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Nuclear receptor corepressors non-canonically drive glucocorticoid receptor-dependent activation of hepatic gluconeogenesis

Amy K. Hauck, Rashid Mehmood, Bryce J. Carpenter, Maxwell T. Frankfurter, Michael C. Tackenberg, Shin-ichi Inoue, Maria K. Krieg, Fathima N. Cassim Bawa, Mohit K. Midha, Delaine M. Zundell, Kirill Batmanov, & Mitchell A. Lazar. Nuclear receptor corepressors non-canonically drive glucocorticoid receptor-dependent activation of hepatic gluconeogenesis. Nat Metab (2024). https://doi.org/10.1038/s42255-024-01029-4

Abstract

Nuclear receptor corepressors (NCoRs) function in multiprotein complexes containing histone deacetylase 3 (HDAC3) to alter transcriptional output primarily through repressive chromatin remodelling at target loci. In the liver, loss of HDAC3 causes a marked hepatosteatosis largely because of de-repression of genes involved in lipid metabolism; however, the individual roles and contribution of other complex members to hepatic and systemic metabolic regulation are unclear. Here we show that adult loss of both NCoR1 and NCoR2 (double knockout (KO)) in hepatocytes phenocopied the hepatomegalic fatty liver phenotype of HDAC3 KO. In addition, double KO livers exhibited a dramatic reduction in glycogen storage and gluconeogenic gene expression that was not observed with hepatic KO of individual NCoRs or HDAC3, resulting in profound fasting hypoglycaemia. This surprising HDAC3-independent activation function of NCoR1 and NCoR2 is due to an unexpected loss of chromatin accessibility on deletion of NCoRs that prevented glucocorticoid receptor binding and stimulatory effect on gluconeogenic genes. These studies reveal an unanticipated, non-canonical activation function of NCoRs that is required for metabolic health.

Mitch Lazar Lab

The microbiota and T cells non-genetically modulate inherited phenotypes transgenerationally

Jordan C. Harris, Natalie A. Trigg, Bruktawit Goshu, Yuichi Yokoyama, Lenka Dohnalová, Ellen K. White, Adele Harman, Sofía M. Murga-Garrido, Jamie Ting-Chun Pan, Preeti Bhanap, Christoph A. Thaiss, Elizabeth A. Grice, Colin C. Conine, Taku Kambayashi. The microbiota and T cells non-genetically modulate inherited phenotypes transgenerationally. Cell Reports, Volume 43, Issue 4 (2024). https://doi.org/10.1038/s41586-024-07278-3

Abstract

The host-microbiota relationship has evolved to shape mammalian physiology, including immunity, metabolism, and development. Germ-free models are widely used to study microbial effects on host processes such as immunity. Here, we find that both germ-free and T cell-deficient mice exhibit a robust sebum secretion defect persisting across multiple generations despite microbial colonization and T cell repletion. These phenotypes are inherited by progeny conceived during in vitro fertilization using germ-free sperm and eggs, demonstrating that non-genetic information in the gametes is required for microbial-dependent phenotypic transmission. Accordingly, gene expression in early embryos derived from gametes from germ-free or T cell-deficient mice is strikingly and similarly altered. Our findings demonstrate that microbial- and immune-dependent regulation of non-genetic information in the gametes can transmit inherited phenotypes transgenerationally in mice. This mechanism could rapidly generate phenotypic diversity to enhance host adaptation to environmental perturbations.

Conine Lab

The variation and evolution of complete human centromeres

Glennis A. Logsdon, Allison N. Rozanski, Fedor Ryabov, Tamara Potapova, Valery A. Shepelev, Claudia R. Catacchio, David Porubsky, Yafei Mao, DongAhn Yoo, Mikko Rautiainen, Sergey Koren, Sergey Nurk, Julian K. Lucas, Kendra Hoekzema, Katherine M. Munson, Jennifer L. Gerton, Adam M. Phillippy, Mario Ventura, Ivan A. Alexandrov & Evan E. Eichler. The variation and evolution of complete human centromeres. Nature (2024). https://doi.org/10.1038/s41586-024-07278-3

Abstract

Human centromeres have been traditionally very difficult to sequence and assemble owing to their repetitive nature and large size1. As a result, patterns of human centromeric variation and models for their evolution and function remain incomplete, despite centromeres being among the most rapidly mutating regions. Here, using long-read sequencing, we completely sequenced and assembled all centromeres from a second human genome and compared it to the finished reference genome. We find that the two sets of centromeres show at least a 4.1-fold increase in single-nucleotide variation when compared with their unique flanks and vary up to 3-fold in size. Moreover, we find that 45.8% of centromeric sequence cannot be reliably aligned using standard methods owing to the emergence of new α-satellite higher-order repeats (HORs). DNA methylation and CENP-A chromatin immunoprecipitation experiments show that 26% of the centromeres differ in their kinetochore position by >500 kb. To understand evolutionary change, we selected six chromosomes and sequenced and assembled 31 orthologous centromeres from the common chimpanzee, orangutan and macaque genomes. Comparative analyses reveal a nearly complete turnover of α-satellite HORs, with characteristic idiosyncratic changes in α-satellite HORs for each species. Phylogenetic reconstruction of human haplotypes supports limited to no recombination between the short (p) and long (q) arms across centromeres and reveals that novel α-satellite HORs share a monophyletic origin, providing a strategy to estimate the rate of saltatory amplification and mutation of human centromeric DNA.

Logsdon Lab

Iterative oxidation by TET1 is required for reprogramming of imprinting control regions and patterning of mouse sperm hypomethylated regions

Rexxi D. Prasasya, Blake A. Caldwell, Zhengfeng Liu, Songze Wu, N. Adrian Leu, Johanna M. Fowler, Steven A. Cincotta, Diana J. Laird, Rahul M. Kohli, and Marisa S. Bartolomei. Iterative oxidation by TET1 is required for reprogramming of imprinting control regions and patterning of mouse sperm hypomethylated regions. Developmental Cell. April 2, 2024. DOI: https://doi.org/10.1016/j.devcel.2024.02.012

Summary

Ten-eleven translocation (TET) enzymes iteratively oxidize 5-methylcytosine (5mC) to generate 5-hydroxymethylcytosine (5hmC), 5-formylcytosine, and 5-carboxylcytosine to facilitate active genome demethylation. Whether these bases are required to promote replication-coupled dilution or activate base excision repair during mammalian germline reprogramming remains unresolved due to the inability to decouple TET activities. Here, we generated two mouse lines expressing catalytically inactive TET1 (Tet1-HxD) and TET1 that stalls oxidation at 5hmC (Tet1-V). Tet1 knockout and catalytic mutant primordial germ cells (PGCs) fail to erase methylation at select imprinting control regions and promoters of meiosis-associated genes, validating the requirement for the iterative oxidation of 5mC for complete germline reprogramming. TET1V and TET1HxD rescue most hypermethylation of Tet1−/− sperm, suggesting the role of TET1 beyond its oxidative capability. We additionally identify a broader class of hypermethylated regions in Tet1 mutant mouse sperm that depend on TET oxidation for reprogramming. Our study demonstrates the link between TET1-mediated germline reprogramming and sperm methylome patterning.

Marisa Bartolomei Lab Rahul Kohli Lab

Efficient formation of single-copy human artificial chromosomes

Craig W. Gambogi, Gabriel J. Birchak, Elie Mer, David M. Brown, George Yankson, Kathryn Kixmoeller, Janardan N. Gavade, Josh L. Espinoza, Prakriti Kashyap, Chris L. Duypont, Glennis A. Logsdon, Patrick Heun, John I. Glass, and Ben E. Black. Efficient formation of single-copy human artificial chromosomes. Science383,1344-1349(2024). DOI:10.1126/science.adj3566

Abstract

Large DNA assembly methodologies underlie milestone achievements in synthetic prokaryotic and budding yeast chromosomes. While budding yeast control chromosome inheritance through ~125-base pair DNA sequence-defined centromeres, mammals and many other eukaryotes use large, epigenetic centromeres. Harnessing centromere epigenetics permits human artificial chromosome (HAC) formation but is not sufficient to avoid rampant multimerization of the initial DNA molecule upon introduction to cells. We describe an approach that efficiently forms single-copy HACs. It employs a ~750-kilobase construct that is sufficiently large to house the distinct chromatin types present at the inner and outer centromere, obviating the need to multimerize. Delivery to mammalian cells is streamlined by employing yeast spheroplast fusion. These developments permit faithful chromosome engineering in the context of metazoan cells.
Ben Black Lab

Structural basis for the phase separation of the chromosome passenger complex

Bryan NW, Ali A, Niedzialkowska E, Mayne L, Stukenberg PT, Black BE. Structural basis for the phase separation of the chromosome passenger complex. Elife. 2024 Mar 8;13:e92709. doi: 10.7554/eLife.92709. Epub ahead of print. PMID: 38456462.

Abstract

The physical basis of phase separation is thought to consist of the same types of bonds that specify conventional macromolecular interactions yet is unsatisfyingly often referred to as ‘fuzzy’. Gaining clarity on the biogenesis of membraneless cellular compartments is one of the most demanding challenges in biology. Here, we focus on the chromosome passenger complex (CPC), that forms a chromatin body that regulates chromosome segregation in mitosis. Within the three regulatory subunits of the CPC implicated in phase separation – a heterotrimer of INCENP, Survivin, and Borealin – we identify the contact regions formed upon droplet formation using hydrogen/deuterium-exchange mass spectrometry (HXMS). These contact regions correspond to some of the interfaces seen between individual heterotrimers within the crystal lattice they form. A major contribution comes from specific electrostatic interactions that can be broken and reversed through initial and compensatory mutagenesis, respectively. Our findings reveal structural insight for interactions driving liquid-liquid demixing of the CPC. Moreover, we establish HXMS as an approach to define the structural basis for phase separation.

Ben Black Lab

Growth factor–induced activation of MSK2 leads to phosphorylation of H3K9me2S10 and corresponding changes in gene expression

Karen G. Wong, Yu-Chia F. Cheng, Vincent H. Wu, Anna A. Kiselva, Jun Li, Andrey Poleshko, Cheryl M. Smith, and Jonathan A. Eptstein.Growth factor–induced activation of MSK2 leads to phosphorylation of H3K9me2S10 and corresponding changes in gene expression.Sci. Adv.10,eadm9518(2024).DOI:10.1126/sciadv.adm9518

Abstract

Extracellular signals are transmitted through kinase cascades to modulate gene expression, but it remains unclear how epigenetic changes regulate this response. Here, we provide evidence that growth factor–stimulated changes in the transcript levels of many responsive genes are accompanied by increases in histone phosphorylation levels, specifically at histone H3 serine-10 when the adjacent lysine-9 is dimethylated (H3K9me2S10). Imaging and proteomic approaches show that epidermal growth factor (EGF) stimulation results in H3K9me2S10 phosphorylation, which occurs in genomic regions enriched for regulatory enhancers of EGF-responsive genes. We also demonstrate that the EGF-induced increase in H3K9me2S10ph is dependent on the nuclear kinase MSK2, and this subset of EGF-induced genes is dependent on MSK2 for transcription. Together, our work indicates that growth factor–induced changes in chromatin state can mediate the activation of downstream genes.
Jon Epstein Lab

Dynamic microenvironments shape nuclear organization and gene expression

Gabriela Hayward-Lara, Matthew D Fischer, and Mustafa Mir. Dynamic microenvironments shape nuclear organization and gene expression. Current Opinion in Genetics & Development. Volume 86, 2024. 102177. ISSN 0959-437X. https://doi.org/10.1016/j.gde.2024.102177.

Highlights

  • Microenvironments are local high concentrations of multiple nuclear factors.
  • Microenvironments form due to protein–protein and protein–chromatin interactions.
  • Local concentrations of protein modulate binding frequency rather than duration.
  • Microenvironments can bridge multiple genes and regulatory elements.
  • Microenvironment lifetimes vary and correlate with regulatory function.

Live imaging has revealed that the regulation of gene expression is largely driven by transient interactions. For example, many regulatory proteins bind chromatin for just seconds, and loop-like genomic contacts are rare and last only minutes. These discoveries have been difficult to reconcile with our canonical models that are predicated on stable and hierarchical interactions. Proteomic microenvironments that concentrate nuclear factors may explain how brief interactions can still mediate gene regulation by creating conditions where reactions occur more frequently. Here, we summarize new imaging technologies and recent discoveries implicating microenvironments as a potential driver of nuclear function. Finally, we propose that key properties of proteomic microenvironments, such as their size, enrichment, and lifetimes, are directly linked to regulatory function.

Mustafa Mir Lab

A genome-wide CRISPR screen identifies BRD4 as a regulator of cardiomyocyte differentiation

Arun Padmanabhan, T. Yvanka de Soysa, Angelo Pelonero, Valerie Sapp, Parisha P. Shah, Qiaohong Wang, Li Li, Clara Youngna Lee, Nandhini Sadagopan, Tomohiro Nishino, Lin Ye, Rachel Yang, Ashley Karnay, Andrey Poleshko, Nikhita Bolar, Ricardo Linares-Saldana, Sanjeev S. Ranade, Michael Alexanian, Sarah U. Morton, Mohit Jain, Saptarsi M. Haldar, Deepak Srivastava, Rajan Jain. A genome-wide CRISPR screen identifies BRD4 as a regulator of cardiomyocyte differentiation. Nat Cardiovasc Res (2024). https://doi.org/10.1038/s44161-024-00431-1 

Abstract

Human induced pluripotent stem cell (hiPSC) to cardiomyocyte (CM) differentiation has reshaped approaches to studying cardiac development and disease. In this study, we employed a genome-wide CRISPR screen in a hiPSC to CM differentiation system and reveal here that BRD4, a member of the bromodomain and extraterminal (BET) family, regulates CM differentiation. Chemical inhibition of BET proteins in mouse embryonic stem cell (mESC)-derived or hiPSC-derived cardiac progenitor cells (CPCs) results in decreased CM differentiation and persistence of cells expressing progenitor markers. In vivo, BRD4 deletion in second heart field (SHF) CPCs results in embryonic or early postnatal lethality, with mutants demonstrating myocardial hypoplasia and an increase in CPCs. Single-cell transcriptomics identified a subpopulation of SHF CPCs that is sensitive to BRD4 loss and associated with attenuated CM lineage-specific gene programs. These results highlight a previously unrecognized role for BRD4 in CM fate determination during development and a heterogenous requirement for BRD4 among SHF CPCs.

Rajan Jain Lab

The conneXion between sex and immune responses

Katherine S. Forsyth, Nikhil Jiwrajka, Claudia D. Lovell, Natalie E. Toothacre, Montserrat C. Anguera. The conneXion between sex and immune responses. Nat Rev Immunol (2024). https://doi.org/10.1038/s41577-024-00996-9

Abstract

There are notable sex-based differences in immune responses to pathogens and self-antigens, with female individuals exhibiting increased susceptibility to various autoimmune diseases, and male individuals displaying preferential susceptibility to some viral, bacterial, parasitic and fungal infections. Although sex hormones clearly contribute to sex differences in immune cell composition and function, the presence of two X chromosomes in female individuals suggests that differential gene expression of numerous X chromosome-linked immune-related genes may also influence sex-biased innate and adaptive immune cell function in health and disease. Here, we review the sex differences in immune system composition and function, examining how hormones and genetics influence the immune system. We focus on the genetic and epigenetic contributions responsible for altered X chromosome-linked gene expression, and how this impacts sex-biased immune responses in the context of pathogen infection and systemic autoimmunity.

Montserrat Anguera Lab

Cooperativity between Cas9 and hyperactive AID establishes broad and diversifying mutational footprints in base editors

Kiara N Berríos, Aleksia Barka, Jasleen Gill, Juan C Serrano, Peter F Bailer, Jared B Parker, Niklaus H Evitt, Kiran S Gajula, Junwei Shi, Rahul M Kohli, Cooperativity between Cas9 and hyperactive AID establishes broad and diversifying mutational footprints in base editors, Nucleic Acids Research, 2024;, gkae024, https://doi.org/10.1093/nar/gkae024

Abstract

The partnership of DNA deaminase enzymes with CRISPR-Cas nucleases is now a well-established method to enable targeted genomic base editing. However, an understanding of how Cas9 and DNA deaminases collaborate to shape base editor (BE) outcomes has been lacking. Here, we support a novel mechanistic model of base editing by deriving a range of hyperactive activation-induced deaminase (AID) base editors (hBEs) and exploiting their characteristic diversifying activity. Our model involves multiple layers of previously underappreciated cooperativity in BE steps including: (i) Cas9 binding can potentially expose both DNA strands for ‘capture’ by the deaminase, a feature that is enhanced by guide RNA mismatches; (ii) after strand capture, the intrinsic activity of the DNA deaminase can tune window size and base editing efficiency; (iii) Cas9 defines the boundaries of editing on each strand, with deamination blocked by Cas9 binding to either the PAM or the protospacer and (iv) non-canonical edits on the guide RNA bound strand can be further elicited by changing which strand is nicked by Cas9. Leveraging insights from our mechanistic model, we create novel hBEs that can remarkably generate simultaneous C > T and G > A transitions over >65 bp with significant potential for targeted gene diversification.

Junwei Shi Lab Rahul Kohli Lab

Histone acetylation in an Alzheimer’s disease cell model promotes homeostatic amyloid-reducing pathways

Daniel C. Xu, Hanna Sas-Nowosielska, Greg Donahue, Hua Huang, Naemeh Pourshafie, Charly R. Good & Shelley L. Berger. Histone acetylation in an Alzheimer’s disease cell model promotes homeostatic amyloid-reducing pathways. acta neuropathol commun 12, 3 (2024). https://doi.org/10.1186/s40478-023-01696-6

Abstract

Alzheimer’s Disease (AD) is a disorder characterized by cognitive decline, neurodegeneration, and accumulation of amyloid plaques and tau neurofibrillary tangles in the brain. Dysregulation of epigenetic histone modifications may lead to expression of transcriptional programs that play a role either in protecting against disease genesis or in worsening of disease pathology. One such histone modification, acetylation of histone H3 lysine residue 27 (H3K27ac), is primarily localized to genomic enhancer regions and promotes active gene transcription. We previously discovered H3K27ac to be more abundant in AD patient brain tissue compared to the brains of age-matched non-demented controls. In this study, we use iPSC-neurons derived from familial AD patients with an amyloid precursor protein (APP) duplication (APPDup neurons) as a model to study the functional effect of lowering CBP/P300 enzymes that catalyze H3K27ac. We found that homeostatic amyloid-reducing genes were upregulated in the APPDup neurons compared to non-demented controls. We lowered CBP/P300 to reduce H3K27ac, which led to decreased expression of numerous of these homeostatic amyloid-reducing genes, along with increased extracellular secretion of a toxic amyloid-β species, Aβ(1–42). Our findings suggest that epigenomic histone acetylation, including H3K27ac, drives expression of compensatory genetic programs in response to AD-associated insults, specifically those resulting from APP duplication, and thus may play a role in mitigating AD pathology in neurons.

Shelley Berger Lab

Spatially coordinated heterochromatinization of long synaptic genes in fragile X syndrome

Malachowski T, Chandradoss KR, Boya R, Zhou L, Cook AL, Su C, Pham K, Haws SA, Kim JH, Ryu HS, Ge C, Luppino JM, Nguyen SC, Titus KR, Gong W, Wallace O, Joyce EF, Wu H, Rojas LA, Phillips-Cremins JE. Spatially coordinated heterochromatinization of long synaptic genes in fragile X syndrome. Cell. 2023 Dec 21;186(26):5840-5858.e36. doi: 10.1016/j.cell.2023.11.019. PMID: 38134876; PMCID: PMC10794044.

Abstract

Short tandem repeat (STR) instability causes transcriptional silencing in several repeat expansion disorders. In fragile X syndrome (FXS), mutation-length expansion of a CGG STR represses FMR1 via local DNA methylation. Here, we find megabase-scale H3K9me3 domains on autosomes and encompassing FMR1 on the X chromosome in FXS patient-derived iPSCs, iPSC-derived neural progenitors, EBV-transformed lymphoblasts, and brain tissue with mutation-length CGG expansion. H3K9me3 domains connect via inter-chromosomal interactions and demarcate severe misfolding of TADs and loops. They harbor long synaptic genes replicating at the end of S phase, replication-stress-induced double-strand breaks, and STRs prone to stepwise somatic instability. CRISPR engineering of the mutation-length CGG to premutation length reverses H3K9me3 on the X chromosome and multiple autosomes, refolds TADs, and restores gene expression. H3K9me3 domains can also arise in normal-length iPSCs created with perturbations linked to genome instability, suggesting their relevance beyond FXS. Our results reveal Mb-scale heterochromatinization and trans interactions among loci susceptible to instability.

Eric Joyce Lab Jennifer Phillips-Cremins Lab Hao Wu Lab

Disruption of H3K36 methylation provokes cellular plasticity to drive aberrant glandular formation and squamous carcinogenesis

Eun Kyung Ko, Amy Anderson, Carina D’souza, Jonathan Zou, Sijia Huang, Sohyun Cho, Faizan Alawi, Stephen Prouty, Vivian Lee, Sora Yoon, Keegan Krick, Yoko Horiuchi, Kai Ge, John T. Seykora, Brian C. Capell. Disruption of H3K36 methylation provokes cellular plasticity to drive aberrant glandular formation and squamous carcinogenesis. Developmental Cell. January 9, 2024. doi: https://doi.org/10.1016/j.devcel.2023.12.007.

Highlights

• Disruption of H3K36 methylation via H3K36M expression drives epithelial plasticity
• This triggers epithelial glandulogenesis while also increasing cancer susceptibility
• H3K36M rewires the global and genome-wide H3K36me2 and H3K27me3 epigenetic landscape
• These chromatin changes suppress differentiation genes while activating glandular genes

Summary

Chromatin organization is essential for maintaining cell-fate trajectories and developmental programs. Here, we find that disruption of H3K36 methylation dramatically impairs normal epithelial differentiation and development, which promotes increased cellular plasticity and enrichment of alternative cell fates. Specifically, we observe a striking increase in the aberrant generation of excessive epithelial glandular tissues, including hypertrophic salivary, sebaceous, and meibomian glands, as well as enhanced squamous tumorigenesis. These phenotypic and gene expression manifestations are associated with loss of H3K36me2 and rewiring of repressive H3K27me3, changes we also observe in human patients with glandular hyperplasia. Collectively, these results have identified a critical role for H3K36 methylation in both in vivo epithelial cell-fate decisions and the prevention of squamous carcinogenesis and suggest that H3K36 methylation modulation may offer new avenues for the treatment of numerous common disorders driven by altered glandular function, which collectively affect large segments of the human population.

Brian Capell Lab

Centromere innovations within a mouse species

Gambogi CW, Pandey N, Dawicki-McKenna JM, Arora UP, Liskovykh MA, Ma J, Lamelza P, Larionov V, Lampson MA, Logsdon GA, Dumont BL, Black BE. Centromere innovations within a mouse species. Sci Adv. 2023 Nov 17;9(46):eadi5764. doi: 10.1126/sciadv.adi5764. Epub 2023 Nov 15. PMID: 37967185; PMCID: PMC10651114.

Abstract

Mammalian centromeres direct faithful genetic inheritance and are typically characterized by regions of highly repetitive and rapidly evolving DNA. We focused on a mouse species, Mus pahari, that we found has evolved to house centromere-specifying centromere protein-A (CENP-A) nucleosomes at the nexus of a satellite repeat that we identified and termed π-satellite (π-sat), a small number of recruitment sites for CENP-B, and short stretches of perfect telomere repeats. One M. pahari chromosome, however, houses a radically divergent centromere harboring ~6 mega-base pairs of a homogenized π-sat-related repeat, π-satB, that contains >20,000 functional CENP-B boxes. There, CENP-B abundance promotes accumulation of microtubule-binding components of the kinetochore and a microtubule-destabilizing kinesin of the inner centromere. We propose that the balance of pro- and anti-microtubule binding by the new centromere is what permits it to segregate during cell division with high fidelity alongside the older ones whose sequence creates a markedly different molecular composition.

Ben Black Lab

Lead-Oriented Synthesis of Epigenetic Relevant Scaffolds

Timothe Maujean, Prakash Kannaboina, Adam I Green, and George Burslem. Lead-Oriented Synthesis of Epigenetic Relevant Scaffolds. Chemical Communications. 15 Nov 2023. https://doi.org/10.1039/D3CC04317G 

Abstract

A simple and rationale method to rank molecules’ lead-likeness using continuous evaluation functions was hereby developed. This strategy proved to be competitive against known methods and finally helped driving synthetic efforts towards candidates of interest for epigenetic applications towards HDAC6, BRD4 and EZH2

George Burslem Lab

Benchmarking algorithms for joint integration of unpaired and paired single-cell RNA-seq and ATAC-seq data

Michelle Y.Y. Lee, Klaus H. Kaestner, Mingyao Li. Benchmarking algorithms for joint integration of unpaired and paired single-cell RNA-seq and ATAC-seq data. Genome Biol 24, 244 (2023). https://doi.org/10.1186/s13059-023-03073-x

Abstract

Background

Single-cell RNA-sequencing (scRNA-seq) measures gene expression in single cells, while single-nucleus ATAC-sequencing (snATAC-seq) quantifies chromatin accessibility in single nuclei. These two data types provide complementary information for deciphering cell types and states. However, when analyzed individually, they sometimes produce conflicting results regarding cell type/state assignment. The power is compromised since the two modalities reflect the same underlying biology. Recently, it has become possible to measure both gene expression and chromatin accessibility from the same nucleus. Such paired data enable the direct modeling of the relationships between the two modalities. Given the availability of the vast amount of single-modality data, it is desirable to integrate the paired and unpaired single-modality datasets to gain a comprehensive view of the cellular complexity.

Results

We benchmark nine existing single-cell multi-omic data integration methods. Specifically, we evaluate to what extent the multiome data provide additional guidance for analyzing the existing single-modality data, and whether these methods uncover peak-gene associations from single-modality data. Our results indicate that multiome data are helpful for annotating single-modality data. However, we emphasize that the availability of an adequate number of nuclei in the multiome dataset is crucial for achieving accurate cell type annotation. Insufficient representation of nuclei may compromise the reliability of the annotations. Additionally, when generating a multiome dataset, the number of cells is more important than sequencing depth for cell type annotation.

Conclusions

Seurat v4 is the best currently available platform for integrating scRNA-seq, snATAC-seq, and multiome data even in the presence of complex batch effects.

Klaus Kaestner Lab

Telomouse—a mouse model with human-length telomeres generated by a single amino acid change in RTEL1

Linyang Ju, Karl M. Glastad, Lihong Sheng, Janko Gospocic, Callum J. Kingwell, Shawn M. Davidson, Sarah D. Kocher, Roberto Bonasio, Shelley L. Berger. Hormonal gatekeeping via the blood-brain barrier governs caste-specific behavior in ants. Cell.  September 7, 2023. DOI: https://doi.org/10.1016/j.cell.2023.08.002

Abstract

Telomeres, the ends of eukaryotic chromosomes, protect genome integrity and enable cell proliferation. Maintaining optimal telomere length in the germline and throughout life limits the risk of cancer and enables healthy aging. Telomeres in the house mouse, Mus musculus, are about five times longer than human telomeres, limiting the use of this common laboratory animal for studying the contribution of telomere biology to aging and cancer. We identified a key amino acid variation in the helicase RTEL1, naturally occurring in the short-telomere mouse species M. spretus. Introducing this variation into M. musculus is sufficient to reduce the telomere length set point in the germline and generate mice with human-length telomeres. While these mice are fertile and appear healthy, the regenerative capacity of their colonic epithelium is compromised. The engineered Telomouse reported here demonstrates a dominant role of RTEL1 in telomere length regulation and provides a unique model for aging and cancer.

Klaus Kaestner Lab

Hormonal gatekeeping via the blood-brain barrier governs caste-specific behavior in ants

Linyang Ju, Karl M. Glastad, Lihong Sheng, Janko Gospocic, Callum J. Kingwell, Shawn M. Davidson, Sarah D. Kocher, Roberto Bonasio, Shelley L. Berger. Hormonal gatekeeping via the blood-brain barrier governs caste-specific behavior in ants. Cell.  September 7, 2023. DOI: https://doi.org/10.1016/j.cell.2023.08.002

Summary

Here, we reveal an unanticipated role of the blood-brain barrier (BBB) in regulating complex social behavior in ants. Using scRNA-seq, we find localization in the BBB of a key hormone-degrading enzyme called juvenile hormone esterase (Jhe), and we show that this localization governs the level of juvenile hormone (JH3) entering the brain. Manipulation of the Jhe level reprograms the brain transcriptome between ant castes. Although ant Jhe is retained and functions intracellularly within the BBB, we show that Drosophila Jhe is naturally extracellular. Heterologous expression of ant Jhe into the Drosophila BBB alters behavior in fly to mimic what is seen in ants. Most strikingly, manipulation of Jhe levels in ants reprograms complex behavior between worker castes. Our study thus uncovers a remarkable, potentially conserved role of the BBB serving as a molecular gatekeeper for a neurohormonal pathway that regulates social behavior.

Shelley Berger Lab Roberto Bonasio Lab

G-quadruplexes associated with R-loops promote CTCF binding

Phillip Wulfridge, Qingqing Yan, Nathaniel Rell, John Doherty, Skye Jacobson, Sarah Offley, Sandra Deliard, Kelly Feng, Jennifer E. Phillips-Cremins, Alessandro Gardini, Kavitha Sarma. G-quadruplexes associated with R-loops promote CTCF binding. Molecular Cell. Volume 82, Issue 17. P3064-3079.E5, August 7, 2023. DOI: https://doi.org/10.1016/j.molcel.2023.07.009

Summary

CTCF is a critical regulator of genome architecture and gene expression that binds thousands of sites on chromatin. CTCF genomic localization is controlled by the recognition of a DNA sequence motif and regulated by DNA modifications. However, CTCF does not bind to all its potential sites in all cell types, raising the question of whether the underlying chromatin structure can regulate CTCF occupancy. Here, we report that R-loops facilitate CTCF binding through the formation of associated G-quadruplex (G4) structures. R-loops and G4s co-localize with CTCF at many genomic regions in mouse embryonic stem cells and promote CTCF binding to its cognate DNA motif in vitro. R-loop attenuation reduces CTCF binding in vivo. Deletion of a specific G4-forming motif in a gene reduces CTCF binding and alters gene expression. Conversely, chemical stabilization of G4s results in CTCF gains and accompanying alterations in chromatin organization, suggesting a pivotal role for G4 structures in reinforcing long-range genome interactions through CTCF.
Kavitha Sarma Lab Jennifer Phillips-Cremins Lab

Mettl3-catalyzed m6A regulates histone modifier and modification expression in self-renewing somatic tissue

Alexandra M. Maldonado López, Eun Kyung Ko, Sijia Huang, Gina Pacella, Nina Kuprasertkul, Carina A. D’Souza, Raúl A. Reyes Hueros, Hui Shen, Julian Stoute, Heidi Elashal, Morgan Sinkfield, Amy Anderson, Stephen Pourty, Hua-Bing Li, John T. Seykora, Kathy Fange Liu, Brian C. Capell. Mettl3-catalyzed m6A regulates histone modifier and modification expression in self-renewing somatic tissue.Sci. Adv.9,eadg5234(2023).DOI:10.1126/sciadv.adg5234

Abstract

N6-methyladenosine (m6A) is the most abundant modification on messenger RNAs (mRNAs) and is catalyzed by methyltransferase-like protein 3 (Mettl3). To understand the role of m6A in a self-renewing somatic tissue, we deleted Mettl3 in epidermal progenitors in vivo. Mice lacking Mettl3 demonstrate marked features of dysfunctional development and self-renewal, including a loss of hair follicle morphogenesis and impaired cell adhesion and polarity associated with oral ulcerations. We show that Mettl3 promotes the m6A-mediated degradation of mRNAs encoding critical histone modifying enzymes. Depletion of Mettl3 results in the loss of m6A on these mRNAs and increases their expression and associated modifications, resulting in widespread gene expression abnormalities that mirror the gross phenotypic abnormalities. Collectively, these results have identified an additional layer of gene regulation within epithelial tissues, revealing an essential role for m6A in the regulation of chromatin modifiers, and underscoring a critical role for Mettl3-catalyzed m6A in proper epithelial development and self-renewal.
Brian Capell Lab

Centromere-specifying nucleosomes persist in aging mouse oocytes in the absence of nascent assembly

Das A, Boese KG, Tachibana K, Baek SH, Lampson MA, Black BE. Centromere-specifying nucleosomes persist in aging mouse oocytes in the absence of nascent assembly. Curr Biol. 2023 Aug 4:S0960-9822(23)00971-5. doi: 10.1016/j.cub.2023.07.032. Epub ahead of print. PMID: 37582374.

Abstract

Centromeres direct genetic inheritance but are not themselves genetically encoded. Instead, centromeres are defined epigenetically by the presence of a histone H3 variant, CENP-A.1 In cultured somatic cells, an established paradigm of cell-cycle-coupled propagation maintains centromere identity: CENP-A is partitioned between sisters during replication and replenished by new assembly, which is restricted to G1. The mammalian female germ line challenges this model because of the cell-cycle arrest between pre-meiotic S phase and the subsequent G1, which can last for the entire reproductive lifespan (months to decades). New CENP-A chromatin assembly maintains centromeres during prophase I in worm and starfish oocytes,2,3 suggesting that a similar process may be required for centromere inheritance in mammals. To test this hypothesis, we developed an oocyte-specific conditional knockout (cKO) mouse for Mis18α, an essential component of the assembly machinery. We find that embryos derived from Mis18α knockout oocytes fail to assemble CENP-A nucleosomes prior to zygotic genome activation (ZGA), validating the knockout model. We show that deletion of Mis18α in the female germ line at the time of birth has no impact on centromeric CENP-A nucleosome abundance, even after 6-8 months of aging. In addition, there is no detectable detriment to fertility. Thus, centromere chromatin is maintained long-term, independent of new assembly during the extended prophase I arrest in mouse oocytes.

Ben Black Lab

Joint single-cell profiling resolves 5mC and 5hmC and reveals their distinct gene regulatory effects

Emily B. Fabyanic, Peng Hu, Qi Qiu, Kiara N. Berríos, Daniel R. Connolly, Tong Wang, Jennifer Flournoy, Zhaolan Zhou, Rahul M. Kohli, Hao Wu. Joint single-cell profiling resolves 5mC and 5hmC and reveals their distinct gene regulatory effects. Nat Biotechnol (2023). https://doi.org/10.1038/s41587-023-01909-2

Abstract

Oxidative modification of 5-methylcytosine (5mC) by ten-eleven translocation (TET) DNA dioxygenases generates 5-hydroxymethylcytosine (5hmC), the most abundant form of oxidized 5mC. Existing single-cell bisulfite sequencing methods cannot resolve 5mC and 5hmC, leaving the cell-type-specific regulatory mechanisms of TET and 5hmC largely unknown. Here, we present joint single-nucleus (hydroxy)methylcytosine sequencing (Joint-snhmC-seq), a scalable and quantitative approach that simultaneously profiles 5hmC and true 5mC in single cells by harnessing differential deaminase activity of APOBEC3A toward 5mC and chemically protected 5hmC. Joint-snhmC-seq profiling of single nuclei from mouse brains reveals an unprecedented level of epigenetic heterogeneity of both 5hmC and true 5mC at single-cell resolution. We show that cell-type-specific profiles of 5hmC or true 5mC improve multimodal single-cell data integration, enable accurate identification of neuronal subtypes and uncover context-specific regulatory effects on cell-type-specific genes by TET enzymes.

Zhaolan Zhou Lab Rahul Kohli Lab Hao Wu Lab

Intrinsically disordered domain of transcription factor TCF-1 is required for T cell developmental fidelity

Naomi Goldman, Aditi Candra, Isabelle Johnson, Matthew A. Sullivan, Abhijeet R. Patil, Ashley Vanderbeck, Atishay Jay, Yeqiao Zhou, Emily K. Ferrari, Leland Mayne, Jennifer Aguilan, Hai-Hui Xue, Robert B. Faryabi, E. John Wherry, Simone Sidoli, Ivan Maillard & Golnaz Vahedi. Intrinsically disordered domain of transcription factor TCF-1 is required for T cell developmental fidelity. Nat Immunol (2023). https://doi.org/10.1038/s41590-023-01599-7

Abstract

In development, pioneer transcription factors access silent chromatin to reveal lineage-specific gene programs. The structured DNA-binding domains of pioneer factors have been well characterized, but whether and how intrinsically disordered regions affect chromatin and control cell fate is unclear. Here, we report that deletion of an intrinsically disordered region of the pioneer factor TCF-1 (termed L1) leads to an early developmental block in T cells. The few T cells that develop from progenitors expressing TCF-1 lacking L1 exhibit lineage infidelity distinct from the lineage diversion of TCF-1-deficient cells. Mechanistically, L1 is required for activation of T cell genes and repression of GATA2-driven genes, normally reserved to the mast cell and dendritic cell lineages. Underlying this lineage diversion, L1 mediates binding of TCF-1 to its earliest target genes, which are subject to repression as T cells develop. These data suggest that the intrinsically disordered N terminus of TCF-1 maintains T cell lineage fidelity.

R. Babak Faryabi Lab Golnaz Vahedi Lab

High-throughput Oligopaint screen identifies druggable 3D genome regulators

Daniel S. Park, Son C. Nguyen, Randi Isenhart, Parisha P. Shah, Wonho Kim, R. Jordan Barnett, Aditi Chandra, Jennifer M. Luppino, Jailynn Harke, May Wai, Patrick J. Walsh, Richard J. Abdill, Rachel Yang, Yemin Lan, Sora Yoon, Rebecca Yunker, Masato T. Kanemaki, Golnaz Vahedi, Jennifer E. Phillips-Cremins, Rajan Jain & Eric F. Joyce. High-throughput Oligopaint screen identifies druggable 3D genome regulators. Nature (2023). https://doi.org/10.1038/s41586-023-06340-w

Abstract

The human genome functions as a three-dimensional chromatin polymer, driven by a complex collection of chromosome interactions. Although the molecular rules governing these interactions are being quickly elucidated, relatively few proteins regulating this process have been identified. Here, to address this gap, we developed high-throughput DNA or RNA labelling with optimized Oligopaints (HiDRO)—an automated imaging pipeline that enables the quantitative measurement of chromatin interactions in single cells across thousands of samples. By screening the human druggable genome, we identified more than 300 factors that influence genome folding during interphase. Among these, 43 genes were validated as either increasing or decreasing interactions between topologically associating domains. Our findings show that genetic or chemical inhibition of the ubiquitous kinase GSK3A leads to increased long-range chromatin looping interactions in a genome-wide and cohesin-dependent manner. These results demonstrate the importance of GSK3A signalling in nuclear architecture and the use of HiDRO for identifying mechanisms of spatial genome organization.

Eric Joyce Lab Jennifer Phillips-Cremins Lab Rajan Jain Lab Golnaz Vahedi Lab

Mutant NPM1 hijacks transcriptional hub to maintain pathogenic gene programs in acute myeloid leukemia.

Mutant NPM1 hijacks transcriptional hub to maintain pathogenic gene programs in acute myeloid leukemia.Wang X*, Fan D*, Han Q*, Liu Y*, Miao H, Wang X, Li Q, Chen D, Gore H, Himadewi P, Pfeifer GP, Cierpicki T, Grembecka J, Su J, Chong S#, Wan L#, Zhang X#. Cancer Discovery https://doi.org/10.1158/2159-8290.CD-22-0424. (*co-first; #co-corresponding)

Spatial / Architectural Cancer and Metabolism Liling Wan Lab

A pioneer factor locally opens compacted chromatin to enable targeted ATP-dependent nucleosome remodeling

A pioneer factor locally opens compacted chromatin to enable targeted ATP-dependent nucleosome remodeling Frederick MA, Williamson KE, Garcia MF, Ferretti MB, McCarthy RL, Donahue G, Monteiro EL, Takenaka N, Reynaga J, Kadoch C, Zaret KS. Nat Struct Mol Biol. 2022 Dec 19; doi: 10.1038/s41594-022-00886-5

Ken Zaret Lab

CTCF blocks antisense transcription initiation at divergent promoters

CTCF blocks antisense transcription initiation at divergent promoters.

Luan J, Vermunt MW, Syrett CM, Coté A, Tome JM, Zhang H, Huang A, Luppino JM, Keller CA, Giardine BM, Zhang S, Dunagin MC, Zhang Z, Joyce EF, Lis JT, Raj A, Hardison RC, Blobel GA. Nat Struct Mol Biol. 2022 Nov;29(11):1136-1144. doi: 10.1038/s41594-022-00855-y. Epub 2022 Nov 11. PMID: 36369346

Gerd Blobel Lab

Hotspot mutations in the structured ENL YEATS domain link aberrant transcriptional condensates and cancer.

Hotspot mutations in the structured ENL YEATS domain link aberrant transcriptional condensates and cancer. Song L*, Yao X*,  Li H, Peng B, Boka AP, Liu Y, Chen G, Liu Z, Mathias KM, Xia L, Li Q, Mir M, Li Y#, Li H#, Wan L#.  Molecular Cell, 2022 Nov 3;82(21):4080-4098.e12. (featured in cover) PMID:36272410 (*co-first;#co-corresponding)

 

Spatial / Architectural Cancer and Metabolism Liling Wan Lab

Small-molecule inhibition of the acyl-lysine reader ENL as a strategy against acute myeloid leukemia

Small-molecule inhibition of the acyl-lysine reader ENL as a strategy against acute myeloid leukemia. Liu Y, Li H, Alikarami F, Barrett DR, Khan TA, Michino M, Hill C, Mahdavi L, Song L, Tang S, Yang L, Li Y, Pokharel SP, Li Q, Stamford AW, Liverton N, Renzetti LM, Taylor S, Watt GF, Ladduwahetty T, Kargman S, Meinke PT, Foley MA, Shi J, Li H, Chen CW, Gardini A, Huggins DJ, Bernt KM#, Wan L#.  Cancer Discovery, September 2022.

Spatial / Architectural Liling Wan Lab

Quantitative sub-cellular acyl-CoA analysis reveals distinct nuclear metabolism and isoleucine-dependent histone propionylation.

Quantitative sub-cellular acyl-CoA analysis reveals distinct nuclear metabolism and isoleucine-dependent histone propionylation. Trefely S, Huber K, Liu J Noji M, Stransky S, Singh J,  Doan MT, Lovell CD,von Krusenstiern E, Jiang H, Bostwick A, Pepper HL, Izzo L, Zhao Z, Xu JP, Bedi Jr KC, Rame JE,  Bogner-Strauss J, Mesaros C, Sidoli S, Wellen KE*,Snyder NW*. Mol Cell, Jan 20;82(2):447-462    *co-corresponding authors

Cancer and Metabolism Kathryn Wellen Lab

Neuronal YY1 in the prefrontal cortex regulates transcriptional and behavioral responses to chronic stress.

Neuronal YY1 in the prefrontal cortex regulates transcriptional and behavioral responses to chronic stress. Kwon DY, Xu B#, Hu P#, Zhao Y-T, Beagan JA, Nofziger JH, Cui Y, Phillips-Cremins JE, Blendy JA, Wu H, Zhou Z*. Nature Communications 13: 55. doi.org/10.1038/s41467-021-27571-3, 2022.

Zhaolan Zhou Lab Jennifer Phillips-Cremins Lab Hao Wu Lab

Controllable genome editing with split-engineered base editors

Berríos KN, Evitt NH, DeWeerd RA, Ren D, Luo M, Barka A, Wang T, Bartman CR, Lan Y, Green AM, Shi J, Kohli RM. Controllable genome editing with split-engineered base editors. Nat Chem Biol. 2021 Oct 18. doi: 10.1038/s41589-021-00880-w. Epub ahead of print. PMID: 34663942.

Junwei Shi Lab Rahul Kohli Lab

Temporal manipulation of Cdkl5 reveals essential post-developmental functions and reversible CDKL5 deficiency disorder-related deficits.

Temporal manipulation of Cdkl5 reveals essential post-developmental functions and reversible CDKL5 deficiency disorder-related deficits. Terzic B, Davatolhagh MF, Ho Y, Tang S, Liu Y-T, Xia Z, Cui Y, Fuccillo MV and Zhou Z*. Journal of Clinical Investigation 131(20): e143655, 2021.

Zhaolan Zhou Lab

BRD4 orchestrates genome folding to promote neural crest differentiation

Linares-Saldana R, Kim W, Bolar NA, Zhang H, Koch-Bojalad BA, Yoon S, Shah PP, Karnay A, Park DS, Luppino JM, Nguyen SC, Padmanabhan A, Smith CL, Poleshko A, Wang Q, Li L, Srivastava D, Vahedi G, Eom GH, Blobel GA, Joyce EF, Jain R. BRD4 orchestrates genome folding to promote neural crest differentiation. Nat Genet. 2021 Oct;53(10):1480-1492. doi: 10.1038/s41588-021-00934-8. Epub 2021 Oct 5. PMID: 34611363.

Gerd Blobel Lab Eric Joyce Lab Rajan Jain Lab Golnaz Vahedi Lab

Tramtrack acts during late pupal development to direct ant caste identity

Glastad KM, Ju L, Berger SL. PLoS Genet. 2021 Sep 22;17(9):e1009801. doi: 10.1371/journal.pgen.1009801. PMID: 34550980; PMCID: PMC8489709.

Shelley Berger Lab

Responsiveness to perturbations is a hallmark of transcription factors that maintain cell identity in vitro

Mellis IA, Edelstein HI, Truitt R, Goyal Y, Beck LE, Symmons O, Dunagin MC, Linares Saldana RA, Shah PP, Pérez-Bermejo JA, Padmanabhan A, Yang W, Jain R, Raj A. Cell Syst. 2021 Sep 22;12(9):885-899.e8. doi: 10.1016/j.cels.2021.07.003. Epub 2021 Aug 4. PMID: 34352221.

Rajan Jain Lab Arjun Raj Lab

Testing the super-enhancer concept

Blobel GA, Higgs DR, Mitchell JA, Notani D, Young RA. Testing the super-enhancer concept. Nat Rev Genet. 2021 Sep 3. doi: 10.1038/s41576-021-00398-w. Epub ahead of print. PMID: 34480110.

Gerd Blobel Lab

CTCF and transcription influence chromatin structure re-configuration after mitosis

Zhang H, Lam J, Zhang D, Lan Y, Vermunt MW, Keller CA, Giardine B, Hardison RC, Blobel GA. Nat Commun. 2021;12:5157. doi: 10.1038/s41467-021-25418-5.

Gerd Blobel Lab

TooManyPeaks identifies drug-resistant-specific regulatory elements from single-cell leukemic epigenomes

Schwartz GW, Zhou Y, Petrovic J, Pear WS, Faryabi RB. Cell Rep. 2021;36(8):109575. doi: 10.1016/j.celrep.2021.109575. PMID: 34433064.

R. Babak Faryabi Lab

Photochemical Synthesis of an Epigenetic Focused Tetrahydroquinoline Library

Green A and Burslem GM. RSC Med Chem. 2021; Accepted Manuscript. doi: 10.1039/D1MD00193K

George Burslem Lab

Correct dosage of X chromosome transcription is controlled by a nuclear pore component

Aleman JR, Kuhn TM, Pascual-Garcia P, Gospocic J, Lan Y, Bonasio R, Little SC, Capelson M. Cell Rep. 2021 Jun 15;35(11):109236. doi: 10.1016/j.celrep.2021.109236. PMID: 34133927.

Roberto Bonasio Lab Former Faculty Labs

The nuclear periphery is a scaffold for tissue-specific enhancers

Smith CL, Poleshko A, Epstein JA. Nucleic Acids Res. 2021 May 22:gkab392. doi: 10.1093/nar/gkab392. Epub ahead of print. PMID: 34023908

Jon Epstein Lab

p53 mediates target gene association with nuclear speckles for amplified RNA expression

Alexander KA, Coté A, Nguyen SC, Zhang L, Gholamalamdari O, Agudelo-Garcia P, Lin-Shiao E, Tanim KMA, Lim J, Biddle N, Dunagin MC, Good CR, Mendoza MR, Little SC, Belmont A, Joyce EF, Raj A, Berger SL. Mol Cell. 2021 Apr 15;81(8):1666-1681.e6. doi: 10.1016/j.molcel.2021.03.006. Epub 2021 Apr 5. PMID: 33823140

Eric Joyce Lab Shelley Berger Lab Arjun Raj Lab

Pathogenic LMNA variants disrupt cardiac lamina-chromatin interactions and de-repress alternative fate genes

Shah PP, Lv W, Rhoades JH, Poleshko A, Abbey D, Caporizzo MA, Linares-Saldana R, Heffler JG, Sayed N, Thomas D, Wang Q, Stanton LJ, Bedi K, Morley MP, Cappola TP, Owens AT, Margulies KB, Frank DB, Wu JC, Rader DJ, Yang W, Prosser BL, Musunuru K, Jain R. Cell Stem Cell. 2021 May 6;28(5):938-954.e9. doi: 10.1016/j.stem.2020.12.016. Epub 2021 Feb 1. PMID: 33529599

Rajan Jain Lab

Targeting androgen regulation of TMPRSS2 and ACE2 as a therapeutic strategy to combat COVID-19

Deng Q, Rasool RU, Russell RM, Natesan R, Asangani IA. iScience. 2021 Mar 19;24(3):102254. doi: 10.1016/j.isci.2021.102254. Epub 2021 Mar 1. PMID: 33681723

Irfan Asangani Lab

Rapid Detection and Signaling of DNA Damage by PARP-1

Pandey N, Black BE. Trends Biochem Sci. 2021 Mar 2:S0968-0004(21)00028-1. doi: 10.1016/j.tibs.2021.01.014. Epub ahead of print. PMID: 33674152

Ben Black Lab

Functionally distinct roles for TET-oxidized 5-methylcytosine bases in somatic reprogramming to pluripotency

Caldwell BA, Liu MY, Prasasya RD, Wang T, DeNizio JE, Leu NA, Amoh NYA, Krapp C, Lan Y, Shields EJ, Bonasio R, Lengner CJ, Kohli RM, Bartolomei MS. Mol Cell. 2021 Feb 18;81(4):859-869.e8. doi: 10.1016/j.molcel.2020.11.045. Epub 2020 Dec 21. PMID: 33352108

Marisa Bartolomei Lab Rahul Kohli Lab Roberto Bonasio Lab

Distinct properties and functions of CTCF revealed by a rapidly inducible degron system

Luan J, Xiang G, Gómez-García PA, Tome JM, Zhang Z, Vermunt MW, Zhang H, Huang A, Keller CA, Giardine BM, Zhang Y, Lan Y, Lis JT, Lakadamyali M, Hardison RC, Blobel GA. Cell Rep. 2021 Feb 23;34(8):108783. doi: 10.1016/j.celrep.2021.108783. PMID: 33626344

Gerd Blobel Lab Melike Lakadamyali Lab

FoxA-dependent demethylation of DNA initiates epigenetic memory of cellular identity

Reizel Y, Morgan A, Gao L, Schug J, Mukherjee S, García MF, Donahue G, Baur JA, Zaret KS, Kaestner KH. Dev Cell. 2021 Feb 24:S1534-5807(21)00116-7. doi: 10.1016/j.devcel.2021.02.005. Epub ahead of print. PMID: 33636105

Klaus Kaestner Lab Ken Zaret Lab

In vivo CD8+ T cell CRISPR screening reveals control by Fli1 in infection and cancer

Chen Z, Arai E, Khan O, Zhang Z, Ngiow SF, He Y, Huang H, Manne S, Cao Z, Baxter AE, Cai Z, Freilich E, Ali MA, Giles JR, Wu JE, Greenplate AR, Hakeem MA, Chen Q, Kurachi M, Nzingha K, Ekshyyan V, Mathew D, Wen Z, Speck NA, Battle A, Berger SL, Wherry EJ, Shi J. Cell. 2021 Feb 25:S0092-8674(21)00169-0. doi: 10.1016/j.cell.2021.02.019. Epub ahead of print. PMID: 33636129

Junwei Shi Lab Shelley Berger Lab

LEAFY is a pioneer transcription factor and licenses cell reprogramming to floral fate

Jin R, Klasfeld S, Zhu Y, Fernandez Garcia M, Xiao J, Han SK, Konkol A, Wagner D. Nat Commun. 2021 Jan 27;12(1):626. doi: 10.1038/s41467-020-20883-w. PMID: 33504790

Doris Wagner Lab

ALC1 links chromatin accessibility to PARP inhibitor response in homologous recombination-deficient cells

Verma P, Zhou Y, Cao Z, Deraska PV, Deb M, Arai E, Li W, Shao Y, Puentes L, Li Y, Patankar S, Mach RH, Faryabi RB, Shi J, Greenberg RA. Nat Cell Biol. 2021 Jan 18. doi: 10.1038/s41556-020-00624-3. Epub ahead of print. PMID: 33462394

Junwei Shi Lab R. Babak Faryabi Lab Roger Greenberg Lab

Genetic screening for single-cell variability modulators driving therapy resistance

Torre EA, Arai E, Bayatpour S, Jiang CL, Beck LE, Emert BL, Shaffer SM, Mellis IA, Fane ME, Alicea GM, Budinich KA, Weeraratna AT, Shi J, Raj A. Nat Genet. 2021;53(1):76-85. doi: 10.1038/s41588-020-00749-z. Epub 2021 Jan 4. PMID: 33398196

Junwei Shi Lab Arjun Raj Lab

Time to get ill: the intersection of viral infections, sex, and the X chromosome

Forsyth KS, Anguera MC. Curr Opin Physiol. 2021;19:62-72. doi: 10.1016/j.cophys.2020.09.015. PMID: 33073073
Montserrat Anguera Lab

ZNF410 Uniquely Activates the NuRD Component CHD4 to Silence Fetal Hemoglobin Expression

Lan X, Ren R, Feng R, Ly LC, Lan Y, Zhang Z, Aboreden N, Qin K, Horton JR, Grevet JD, Mayuranathan T, Abdulmalik O, Keller CA, Giardine B, Hardison RC, Crossley M, Weiss MJ, Cheng X, Shi J, Blobel GA. Mol Cell. 2020:S1097-2765(20)30784-X. doi: 10.1016/j.molcel.2020.11.006. Online ahead of print. PMID: 33301730

Gerd Blobel Lab

Promoter-anchored chromatin interactions predicted from genetic analysis of epigenomic data

Wu Y, Wang H, Zhang F, Zheng Z, Phillips-Cremins JE, Deary IJ, McRae AF, Wray NR, Zeng J, Yang J. Nat Commun. 2020;11(1):2061. doi: 10.1038/s41467-020-15587-0. PMID: 32345984

Jennifer Phillips-Cremins Lab

3D genome restructuring across timescales of activity-induced neuronal gene expression

Beagan JA, Pastuzyn ED, Fernandez LR, Guo MH, Feng K, Titus KR, Chandrashekar H, Shepherd JD, Phillips-Cremis JE. Nat Neurosci. 2020;23(6):707-717. doi: 10.1038/s41593-020-0634-6. PMID: 32451484

Jennifer Phillips-Cremins Lab

3DeFDR: statistical methods for identifying cell type-specific looping interactions in 5C and Hi-C data

Fernandez LR, Gilgenast TG, Phillips-Cremins JE. Genome Biology. 2020;21(1):219. doi: 10.1186/s13059-020-02061-9. PMID: 32859248

Jennifer Phillips-Cremins Lab

Collapse of the hepatic gene regulatory network in the absence of FoxA factors

Reizel Y, Morgan A, Gao L, Lan Y, Manduchi E, Waite EL, Wang AW, Wells A, Kaestner KH. Genes Dev. 2020;34(15-16):1039-1050. doi: 10.1101/gad.337691.120. PMID: 32561546

Klaus Kaestner Lab

Single-cell transcriptomics of human islet ontogeny defines the molecular basis of β-cell dedifferentiation in T2D

Avrahami D, Wang YJ, Schug J, Feleke E, Gao L, Liu C; HPAP Consortium, Naji A, Glaser B, Kaestner KH. Mol Metab. 2020;42:101057. doi: 10.1016/j.molmet.2020.101057.PMID: 32739450

Klaus Kaestner Lab

Dietary fructose feeds hepatic lipogenesis via microbiota-derived acetate

Zhao S, Jang C, Liu J, Uehara K, Gilbert M, Izzo L, Zeng X, Trefely S, Fernandez S, Carrer A, Miller KD, Schug ZT, Snyder NW, Gade TP, Titchenell PM, Rabinowitz JD, Wellen KE. Nature. 2020;579(7800):586-591. doi: 10.1038/s41586-020-2101-7. PMID: 32214246

Kathryn Wellen Lab

Direct RNA sequencing reveals m 6 A modifications on adenovirus RNA are necessary for efficient splicing

Price AM, Hayer KE, McIntyre ABR, Gokhale NS,  Abebe JS, Fera AND, Mason CE, Horner SM, Wilson AC, Depledge DP, Weitzman MD. Nat Commun. 2020;11(1):6016. doi: 10.1038/s41467-020-19787-6. PMID: 33243990

Matt Weitzman Lab

Cell Cycle Checkpoints Cooperate to Suppress DNA- and RNA-Associated Molecular Pattern Recognition and Anti-Tumor Immune Responses

Chen J, Harding SM, Natesan R, Tian L, Benci JL, Li W, Minn AJ, Asangani IA, Greenberg RA.
Cell Rep. 2020;32(9):108080. doi: 10.1016/j.celrep.2020.108080. PMID: 32877684
Irfan Asangani Lab Roger Greenberg Lab

Targeting cardiac fibrosis with engineered T cells

Aghajanian H, Kimura T, Rurik JG, Hancock AS, Leibowitz MS, Li L, Scholler J, Monslow J, Lo A, Han W, Wang T, Bedi K, Morley MP, Linares Saldana RA, Bolar NA, McDaid K, Assenmacher CA, Smith CL, Wirth D, June CH, Margulies KB, Jain R, Puré E, Albelda SM, Epstein JA. Nature. 2019;573(7774):430-433. doi: 10.1038/s41586-019-1546-z. PMID: 31511695
Jon Epstein Lab

H3K9me2 orchestrates inheritance of spatial positioning of peripheral heterochromatin through mitosis

Poleshko A, Smith CL, Nguyen SC, Sivaramakrishnan P, Wong KG, Murray JI, Lakadamyali M, Joyce EF, Jain R, Epstein JA. Elife. 2019;8:e49278. doi: 10.7554/eLife.49278. PMID: 31573510
Jon Epstein Lab Eric Joyce Lab

Teasing the Immune System to Repair the Heart

Epstein JA, Rosenthal N, Feldman AM. N Engl J Med. 2020;382(17):1660-1662. doi: 10.1056/NEJMcibr2002014. PMID: 32320575
Jon Epstein Lab

Histone methyltransferase activity programs nuclear peripheral genome positioning

See K, Kiseleva AA, Smith CL, Liu F, Li J, Poleshko A, Epstein JA. Dev Biol. 2020;466(1-2):90-98. doi: 10.1016/j.ydbio.2020.07.010. PMID: 32712024

Jon Epstein Lab

Social reprogramming in ants induces longevity-associated glia remodeling

Sheng L, Shields EJ, Gospocic J, Glastad KM, Ratchasanmuang P, Berger SL, Raj A, Little S, Bonasio R. Sci Adv. 2020;6(34):eaba9869. doi: 10.1126/sciadv.aba9869. PMID: 32875108
Shelley Berger Lab Roberto Bonasio Lab Arjun Raj Lab

TET2 chemically modifies tRNAs and regulates tRNA fragment levels

He C, Bozler J, Janssen KA, Wilusz JE, Garcia BA, Schorn AJ, Bonasio R. Nat Struct Mol Biol. 2020. doi: 10.1038/s41594-020-00526-w. PMID: 33230319

Roberto Bonasio Lab Former Faculty Labs

Comparative structure-function analysis of bromodomain and extraterminal motif (BET) proteins in a gene-complementation system

Werner MT, Wang H, Hamagami N, Hsu SC, Yano JA, Stonestrom AJ, Behera V, Zhong Y, Mackay JP, Blobel GA. J Biol Chem. 2020;295(7):1898-1914. doi: 10.1074/jbc.RA119.010679. PMID: 31792058

Gerd Blobel Lab

Understanding heterogeneity of fetal hemoglobin induction through comparative analysis of F and A erythroblasts

Khandros E, Huang P, Peslak SA, Sharma M, Abdulmalik O, Giardine BM, Zhang Z, Keller CA, Hardison RC, Blobel GA. Blood. 2020;135(22):1957-1968. doi: 10.1182/blood.2020005058. PMID: 32268371
Gerd Blobel Lab

The HRI-regulated transcription factor ATF4 activates BCL11A transcription to silence fetal hemoglobin expression

Huang P, Peslak SA, Lan X, Khandros E, Yano JA, Sharma M, Keller CA, Giardine B, Qin K, Abdulmalik O, Hardison RC, Shi J, Blobel GA. Blood. 2020;135(24):2121-2132. doi: 10.1182/blood.2020005301. PMID: 32299090

Gerd Blobel Lab

SIRT1 is downregulated by autophagy in senescence and ageing

Xu C, Wang L, Fozouni P, Evjen G, Chandra V, Jiang J, Lu C, Nicastri M, Bretz C, Winkler JD, Amaravadi R, Garcia BA, Adams PD, Ott M, Tong W, Johansen T, Dou Z, Berger SL. Nat Cell Biol. 2020;22(10):1170-1179. doi: 10.1038/s41556-020-00579-5. PMID: 32989246
Shelley Berger Lab Former Faculty Labs

An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer’s disease

Nativio R, Lan Y, Donahue G, Sidoli S, Berson A, Srinivasan AR, Shcherbakova O, Amlie-Wolf A, Nie J, Cui X, He C, Wang LS, Garcia BA, Trojanowski JQ, Bonini NM, Berger SL. Nat Genet. 2020;52(10):1024-1035. doi: 10.1038/s41588-020-0696-0. PMID: 32989324

Shelley Berger Lab Former Faculty Labs

Assisted reproductive technologies induce temporally specific placental defects and the preeclampsia risk marker sFLT1 in mouse

Vrooman LA, Rhon-Calderon EA, Chao OY, Nguyen DK, Narapareddy L, Dahiya AK, Putt ME, Schultz RM, Bartolomei MS. Development. 2020;147(11):dev186551. doi: 10.1242/dev.186551. PMID: 32471820

Marisa Bartolomei Lab

Temple syndrome and Kagami-Ogata syndrome: clinical presentations, genotypes, models and mechanisms

Prasasya R, Grotheer KV, Siracusa LD, Bartolomei MS. Hum Mol Genet. 2020;29(R1):R107-R116. doi: 10.1093/hmg/ddaa133 PMID: 32592473
Marisa Bartolomei Lab

Genomic imprinting: An epigenetic regulatory system

Bartolomei MS, Oakey RJ, Wutz A. PLoS Genet. 2020 Aug 6;16(8):e1008970. doi: 10.1371/journal.pgen.1008970. PMID: 32760145

Marisa Bartolomei Lab

Loss of epigenetic modifications on the inactive X chromosome and sex-biased gene expression profiles in B cells from NZB/W F1 mice with lupus-like disease

Syrett CM, Sierra I, Beethem ZT, Dubin AH, Anguera MC. J Autoimmun. 2020;107:102357. doi: 10.1016/j.jaut.2019.102357. PMID: 31780316

Montserrat Anguera Lab

Food for Thought

Egervari GGlastad KMBerger SL. Science. 2020;370(657):660-662. doi: 10.1126/science.abb4367.

Shelley Berger Lab

TERMINAL FLOWER 1-FD complex target genes and competition with FLOWERING LOCUS T.

Zhu Y, Klasfeld S, Jeong CW, Jin R, Goto K, Yamaguchi N, Wagner D. Nat Commun. 2020;11(1):5118. doi: 10.1038/s41467-020-18782-1. PMID: 33046692

Doris Wagner Lab

Massively parallel and time-resolved RNA sequencing in single cells with scNT-seq.

Qiu Q, Hu P, Qiu X, Govek KW, Cámara PG, Wu H. Nat Methods. 2020 Aug 31. doi: 10.1038/s41592-020-0935-4. PMID: 32868927

Hao Wu Lab

Alteration of genome folding via contact domain boundary insertion.

Zhang D, Huang P, Sharma M, Keller CA, Giardine B, Zhang H, Gilgenast TG, Phillips-Cremins JE, Hardison RC, Blobel GA. Nat Genet. 2020 Aug 31. doi: 10.1038/s41588-020-0680-8. PMID: 32868908

Gerd Blobel Lab Jennifer Phillips-Cremins Lab

Disruption of ATRX-RNA interactions uncovers roles in ATRX localization and PRC2 function.

Ren W, Medeiros N, Warneford-Thomson R, Wulfridge P, Yan Q, Bian J, Sidoli S, Garcia BA, Skordalakes E, Joyce E, Bonasio R, Sarma K. Nat Commun. 2020;11(1):2219. doi: 10.1038/s41467-020-15902-9. PMID: 32376827

Kavitha Sarma Lab Roberto Bonasio Lab Former Faculty Labs

Structural basis for allosteric PARP-1 retention on DNA breaks.

Zandarashvili L, Langelier MF, Velagapudi UK, Hancock MA, Steffen JD, Billur R, Hannan ZM, Wicks AJ, Krastev DB, Pettitt SJ, Lord CJ, Talele TT, Pascal JM, Black BE. Science. 2020;368(6486). pii: eaax6367. doi: 10.1126/science.aax6367. PMID:32241924

Ben Black Lab

Gene network transitions in embryos depend upon interactions between a pioneer transcription factor and core histones.

Iwafuchi M, Cuesta I, Donahue G, Takenaka N, Osipovich AB, Magnuson MA, Roder H, Seeholzer SH, Santisteban P, Zaret KS. Nat Genet. 2020. doi: 10.1038/s41588-020-0591-8. [Epub ahead of print]. PMID:32203463

Ken Zaret Lab

TooManyCells identifies and visualizes relationships of single-cell clades.

Schwartz GW, Zhou Y, Petrovic J, Fasolino M, Xu L, Shaffer SM, Pear WS, Vahedi G, Faryabi RB. Nat Methods. 2020. doi: 10.1038/s41592-020-0748-5. PMID:32123397

R. Babak Faryabi Lab

Joint profiling of chromatin accessibility and CAR-T integration site analysis at population and single-cell levels.

Wang W, Fasolino M, Cattau B, Goldman N, Kong W, Frederick MA, McCright SJ, Kiani K, Fraietta JA, Vahedi G. Proc. Natl. Acad. Sci. U.S.A. 2020;

Golnaz Vahedi Lab

Genetic Variation in Type 1 Diabetes Reconfigures the 3D Chromatin Organization of T Cells and Alters Gene Expression.

Fasolino M, Goldman N, Wang W, Cattau B, Zhou Y, Petrovic J, Link VM, Cote A, Chandra A, Silverman M, Joyce EF, Little SC; HPAP Consortium, Kaestner KH, Naji A, Raj A, Henao-Mejia J, Faryabi RBVahedi G. Immunity. 2020. pii: S1074-7613(20)30030-3. doi: 10.1016/j.immuni.2020.01.003. [Epub ahead of print]

Klaus Kaestner Lab R. Babak Faryabi Lab Arjun Raj Lab Golnaz Vahedi Lab

Nr4a1 suppresses cocaine-induced behavior via epigenetic regulation of homeostatic target genes.

Carpenter MD, Hu Q, Bond AM, Lombroso SI, Czarnecki KS, Lim CJ, Song H, Wimmer ME, Pierce RC, Heller EA. Nat Commun. 2020;11(504). doi: 110.1038/s41467-020-14331-y.

Elizabeth Heller Lab

On the existence and functionality of topologically associating domains

Beagan J, Phillips-Cremins JE. Nat Genet. 2020;52(1):8-16. doi: 10.1038/s41588-019-0561-1. PMID: 31925403

Jennifer Phillips-Cremins Lab

A Patient-Derived Glioblastoma Organoid Model and Biobank Recapitulates Inter- and Intra-tumoral Heterogeneity

Jacob F, Salinas RD, Zhang DY, Nguyen PTT, Schnoll JG, Wong SZH, Thokala R, Sheikh S, Saxena D, Prokop S, Liu D-A, Qian X, Petrov D, Lucas T, Chen HI, Dorsey JF, Christian KM, Binder ZA, Nasrallah M, Brem S, O’Rourke DM, Ming G-L, Song H. Cell. 2020;180(1):188-204.e22. doi: 10.1016/j.cell.2019.11.036. PMID: 31883794

Hongjun Song Lab

Chromatin structure dynamics during the mitosis-to-G1 phase transition.

Zhang H, Emerson DJ, Gilgenast TG, Titus KR, Lan Y, Huang P, Zhang D, Wang H, Keller CA, Giardine B, Hardison RC, Phillips-Cremins JE, Blobel GA. Nature. 2019;576:158-162. doi: 10.1038/s41586-019-1778-y. PMID: 31776509

Gerd Blobel Lab

Metabolic control of BRISC-SHMT2 assembly regulates immune signalling

Walden M, Tian L, Ross RL, Sykora UM, Byrne DP, Hesketh EL, Masandi SK, Cassel J, George R, Ault JR, El Oualid F, Pawłowski K, Salvino JM, Eyers PA, Ranson NA, Del Galdo F, Greenberg RA, Zeqiraj E. Nature. 2019;570(7760):194-199. doi: 10.1038/s41586-019-1232-1. PMID: 31142841

Roger Greenberg Lab

Altered X-chromosome inactivation in T cells may promote sex-biased autoimmune diseases

Syrett CM, Paneru B, Sandoval-Heglund D, Wang J, Banerjee S, Sindhava V, Behrens EM, Atchison M, Anguera MC. JCI Insight. 2019;4(7):e126751. doi: 10.1172/jci.insight.126751. PMID: 30944248
Montserrat Anguera Lab

Enjoy the silence: X-chromosome inactivation diversity in somatic cells

Sierra I, Anguera MC. Curr Opin Genet Dev. 2019;55:26-31. doi: 10.1016/j.gde.2019.04.012. PMID: 31108425

Montserrat Anguera Lab

Mapping Native R-Loops Genome-wide Using aTargeted Nuclease Approach

Yan et al., 2019, Cell Reports29, 1369–1380 October 29, 2019ª2019 The Author(s).https://doi.org/10.1016/j.celrep.2019.09.052

Kavitha Sarma Lab Roberto Bonasio Lab

Mapping Native R-Loops Genome-wide Using a Targeted Nuclease Approach.

Yan Q, Shields EJ, Bonasio R, Sarma K. Cell Rep. 2019 Oct 29;29(5):1369-1280.e5. doi: 10.1016/j.celrep.2019.09.052. PMID: 3166564

Kavitha Sarma Lab

Structural Features of Transcription Factors Associating with Nucleosome Binding.

Fernandez Garcia M, Moore CD, Schulz KN, Alberto O, Donague G, Harrison MM, Zhu H, Zaret KS. Mol Cell. 2019 Sept 5;75(5):921-932.e6. doi: 10.1016/j.molcel.2019.06.009. PMID: 31303471

Ken Zaret Lab

Chromatin targeting of nuclear pore proteins induces chromatin decondensation.

Kuhn TM, Pascual-Garcia P, Gozalo A, Little SC, Capelson M. J Cell Biol. 2019 Sep 2;218(9):2945-2961. doi: 10.1083/jcb.201807139. Epub 2019 Jul 31. PMID:31366666

Former Faculty Labs

CDK7 inhibition suppresses Castration-Resistant Prostate Cancer through MED1 inactivation.

Rasool RU, Natesan R, Deng Q, Aras S, Lal P, Sander Effron S, Mitchell-Velasquez E, Posimo JM, Carskadon S, Baca SC, Pomerantz MM, Siddiqui J, Schwartz LE, Lee DJ, Palanisamy N, Narla G, Den RB, Freedman ML, Brady DC, Asangani IA. Cancer Discov. 2019 Aug 29. pii: CD-19-0189. doi: 10.1158/2159-8290.CD-19-0189. [Epub ahead of print] PMID:31466944

Irfan Asangani Lab

Circadian lipid synthesis in brown fat maintains murine body temperature during chronic cold.

Adlanmerini M, Carpenter BJ, Remsberg JR, Aubert Y, Peed LC, Richter HJ, Lazar MA. Proc Natl Acad Sci U S A. 2019 Aug 26. pii: 201909883. doi: 10.1073/pnas.1909883116. [Epub ahead of print] PMID:31451658

Mitch Lazar Lab

LSD1 Inhibition Promotes Epithelial Differentiation through Derepression of Fate-Determining Transcription Factors.

Egolf S, Aubert Y, Doepner M, Anderson A, Maldonado-Lopez A, Pacella G, Lee J, Ko EK, Zou J, Lan Y, Simpson CL, Ridky T, Capell BC. Cell Rep. 2019 Aug 20;28(8):1981-1992.e7. doi: 10.1016/j.celrep.2019.07.058. PMID:31433976

Brian Capell Lab

Structure of the Human Core Centromeric Nucleosome Complex.

Allu PK, Dawicki-McKenna JM, Van Eeuwen T, Slavin M, Braitbard M, Xu C, Kalisman N, Murakami K, Black BE. Curr Biol. 2019 Aug 19;29(16):2625-2639.e5. doi: 10.1016/j.cub.2019.06.062. Epub 2019 Jul 25. PMID:31353180

Ben Black Lab

Human Artificial Chromosomes that Bypass Centromeric DNA.

Logsdon GA, Gambogi CW, Liskovykh MA, Barrey EJ, Larionov V, Miga KH, Heun P, Black BE. Cell. 2019 Jul 25;178(3):624-639.e19. doi: 10.1016/j.cell.2019.06.006. PMID:31348889

Ben Black Lab

The Unexpected Noncatalytic Roles of Histone Modifiers in Development and Disease.

Aubert Y, Egolf S, Capell BC. Trends Genet. 2019 Sep;35(9):645-657. doi: 10.1016/j.tig.2019.06.004. Epub 2019 Jul 10. Review. PMID:31301850

Brian Capell Lab

A subset of topologically associating domains fold into mesoscale core-periphery networks.

Huang H, Chen ST, Titus KR, Emerson DJ, Bassett DS, Phillips-Cremins JE. Sci Rep. 2019 Jul 2;9(1):9526. doi: 10.1038/s41598-019-45457-9. PMID:31266973

Jennifer Phillips-Cremins Lab

SAMHD1 Modulates Early Steps during Human Cytomegalovirus Infection by Limiting NF-κB Activation

SAMHD1 Modulates Early Steps during Human Cytomegalovirus Infection by Limiting NF-κB Activation. Kim ET, Roche KL, Kulej K, Spruce LA, Seeholzer SH, Coen DM, Diaz-Griffero F, Murphy EA, Weitzman MD. Cell Rep. 2019 Jul 9;28(2):434-448.e6. doi: 10.1016/j.celrep.2019.06.027. PMID:31291579

Matt Weitzman Lab

LADL: light-activated dynamic looping for endogenous gene expression control

LADL: light-activated dynamic looping for endogenous gene expression control.
Kim JH, Rege M, Valeri J, Dunagin MC, Metzger A, Titus KR, Gilgenast TG, Gong W, Beagan JA, Raj A, Phillips-Cremins JE. Nat Methods. 2019 Jul;16(7):633-639. doi: 10.1038/s41592-019-0436-5. Epub 2019 Jun 24. PMID:31235883

Jennifer Phillips-Cremins Lab

Altered NMDAR Signaling Underlies Autistic-like Features in Mouse Models of CDKL5 Deficiency Disorder.

Altered NMDAR signaling underlies autistic-like features in mouse models of CDKL5 deficiency disorder. Tang S, Terzic B, Wang I-T, Sarmieto N, Sizov K, Cui Y, Takano H, Marsh ED, Zhou Z and Coulter DA. Nature Communications 10: 2655. doi: 10.1038/s41467-019-10689-w. 2019.

Zhaolan Zhou Lab

The E3 ligase adaptor molecule SPOP regulates fetal hemoglobin levels in adult erythroid cells.

Lan X, Khandros E, Huang P, Peslak SA, Bhardwaj SK, Grevet JD, Abdulmalik O, Wang H, Keller CA, Giardine B, Baeza J, Duffner ER, El Demerdash O, Wu XS, Vakoc CR, Garcia BA, Hardison RC, Shi J, Blobel GA. Blood Adv. 2019 May 28;3(10):1586-1597. doi: 10.1182/bloodadvances.2019032318. PMID:31126914

Gerd Blobel Lab Former Faculty Labs

Diversification and collapse of a telomere elongation mechanism.

Saint-Leandre B, Nguyen SC, Levine MT. Genome Res. 2019 Jun;29(6):920-931. doi: 10.1101/gr.245001.118. Epub 2019 May 28. PMID: 31138619

Mia Levine Lab

SR9009 has REV-ERB-independent effects on cell proliferation and metabolism.

Dierickx P, Emmett MJ, Jiang C, Uehara K, Liu M, Adlanmerini M, Lazar MA. Proc Natl Acad Sci U S A. 2019 Jun 18;116(25):12147-12152. doi: 10.1073/pnas.1904226116. Epub 2019 May 24. PMID:31127047

Mitch Lazar Lab

One minute analysis of 200 histone posttranslational modifications by direct injection mass spectrometry.

Sidoli S, Kori Y, Lopes M, Yuan ZF, Kim HJ, Kulej K, Janssen KA, Agosto LM, Cunha JPCD, Andrews AJ, Garcia BA. Genome Res. 2019 Jun;29(6):978-987. doi: 10.1101/gr.247353.118. Epub 2019 May 23. PMID:31123082

Former Faculty Labs

p63 establishes epithelial enhancers at critical craniofacial development genes.

Lin-Shiao E, Lan Y, Welzenbach J, Alexander KA, Zhang Z, Knapp M, Mangold E, Sammons M, Ludwig KU, Berger SL. Sci Adv. 2019 May 1;5(5):eaaw0946. doi: 10.1126/sciadv.aaw0946. eCollection 2019 May. PMID:31049400

Shelley Berger Lab

The HIRA histone chaperone complex subunit UBN1 harbors H3/H4- and DNA-binding activity.

Ricketts MD, Dasgupta N, Fan J, Han J, Gerace M, Tang Y, Black BE, Adams PD, Marmorstein R. J Biol Chem. 2019 Jun 7;294(23):9239-9259. doi: 10.1074/jbc.RA119.007480. Epub 2019 Apr 30. PMID:31040182

Ronen Marmostein Lab

Sex-Specific Regulation of Fear Memory by Targeted Epigenetic Editing of Cdk5.

Sase AS, Lombroso SI, Santhumayor BA, Wood RR, Lim CJ, Neve RL, Heller EA. Biol Psychiatry. 2019 Apr 15;85(8):623-634. doi: 10.1016/j.biopsych.2018.11.022. Epub 2018 Dec 5. PMID:30661667

Elizabeth Heller Lab

Interrogating Histone Acetylation and BRD4 as Mitotic Bookmarks of Transcription.

Behera V, Stonestrom AJ, Hamagami N, Hsiung CC, Keller CA, Giardine B, Sidoli S, Yuan Z-F, Bhanu NV, Werner MT, Wang H, Garcia BA, Hardison RC, Blobel GA. Cell Rep. 2019 Apr 9;27(2):400-415.e5. doi: 10.1016/j.celrep.2019.03.057. PMID: 30970245

Gerd Blobel Lab Former Faculty Labs

Epigenomic reordering induced by Polycomb loss drives oncogenesis but leads to therapeutic vulnerabilities in malignant peripheral nerve sheath tumors.

Wojcik JB, Marchione DM, Sidoli S, Djedid A, Lisby A, Majewski J, Garcia BA. Cancer Res. 2019 Mar 21. pii: canres.3704.2018. doi: 10.1158/0008-5472.CAN-18-3704. [Epub ahead of print] PMID:30898839

Former Faculty Labs

Systematic Evaluation of Statistical Methods for Identifying Looping Interactions in 5C Data.

Gilgenast TG, Phillips-Cremins JE. Cell Syst. 2019 Mar 27;8(3): 197-211. e13. doi: 10.10.16/j.cels.2019.02.006. Epub 2019 Mar 20. PMID:30904376

Jennifer Phillips-Cremins Lab

ATP-citrate lyase multimerization is required for coenzyme-A substrate binding and catalysis.

Bazilevsky GA, Affronti HC, Wei X, Campbell SL, Wellen KE, Marmorstein R. J Biol Chem. 2019 May 3;294(18):7259-7268. doi: 10.1074/jbc.RA118.006685. Epub 2019 Mar 15.
PMID:30877197

Ronen Marmostein Lab

Multiplexed in Situ Imaging Mass Cytometry Analysis of the Human Endocrine Pancreas and Immune System in Type 1 Diabetes.

Wang YJ, Traum D, Schug J, Gao L, Liu C; HPAP Consortium, Atkinson MA, Powers AC, Feldman MD, Naji A, Chang KM, Kaestner KH. Cell Metab. 2019 Mar 5;29(3):769-783.e4. doi: 10.1016/j.cmet.2019.01.003. Epub 2019 Jan 31. PMID:30713110

Klaus Kaestner Lab

The effects of Assisted Reproductive Technologies on genomic imprinting in the placenta.

Rhon-Calderon EA, Vrooman LA, Riesche L, Bartolomei MS. Placenta. 2019 Mar 4. pii: S0143-4004(19)30002-5. doi: 10.1016/j.placenta.2019.02.013. [Epub ahead of print] Review. PMID:30871810

Marisa Bartolomei Lab

Auxin Response Factors promote organogenesis by chromatin-mediated repression of the pluripotency gene SHOOTMERISTEMLESS.

Chung Y, Zhu Y, Wu MF, Simonini S, Kuhn A, Armenta-Medina A, Jin R, Østergaard L, Gillmor CS, Wagner D. Nat Commun. 2019 Feb 21;10(1):886. doi: 10.1038/s41467-019-08861-3. PMID:30792395

Doris Wagner Lab

Coordination between TGF-β cellular signaling and epigenetic regulation during epithelial to mesenchymal transition.

Lu C, Sidoli S, Kulej K, Ross K, Wu CH, Garcia BA. Epigenetics Chromatin. 2019 Feb 8;12(1):11. doi: 10.1186/s13072-019-0256-y. PMID:30736855

Former Faculty Labs

Histone Acetyltransferase p300 Induces De Novo Super-Enhancers to Drive Cellular Senescence.

Sen P, Lan Y, Li CY, Sidoli S, Donahue G, Dou Z, Frederick B, Chen Q, Luense LJ, Garcia BA, Dang W, Johnson FB, Adams PD, Schultz DC, Berger SL. Mol Cell. 2019 Feb 8. pii: S1097-2765(19)30041-3. doi: 10.1016/j.molcel.2019.01.021. [Epub ahead of print] PMID:30773298

Shelley Berger Lab Former Faculty Labs

Patient Adipose Stem Cell-Derived Adipocytes Reveal Genetic Variation that Predicts Antidiabetic Drug Response.

Hu W, Jiang C, Guan D, Dierickx P, Zhang R, Moscati A, Nadkarni GN, Steger DJ, Loos RJF, Hu C, Jia W, Soccio RE, Lazar MA. Cell Stem Cell. 2019 Feb 7;24(2):299-308.e6. doi: 10.1016/j.stem.2018.11.018. Epub 2019 Jan 10. PMID:30639037

Mitch Lazar Lab

Transcriptional Burst Initiation and Polymerase Pause Release Are Key Control Points of Transcriptional Regulation.

Bartman CR, Hamagami N, Keller CA, Giardine B, Hardison RC, Blobel GA, Raj A. Mol Cell. 2019 Feb 7;73(3):519-532.e4. doi: 10.1016/j.molcel.2018.11.004. Epub 2018 Dec 13.
PMID:30554946

Gerd Blobel Lab Arjun Raj Lab

Lineage-specific reorganization of nuclear peripheral heterochromatin and H3K9me2 domains.

See K, Lan Y, Rhoades J, Jain R, Smith CL, Epstein JA. Development. 2019 Feb 5;146(3). pii: dev174078. doi: 10.1242/dev.174078. PMID:30723106

Jon Epstein Lab

High performance of cerebrospinal fluid immunoglobulin G analysis for diagnosis of multiple sclerosis

Gamraoui S, Mathey G, Debouverie M, Malaplate C, Anxionnat R, Guillemin F, Epstein J. J Neurol. 2019 Apr;266(4):902-909. doi: 10.1007/s00415-019-09212-4. Epub 2019 Feb 1. PMID:30707357

Jon Epstein Lab

A Time to Press Reset and Regenerate Cardiac Stem Cell Biology.

Epstein JA. JAMA Cardiol. 2019 Feb 1;4(2):95-96. doi: 10.1001/jamacardio.2018.4435. No abstract available. PMID:30480702

Jon Epstein Lab

RAD52 and SLX4 act nonepistatically to ensure telomere stability during alternative telomere lengthening.

Verma P, Dilley RL, Zhang T, Gyparaki MT, Li Y, Greenberg RA. Genes Dev. 2019 Feb 1;33(3-4):221-235. doi: 10.1101/gad.319723.118. Epub 2019 Jan 28. PMID:30692206

Roger Greenberg Lab

H3K9me3-heterochromatin loss at protein-coding genes enables developmental lineage specification.

Nicetto D, Donahue G, Jain T, Peng T, Sidoli S, Sheng L, Montavon T, Becker JS, Grindheim JM, Blahnik K, Garcia BA, Tan K, Bonasio R, Jenuwein T, Zaret KS. Science. 2019 Jan 18;363(6424):294-297. doi: 10.1126/science.aau0583. Epub 2019 Jan 3. PMID:30606806

Ken Zaret Lab Roberto Bonasio Lab Former Faculty Labs

Allele-specific RNA imaging shows that allelic imbalances can arise in tissues through transcriptional bursting.

Symmons O, Chang M, Mellis IA, Kalish JM, Park J, Suszták K, Bartolomei MS, Raj A. PLoS Genet. 2019 Jan 9;15(1):e1007874. doi: 10.1371/journal.pgen.1007874. eCollection 2019 Jan.
PMID:30605160

Arjun Raj Lab

Diversity of Epigenetic Features of the Inactive X-Chromosome in NK Cells, Dendritic Cells, and Macrophages.

Syrett CM, Sindhava V, Sierra I, Dubin AH, Atchison M, Anguera MC. Front Immunol. 2019 Jan 8;9:3087. doi: 10.3389/fimmu.2018.03087. eCollection 2018.

Montserrat Anguera Lab

Resistance to BET Inhibitor Leads to Alternative Therapeutic Vulnerabilities in Castration-Resistant Prostate Cancer

Pawar A, Gollavilli PN, Wang S, Asangani IA. Cell Rep. 2018;22(9):2236-2245. doi: 10.1016/j.celrep.2018.02.011 PMID: 29490263

Irfan Asangani Lab

Targeted demethylation at the CDKN1C/p57 induces human β cell replication.

Ou K, Yu M, Moss NG, Wang YJ, Wang AW, Nguyen SC, Jiang C, Feleke E, Kameswaran V, Joyce EF, Naji A, Glaser B, Avrahami D, Kaestner KHJ Clin Invest. 2018 Oct 23. pii: 99170. doi: 10.1172/JCI99170.

Klaus Kaestner Lab

Recurrent Amplification of the Heterochromatin Protein 1 (HP1) Gene Family across Diptera.

Helleu Q, Levine MT. Mol Biol Evol. 2018 Oct 1;35(10):2375-2389. doi: 10.1093/molbev/msy128. PMID: 29924345

Mia Levine Lab

Sex-Specific Gene Expression Differences Are Evident in Human Embryonic Stem Cells and During In Vitro Differentiation of Human Placental Progenitor Cells.

Syrett CM, Sierra I, Berry CL, Beiting D, Anguera MC. Stem Cells Dev. 2018 Oct 1;27(19):1360-1375. doi: 10.1089/scd.2018.0081. Epub 2018 Aug 21. PMID: 29993333

Montserrat Anguera Lab

Hydrogen-Deuterium Exchange Coupled to Top- and Middle-Down Mass Spectrometry Reveals Histone Tail Dynamics before and after Nucleosome Assembly.

Karch KR, Coradin M, Zandarashvili L, Kan ZY, Gerace M, Englander SW, Black BE, Garcia BA. Structure. 2018 Aug 25. pii: S0969-2126(18)30294-6. doi: 10.1016/j.str.2018.08.006. [Epub ahead of print] PMID: 30293810

Former Faculty Labs

Long genes linked to autism spectrum disorders harbor broad enhancer-like chromatin domains

Long genes linked to autism spectrum disorders harbor broad enhancer-like chromatin domains. Zhao YT, Kwon DY, Johnson BS, Fasolino M, Lamonica JM, Kim YJ, Zhao BS, He C, Vahedi G, Kim TH, Zhou ZGenome Res. 2018 Jul;28(7):933-942. doi: 10.1101/gr.233775.117. Epub 2018 May 30.

Zhaolan Zhou Lab

Domain-focused CRISPR screen identifies HRI as a fetal hemoglobin regulator in human erythroid cells

Domain-focused CRISPR screen identifies HRI as a fetal hemoglobin regulator in human erythroid cells. Grevet JD, Lan X, Hamagami N, Edwards CR, Sankaranarayanan L, Ji X, Bhardwaj SK, Face CJ, Posocco DF, Abdulmalik O, Keller CA, Giardine B, Sidoli S, Garcia BA, Chou ST, Liebhaber SA, Hardison RC, Shi J, Blobel GAScience. 2018 Jul 20;361(6399):285-290. doi: 10.1126/science.aao0932

Gerd Blobel Lab

EpiProfile 2.0: A Computational Platform for Processing Epi-Proteomics Mass Spectrometry Data

EpiProfile 2.0: A Computational Platform for Processing Epi-Proteomics Mass Spectrometry Data. Yuan ZF, Sidoli S, Marchione DM, Simithy J, Janssen KA, Szurgot MR, Garcia BAJ Proteome Res. 2018 Jul 6;17(7):2533-2541. doi: 10.1021/acs.jproteome.8b00133. Epub 2018 May 30.

Former Faculty Labs

Structure of Human NatA and Its Regulation by the Huntingtin Interacting Protein HYPK

Structure of Human NatA and Its Regulation by the Huntingtin Interacting Protein HYPK. Gottlieb L, Marmorstein R. Structure. 2018 Jul 3;26(7):925-935.e8. doi: 10.1016/j.str.2018.04.003.

Ronen Marmostein Lab

Recurrent amplification of the Heterochromatin Protein 1 (HP1) gene family across Dipter

Recurrent amplification of the Heterochromatin Protein 1 (HP1) gene family across Dipter. Helleu Q, Levine MT. Mol Biol Evol. 2018 Jun 19. doi: 10.1093/molbev/msy128. [Epub ahead of print]

Mia Levine Lab

N-(7-Cyano-6-(4-fluoro-3-(2-(3-(trifluoromethyl)phenyl)acetamido)phenoxy)benzo[d]thiazol-2-yl)cyclopropanecarboxamide (TAK632) Promotes Inhibition of BRAF through the Induction of Inhibited Dimers

N-(7-Cyano-6-(4-fluoro-3-(2-(3-(trifluoromethyl)phenyl)acetamido)phenoxy)benzo[d]thiazol-2-yl)cyclopropanecarboxamide (TAK632) Promotes Inhibition of BRAF through the Induction of Inhibited Dimers. Grasso M, Estrada MA, Berrios KN, Winkler JD, Marmorstein R. J Med Chem. 2018 Jun 14;61(11):5034-5046. doi: 10.1021/acs.jmedchem.8b00499.

Ronen Marmostein Lab

EWS/ETS-driven Ewing Sarcoma requires BET bromodomain proteins

EWS/ETS-driven Ewing Sarcoma requires BET bromodomain proteins. Gollavilli PN, Pawar A, Wilder-Romans K, Ramakrishnan N, Engelke CG, Dommeti VL, Krishnamurthy PM, Nallasivam A, Apel IJ, Xu T, Qin Z, Feng FY, Asangani IACancer Res. 2018 Jun 13. pii: canres.0484.2018. doi: 10.1158/0008-5472.CAN-18-0484

Irfan Asangani Lab

Emetine inhibits Zika and Ebola virus infections through two molecular mechanisms: inhibiting viral replication and decreasing viral entry

Emetine inhibits Zika and Ebola virus infections through two molecular mechanisms: inhibiting viral replication and decreasing viral entry. Yang S, Xu M, Lee EM, Gorshkov K, Shiryaev SA, He S, Sun W, Cheng YS, Hu X, Tharappel AM, Lu B, Pinto A, Farhy C, Huang CT, Zhang Z, Zhu W, Wu Y, Zhou Y, Song G, Zhu H, Shamim K, Martínez-Romero C, García-Sastre A, Preston RA, Jayaweera DT, Huang R, Huang W, Xia M, Simeonov A, Ming G, Qiu X, Terskikh AV, Tang H, Song H, Zheng W. Cell Discov. 2018 Jun 5;4:31. doi: 10.1038/s41421-018-0034-1. eCollection 2018.

Hongjun Song Lab

High-Quality Genome Assemblies Reveal Long Non-coding RNAs Expressed in Ant Brains

High-Quality Genome Assemblies Reveal Long Non-coding RNAs Expressed in Ant Brains. Shields EJ, Sheng L, Weiner AK, Garcia BA, Bonasio R. Cell Rep. 2018 Jun 5;23(10):3078-3090. doi: 10.1016/j.celrep.2018.05.014.

Roberto Bonasio Lab

5C-ID: Increased resolution Chromosome-Conformation-Capture-Carbon-Copy with in situ 3C and double alternating primer design

5C-ID: Increased resolution Chromosome-Conformation-Capture-Carbon-Copy with in situ 3C and double alternating primer design. Kim JH, Titus KR, Gong W, Beagan JA, Cao Z, Phillips-Cremins JE. Methods. 2018 Jun 1;142:39-46. doi: 10.1016/j.ymeth.2018.05.005. Epub 2018 May 24.

Jennifer Phillips-Cremins Lab

Non-equilibrium repressor binding kinetics link DNA damage dose to transcriptional timing within the SOS gene network

Non-equilibrium repressor binding kinetics link DNA damage dose to transcriptional timing within the SOS gene network. Culyba MJ, Kubiak JM, Mo CY, Goulian M, Kohli RM. PLoS Genet. 2018 Jun 1;14(6):e1007405. doi: 10.1371/journal.pgen.1007405.

Rahul Kohli Lab

Distinct macrophage populations direct inflammatory versus physiological changes in adipose tissue

Distinct macrophage populations direct inflammatory versus physiological changes in adipose tissue. Hill DA, Lim HW, Kim YH, Ho WY, Foong YH, Nelson VL, Nguyen HCB, Chegireddy K, Kim J, Habertheuer A, Vallabhajosyula P, Kambayashi T, Won KJ, Lazar MA. Proc Natl Acad Sci U S A. 2018 May 29;115(22):E5096-E5105. doi: 10.1073/pnas.1802611115. Epub 2018 May 14.

Mitch Lazar Lab

Mice exposed to bisphenol A exhibit depressive-like behavior with neurotransmitter and neuroactive steroid dysfunction

Mice exposed to bisphenol A exhibit depressive-like behavior with neurotransmitter and neuroactive steroid dysfunction. Xin F, Fischer E, Krapp C, Krizman EN, Lan Y, Mesaros C, Snyder NW, Bansal A, Robinson MB, Simmons RA, Bartolomei MS. Horm Behav. 2018 Jun;102:93-104. doi: 10.1016/j.yhbeh.2018.05.010. Epub 2018 May 18.

Marisa Bartolomei Lab

Endocardial Hippo signaling regulates myocardial growth and cardiogenesis

Endocardial Hippo signaling regulates myocardial growth and cardiogenesis. Artap S, Manderfield LJ, Smith CL, Poleshko A, Aghajanian H, See K, Li L, Jain R, Epstein JA. Dev Biol. 2018 Aug 1;440(1):22-30. doi: 10.1016/j.ydbio.2018.04.026. Epub 2018 May 1. PMID: 29727635

Jon Epstein Lab

In vivo clonal analysis reveals spatiotemporal regulation of thalamic nucleogenesis

In vivo clonal analysis reveals spatiotemporal regulation of thalamic nucleogenesis. Wong SZH, Scott EP, Mu W, Guo X, Borgenheimer E, Freeman M, Ming GL, Wu QF, Song H, Nakagawa Y. PLoS Biol. 2018 Apr 23;16(4):e2005211. doi: 10.1371/journal.pbio.2005211. eCollection 2018 Apr.

Hongjun Song Lab

Dysregulation of the epigenetic landscape of normal aging in Alzheimer’s disease

Dysregulation of the epigenetic landscape of normal aging in Alzheimer’s disease. Nativio R, Donahue G, Berson A, Lan Y, Amlie-Wolf A, Tuzer F, Toledo JB, Gosai SJ, Gregory BD, Torres C, Trojanowski JQ, Wang LS, Johnson FB, Bonini NM, Berger SL. Nat Neurosci. 2018 Apr;21(4):497-505. doi: 10.1038/s41593-018-0101-9.

Neuroepigenetics Shelley Berger Lab

Dysregulation of the epigenetic landscape of normal aging in Alzheimer’s disease

Dysregulation of the epigenetic landscape of normal aging in Alzheimer’s disease. Nativio R, Donahue G, Berson A, Lan Y, Amlie-Wolf A, Tuzer F, Toledo JB, Gosai SJ, Gregory BD, Torres C, Trojanowski JQ, Wang LS, Johnson FB, Bonini NM, Berger SL. Nat Neurosci. 2018 Apr;21(4):497-505. doi: 10.1038/s41593-018-0101-9.

Neuroepigenetics Shelley Berger Lab

Imprinted gene dysregulation in a Tet1 null mouse model is stochastic and variable in the germline and offspring

Imprinted gene dysregulation in a Tet1 null mouse model is stochastic and variable in the germline and offspring. SanMiguel JM, Abramowitz LK, Bartolomei MS.Development. 2018 Mar 29;145(7). pii: dev160622. doi: 10.1242/dev.160622.

Marisa Bartolomei Lab

The scaffolding protein JADE1 physically links the acetyltransferase subunit HBO1 with its histone H3-H4 substrate

The scaffolding protein JADE1 physically links the acetyltransferase subunit HBO1 with its histone H3-H4 substrate. Han J, Lachance C, Ricketts MD, McCullough CE, Gerace M, Black BE, Côté J, Marmorstein R. J Biol Chem. 2018 Mar 23;293(12):4498-4509. doi: 10.1074/jbc.RA117.000677.

Ronen Marmostein Lab

Detecting hierarchical genome folding with network modularity

Detecting hierarchical genome folding with network modularity. Norton HK, Emerson DJ, Huang H, Kim J, Titus KR, Gu S, Bassett DS, Phillips-Cremins JE. Nat Methods. 2018 Feb;15(2):119-122. doi: 10.1038/nmeth.4560. Epub 2018 Jan 15. PMID: 29334377

Jennifer Phillips-Cremins Lab

Rare Cell Detection by Single-Cell RNA Sequencing as Guided by Single-Molecule RNA FISH

Rare Cell Detection by Single-Cell RNA Sequencing as Guided by Single-Molecule RNA FISH. Torre E, Dueck H, Shaffer S, Gospocic J, Gupte R, Bonasio R, Kim J, Murray J, Raj A. Cell Syst. 2018 Feb 28;6(2):171-179.e5. doi: 10.1016/j.cels.2018.01.014. Epub 2018 Feb 14. PMID: 29454938

Arjun Raj Lab

Inhibitors of LexA Autoproteolysis and the Bacterial SOS Response Discovered by an Academic-Industry Partnership

Inhibitors of LexA Autoproteolysis and the Bacterial SOS Response Discovered by an Academic-Industry Partnership. Mo CY, Culyba MJ, Selwood T, Kubiak JM, Hostetler ZM, Jurewicz AJ, Keller PM, Pope AJ, Quinn A, Schneck J, Widdowson KL, Kohli RM. ACS Infect Dis. 2018 Mar 9;4(3):349-359. doi: 10.1021/acsinfecdis.7b00122.

Rahul Kohli Lab

Dysregulation of the epigenetic landscape of normal aging in Alzheimer’s disease.

Raffaella native,Greg Donahue, Amit Berson, Yemin Lan, Alexandre Amlie-Wolf, Ferit Tuzer, Jon B. Toledo, Sager J, Gosai, Brian D. Gregory, Claudio Torres, John Q. Trojanowski, Li-San Wang, F. Brad Johnson, Nancy M. Bonini, & Shelley Berger. Nature Neuroscience volume 21, pages497–505 (2018) doi:10.1038/s41593-018-0101-9

Shelley Berger Lab

NAD+ analog reveals PARP-1 substrate-blocking mechanism and allosteric communication from catalytic center to DNA-binding domains

NAD+ analog reveals PARP-1 substrate-blocking mechanism and allosteric communication from catalytic center to DNA-binding domains. Langelier MF, Zandarashvili L, Aguiar PM, Black BE, Pascal JM. Nat Commun. 2018 Feb 27;9(1):844. doi: 10.1038/s41467-018-03234-8. PMID: 29487285

Ben Black Lab

Exploiting genetic variation to uncover rules of transcription factor binding and chromatin accessibility

Exploiting genetic variation to uncover rules of transcription factor binding and chromatin accessibility. Behera V, Evans P, Face CJ, Hamagami N, Sankaranarayanan L, Keller CA, Giardine B, Tan K, Hardison RC, Shi J, Blobel GA. Nat Commun. 2018 Feb 22;9(1):782. doi: 10.1038/s41467-018-03082-6. PMID: 29472540

Gerd Blobel Lab

Lineage-Determining Transcription Factor TCF-1 Initiates the Epigenetic Identity of T Cells

Lineage-Determining Transcription Factor TCF-1 Initiates the Epigenetic Identity of T Cells. Johnson JL, Georgakilas G, Petrovic J, Kurachi M, Cai S, Harly C, Pear WS, Bhandoola A, Wherry EJ, Vahedi G. Immunity. 2018 Feb 20;48(2):243-257.e10. doi: 10.1016/j.immuni.2018.01.012.

Golnaz Vahedi Lab

KMT2D regulates p63 target enhancers to coordinate epithelial homeostasis

KMT2D regulates p63 target enhancers to coordinate epithelial homeostasis. Lin-Shiao E, Lan Y, Coradin M, Anderson A, Donahue G, Simpson CL, Sen P, Saffie R, Busino L, Garcia BA, Berger SL, Capell BC. Genes Dev. 2018 Jan 15;32(2):181-193. doi: 10.1101/gad.306241.117. Epub 2018 Feb 12.

Shelley Berger Lab Brian Capell Lab

Rev-erbα dynamically modulates chromatin looping to control circadian gene transcription

Rev-erbα dynamically modulates chromatin looping to control circadian gene transcription. Kim YH, Marhon SA, Zhang Y, Steger DJ, Won KJ, Lazar MA. Science. 2018 Mar 16;359(6381):1274-1277. doi: 10.1126/science.aao6891. Epub 2018 Feb 8.

Mitch Lazar Lab

Genomic and Proteomic Resolution of Heterochromatin and Its Restriction of Alternate Fate Genes

Genomic and Proteomic Resolution of Heterochromatin and Its Restriction of Alternate Fate Genes.  Justin S. Becker, Ryan L. McCarthy, Simone Sidoli, Greg Donahue, Kelsey E. Kaeding, Zhiying He, Shu Lin, Benjamin A. Garcia, Kenneth S. Zaret.  DOI: http://dx.doi.org/10.1016/j.molcel.2017.11.030

Ken Zaret Lab

Identifying Host Factors Associated with DNA Replicated During Virus Infection

Identifying Host Factors Associated with DNA Replicated During Virus Infection. Reyes ED, Kulej K, Pancholi NJ, Akhtar LN, Avgousti DC, Kim ET, Bricker DK, Spruce LA, Koniski SA, Seeholzer SH, Isaacs SN, Garcia BA, Weitzman MD.  Mol Cell Proteomics. 2017 Dec;16(12):2079-2097. doi: 10.1074/mcp.M117.067116. Epub 2017 Oct 2.

Matt Weitzman Lab

Dissecting Cell-Type Composition and Activity-Dependent Transcriptional State in Mammalian Brains by Massively Parallel Single-Nucleus RNA-Seq

Dissecting Cell-Type Composition and Activity-Dependent Transcriptional State in Mammalian Brains by Massively Parallel Single-Nucleus RNA-Seq. Hu P, Fabyanic E, Kwon DY, Tang S, Zhou Z, Wu H.  Mol Cell. 2017 Dec 7;68(5):1006-1015.e7. doi: 10.1016/j.molcel.2017.11.017.

Neuroepigenetics Hao Wu Lab

BAP1: case report and insight into a novel tumor suppressor

BAP1: case report and insight into a novel tumor suppressor. Ghosh K, Modi B, James WD, Capell BC.  BMC Dermatol. 2017 Nov 22;17(1):

Brian Capell Lab

The nucleosomal surface is the main target of histone ADP-ribosylation in response to DNA damage

The nucleosomal surface is the main target of histone ADP-ribosylation in response to DNA damage. Karch KR, Langelier MF, Pascal JM, Garcia BA.  Mol Biosyst. 2017 Nov 21;13(12):2660-2671.

Former Faculty Labs

Temporal Control of Mammalian Cortical Neurogenesis by m6A Methylation

Temporal Control of Mammalian Cortical Neurogenesis by m6A Methylation. Ki-Jun Yoon, Francisca Rojas Ringeling, Caroline Vissers, Fadi Jacob, Michael Pokrass, Dennisse Jimenez-Cyrus, Yijing SU, Nam-Shik Kim, Yunhua Zhu, Lily Zheng, Sungan Kim, Xinyuan Wang, Lousic C. Dore, Pen Jin, Sergi Regot, Jaoxi Zhuang, Stefan Canzar, Chuan He, Guo-li Ming, Hongjun Song.  DOI: dx.doi.org10.1016/j.cell.2017.09.003.

Neuroepigenetics Hongjun Song Lab

The Crucial Role of DNA Methylation and MeCP2 in Neuronal Function

The Crucial Role of DNA Methylation and MeCP2 in Neuronal Function. Fasolino M, Zhou Z.  Genes. 8(5) pii: E141, 2017.
Zhaolan Zhou Lab

Characterization of histone acylations links chromatin modifications with metabolism

Characterization of histone acylations links chromatin modifications with metabolism Simithy J, Sidoli S, Yuan ZF, Coradin M, Bhanu NV, Marchione DM, Klein BJ, Bazilevsky GA, McCullough CE, Magin RS, Kutateladze TG, Snyder NW, Marmorstein R, Garcia BA.  Nat Commun. 2017 Oct 26;8(1):1141.

Former Faculty Labs

Biotin tagging of MeCP2 in mice reveals contextual insights into the Rett syndrome transcriptome

Biotin tagging of MeCP2 in mice reveals contextual insights into the Rett syndrome transcriptome. Johnson BS, Zhao YT, Fasolino M, Lamonica JM, Kim YJ, Georgakilas G, Wood KH, Bu D, Cui Y, Goffin D, Vahedi G, Kim TH, Zhou Z.  Nat Med. 2017 Oct;23(10):1203-1214.

Neuroepigenetics Zhaolan Zhou Lab

Genome-Nuclear Lamina Interactions Regulate Cardiac Stem Cell Lineage Restriction

Genome-Nuclear Lamina Interactions Regulate Cardiac Stem Cell Lineage Restriction. Poleshko A, Shah PP, Gupta M, Babu A, Morley MP, Manderfield LJ, Ifkovits JL, Calderon D, Aghajanian H, Sierra-Pagán JE, Sun Z, Wang Q, Li L, Dubois NC, Morrisey EE, Lazar MA, Smith CL, Epstein JA, Jain R.  Cell. 2017 Oct 19;171(3):573-587.e14. doi: 10.1016/j.cell.2017.09.018. Epub 2017 Oct 12.

Jon Epstein Lab

Genetic drivers of repeat expansion disorders localize to 3-D chromatin domain boundaries

Genetic drivers of repeat expansion disorders localize to 3-D chromatin domain boundaries. 2017 Sept 20.  James Sun, Linda Zhou, Daniel J Emerson, Thomas G. Gilgenast, Katelyn Titus, Jonathan A. Beagan, Jennifer E. Phillips-Cremins.  DOI: 10.1101/191213

Jennifer Phillips-Cremins Lab

Loss of Xist RNA from the inactive X during B cell development is restored in a dynamic YY1-dependent two-step process in activated B cells

Loss of Xist RNA from the inactive X during B cell development is restored in a dynamic YY1-dependent two-step process in activated B cells.  Syrett CM, Sindhava V, Hodawadekar S, Myles A, Liang G, Zhang Y, Nandi S, Cancro M, Atchison M, Anguera MC. PLoS Genet. 2017 Oct 9;13(10):e1007050

Montserrat Anguera Lab

Cytoplasmic chromatin triggers inflammation in senescence and cancer

Cytoplasmic chromatin triggers inflammation in senescence and cancer. Dou Z, Ghosh K, Vizioli MG, Zhu J, Sen P, Wangensteen KJ, Simithy J, Lan Y, Lin Y, Zhou Z, Capell BC, Xu C, Xu M, Kieckhaefer JE, Jiang T, Shoshkes-Carmel M, Tanim KMAA, Barber GN, Seykora JT, Millar SE, Kaestner KH, Garcia BA, Adams PD, Berger SL.  Nature. 2017 Oct 19;550(7676):402-406. doi: 10.1038/nature24050. Epub 2017 Oct 4.

Shelley Berger Lab

Intramolecular autoinhibition of Checkpoint Kinase 1 is mediated by conserved basic motifs of the C-terminal Kinase Associated-1 domain

Intramolecular autoinhibition of Checkpoint Kinase 1 is mediated by conserved basic motifs of the C-terminal Kinase Associated-1 domain  Emptage RP, Schoenberger MJ, Ferguson KM, Marmorstein R.  J Biol Chem. 2017 Sep 25. pii: jbc.M117.811265. doi: 10.1074/jbc.M117.811265.

Ronen Marmostein Lab

Biotin tagging of MeCP2 in mice reveals contextual insights into the Rest syndrome transcriptome

Biotin tagging of MeCP2 in mice reveals contextual insights into the Rest syndrome transcriptome. Johnson BS, Zhao YT, Fasolino M, Lamonica JM, Kim YJ, Georgakilas G, Wood KH, Bu D, Cui Y, Goffin D, Vahedi G, Kim TH, Zhou Z.  Nat Med. 2017 Sep 18. DOI 10.1038/nm.4406

Zhaolan Zhou Lab

An HDAC3-PROX1 corepressor module acts on HNF4α to control hepatic triglycerides

An HDAC3-PROX1 corepressor module acts on HNF4α to control hepatic triglycerides  Armour SM, Remsberg JR, Damle M, Sidoli S, Ho WY, Li Z, Garcia BA, Lazar MA.  Nat Commun. 2017 Sep 15;8(1):549. doi: 10.1038/s41467-017-00772-5.

Mitch Lazar Lab

Mitotic transcription and waves of gene reactivation during mitotic exit

Mitotic transcription and waves of gene reactivation during mitotic exit. Katherine C. Palozola, Greg, Donahue, Hong Liu, Gregory R Grant, Justin S. Becker, Allison Cote, Hongtao Yu, Arjun Raj, Kenneth S. Zaret. Published Online 12 Sep 2017 full access. doi: 10.1126/science.aal4671

Developmental Ken Zaret Lab

Dense Bicoid hubs accentuate binding along the morphogen gradient.

Dense Bicoid hubs accentuate binding along the morphogen gradient. M. Mir, A. Reimer, J. E. Haines, X.-Y. Li, M. Stadler, H. Garcia, M. B. Eisen, X. Darzacq. Genes Dev. 31: 1784-1794 2017.

Mustafa Mir Lab

A Small-Molecule Inducible Synthetic Circuit for Control of the SOS Gene Network without DNA Damage

A Small-Molecule Inducible Synthetic Circuit for Control of the SOS Gene Network without DNA Damage. Kubiak JM, Culyba MJ, Liu MY, Mo CY, Goulian M, Kohli RM.  ACS Synth Biol. 2017 Sep 1. doi: 10.1021/acssynbio.7b00108.

Rahul Kohli Lab

Proteome-wide acetylation dynamics in human cells

Proteome-wide acetylation dynamics in human cells. Kori Y, Sidoli S, Yuan ZF, Lund PJ, Zhao X, Garcia BA. Sci Rep. 2017 Aug 31;7(1):10296.

Cancer and Metabolism Former Faculty Labs

Cis and trans determinants of epigenetic silencing by Polycomb repressive complex 2 in Arabidopsis

Cis and trans determinants of epigenetic silencing by Polycomb repressive complex 2 in Arabidopsis. Xiao J, Jin R, Yu X, Shen M, Wagner JD, Pai A, Song C, Zhuang M, Klasfeld S, He C, Santos AM, Helliwell C, Pruneda-Paz JL, Kay SA, Lin X, Cui S, Garcia MF, Clarenz O, Goodrich J, Zhang X, Austin RS, Bonasio R, Wagner D.  Nat Genet. 2017 Aug 21. doi: 10.1038/ng.3937.

Developmental Doris Wagner Lab Roberto Bonasio Lab

Comparative analysis of three-dimensional chromosomal architecture identifies a novel fetal hemoglobin regulatory element

Comparative analysis of three-dimensional chromosomal architecture identifies a novel fetal hemoglobin regulatory element. Huang P, Keller CA, Giardine B, Grevet JD, Davies JOJ, Hughes JR, Kurita R, Nakamura Y, Hardison RC, Blobel GA.  Genes Dev. 2017 Aug 15;31(16):1704-1713.

Gerd Blobel Lab

The Neuropeptide Corazonin Controls Social Behavior and Caste Identity in Ants

The Neuropeptide Corazonin Controls Social Behavior and Caste Identity in Ants.  Gospocic J, Shields EJ, Glastad KM, Lin Y, Penick CA, Yan H, Mikheyev AS, Linksvayer TA, Garcia BA, Berger SL, Liebig J, Reinberg D, Bonasio R.  Cell. 2017 Aug 10;170(4):748-759.e12. doi: 10.1016/j.cell.2017.07.014

Developmental Roberto Bonasio Lab

Adenovirus core protein VII down-regulates the DNA damage response on the host genome

Adenovirus core protein VII down-regulates the DNA damage response on the host genome. Avgousti DC, Della Fera AN, Otter CJ, Herrmann C, Pancholi NJ, Weitzman MD.  J Virol. 2017 Aug 9. pii: JVI.01089-17. doi: 10.1128/JVI.01089-17.

Matt Weitzman Lab

Expanded Satellite Repeats Amplify a Discrete CENP-A Nucleosome Assembly Site on Chromosomes that Drive in Female Meiosis

Expanded Satellite Repeats Amplify a Discrete CENP-A Nucleosome Assembly Site on Chromosomes that Drive in Female Meiosis  Iwata-Otsubo A, Dawicki-McKenna JM, Akera T, Falk SJ, Chmátal L, Yang K, Sullivan BA, Schultz RM, Lampson MA, Black BE.  Curr Biol. 2017 Aug 7;27(15):2365-2373.e8. doi: 10.1016/j.cub.2017.06.069.

Ben Black Lab

Bile Acids and Tryptophan Metabolism Are Novel Pathways Involved in Metabolic Abnormalities in BPA-Exposed Pregnant Mice and Male Offspring

Bile Acids and Tryptophan Metabolism Are Novel Pathways Involved in Metabolic Abnormalities in BPA-Exposed Pregnant Mice and Male Offspring. Susiarjo M, Xin F, Stefaniak M, Mesaros C, Simmons RA, Bartolomei MS.  Endocrinology. 2017 Aug 1;158(8):2533-2542. DOI: 10.1210/en.2017-00046.

Marisa Bartolomei Lab

Diverse BRCA1 and BRCA2 Reversion Mutations in Circulating Cell-Free DNA of Therapy-Resistant Breast or Ovarian Cancer

Diverse BRCA1 and BRCA2 Reversion Mutations in Circulating Cell-Free DNA of Therapy-Resistant Breast or Ovarian Cancer. Weigelt B, Comino-Méndez I, de Bruijn I, Tian L, Meisel JL, Garcia-Murillas I, Fribbens C, Cutts R, Martelotto LG, Ng CKY, Lim RS, Selenica P, Piscuoglio S, Aghajanian C, Norton L, Murali R, Hyman DM, Borsu L, Arcila ME, Konner J, Reis-Filho JS, Robson M, Turner NC, Greenberg RA.  Clin Cancer Res. 2017 Aug 1. pii: clincanres.0544.2017. DOI: 10.1158/1078-0432.CCR-17-0544.

Roger Greenberg Lab

Mitotic progression following DNA damage enables pattern recognition within micronuclei

Mitotic progression following DNA damage enables pattern recognition within micronuclei. Harding SM, Benci JL, Irianto J, Discher DE, Minn AJ, Greenberg RA.  Nature. 2017 Aug 24;548(7668):466-470. DOI: 10.1038/nature23470. Epub 2017 Jul 31 PMID: 28759889

Cancer and Metabolism Roger Greenberg Lab

YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment

YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment. Beagan JA, Duong MT, Titus KR, Zhou L, Cao Z, Ma J, Lachanski CV, Gillis DR, Phillips-Cremins JE.  Genome Res. 2017 Jul;27(7):1139-1152.

Spatial / Architectural Jennifer Phillips-Cremins Lab

APOBEC3A efficiently deaminates methylated, but not TET-oxidized, cytosine bases in DNA

APOBEC3A efficiently deaminates methylated, but not TET-oxidized, cytosine bases in DNA. Schutsky EK, Nabel CS, Davis AKF, DeNizio JE, Kohli RM.  Nucleic Acids Res. 2017 Jul 27;45(13):7655-7665. doi: 10.1093/nar/gkx345.

Rahul Kohli Lab

The hepatic circadian clock fine-tunes the lipogenic response to feeding through RORα/γ

The hepatic circadian clock fine-tunes the lipogenic response to feeding through RORα/γ  Zhang Y, Papazyan R, Damle M, Fang B, Jager J, Feng D, Peed LC, Guan D, Sun Z, Lazar MA.  Genes Dev. 2017 Jul 26. doi: 10.1101/gad.302323.117.

Mitch Lazar Lab

Detection of early pancreatic ductal adenocarcinoma with thrombospondin-2 and CA19-9 blood markers

Detection of early pancreatic ductal adenocarcinoma with thrombospondin-2 and CA19-9 blood markers  Kim J, Bamlet WR, Oberg AL, Chaffee KG, Donahue G, Cao XJ, Chari S, Garcia BA, Petersen GM, Zaret KS.  Sci Transl Med. 2017 Jul 12;9(398). pii: eaah5583. DOI: 10.1126/scitranslmed.aah5583.

Ken Zaret Lab

Metabolic labeling in middle-down proteomics allows for investigation of the dynamics of the histone code

Metabolic labeling in middle-down proteomics allows for investigation of the dynamics of the histone code. Sidoli S, Lu C, Coradin M, Wang X, Karch KR, Ruminowicz C, Garcia BA.  Epigenetics Chromatin. 2017 Jul 6;10(1):34. doi: 10.1186/s13072-017-0139-z.

Former Faculty Labs

Nuclear Acetyl-CoA Production by ACLY Promotes Homologous Recombination

Nuclear Acetyl-CoA Production by ACLY Promotes Homologous Recombination. Sivanand S, Rhoades S, Jiang Q, Lee JV, Benci J, Zhang J, Yuan S, Viney I, Zhao S, Carrer A, Bennett MJ, Minn AJ, Weljie AM, Greenberg RA, Wellen KE. Mol Cell. 2017 Jul 20;67(2):252-265.e6. doi: 10.1016/j.molcel.2017.06.008. Epub 2017 2017 Jul 6. PMID:28689661

Cancer and Metabolism Kathryn Wellen Lab

Loss of CDKL5 in Glutamatergic Neurons Disrupts Hippocampal Microcircuitry and Leads to Memory Impairment in Mice

Loss of CDKL5 in Glutamatergic Neurons Disrupts Hippocampal Microcircuitry and Leads to Memory Impairment in Mice  Tang S, Wang IJ, Yue C, Takano H, Terzic B, Pance K, Lee JY, Cui Y, Coulter DA, Zhou Z.  J Neurosci. 2017 Aug 2;37(31):7420-7437. doi: 10.1523/JNEUROSCI.0539-17.2017. Epub 2017 Jul 3.

Zhaolan Zhou Lab

A Molecular Prospective for HIRA Complex Assembly and H3.3-Specific Histone Chaperone Function

A Molecular Prospective for HIRA Complex Assembly and H3.3-Specific Histone Chaperone Function  Ricketts MD, Marmorstein R.  J Mol Biol. 2017 Jun 30;429(13):1924-1933. doi: 10.1016/j.jmb.2016.11.010. Epub 2016 Nov 19. Review.

Ronen Marmostein Lab

Cytosine Deaminase APOBEC3A Sensitizes Leukemia Cells to Inhibition of the DNA Replication Checkpoint

Cytosine Deaminase APOBEC3A Sensitizes Leukemia Cells to Inhibition of the DNA Replication Checkpoint  Green AM, Budagyan K, Hayer KE, Reed MA, Savani MR, Wertheim GB, Weitzman MD.  Cancer Res. 2017 Jun 27. doi: 10.1158/0008-5472.CAN-16-3394.

Matt Weitzman Lab

Photoactivated In Vivo Proximity Labeling

Photoactivated In Vivo Proximity Labeling. Beck DB, Bonasio R.  Curr Protoc Chem Biol. 2017 Jun 19;9(2):128-146. doi: 10.1002/cpch.18.

Roberto Bonasio Lab

The interplay between epigenetic changes and the p53 protein in stem cells

The interplay between epigenetic changes and the p53 protein in stem cells  Levine AJ, Berger SL.  Genes Dev. 2017 Jun 15;31(12):1195-1201. doi: 10.1101/gad.298984.117.

Shelley Berger Lab

Histone Deacetylase 3 prepares brown adipose tissue for acute thermogenic challenge

Histone Deacetylase 3 prepares brown adipose tissue for acute thermogenic challenge  Emmett MJ, Lim HW, Jager J, Richter HJ, Adlanmerini M, Peed LC, Briggs ER, Steger DJ, Ma T, Sims CA, Baur JA, Pei L, Won KJ, Seale P, Gerhart-Hines Z, Lazar MA.  Nature. 2017 Jun 22;546(7659):544-548. doi: 10.1038/nature22819. Epub 2017 Jun 14.

Cancer and Metabolism Mitch Lazar Lab

Histone posttranslational modifications predict specific alternative exon subtypes in mammalian brain

Histone posttranslational modifications predict specific alternative exon subtypes in mammalian brain  Hu Q, Kim EJ, Feng J, Grant GR, Heller EA.  PLoS Comput Biol. 2017 Jun 13;13(6):e1005602.

Elizabeth Heller Lab

Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance

Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance  Shaffer SM, Dunagin MC, Torborg SR, Torre EA, Emert B, Krepler C, Beqiri M, Sproesser K, Brafford PA, Xiao M, Eggan E, Anastopoulos IN, Vargas-Garcia CA, Singh A, Nathanson KL, Herlyn M, Raj A.  Nature. 2017 Jun 15;546(7658):431-435. doi: 10.1038/nature22794. Epub 2017 Jun 7.

Arjun Raj Lab

Acetyl-CoA synthetase regulates histone acetylation and hippocampal memory

Acetyl-CoA synthetase regulates histone acetylation and hippocampal memory  Mews P, Donahue G, Drake AM, Luczak V, Abel T, Berger SL.  Nature. 2017 Jun 15;546(7658):381-386. doi: 10.1038/nature22405. Epub 2017 May 31.

Shelley Berger Lab

Epigenetics meets metabolism through PHB-mediated histone H3.3 deposition by HIRA

Epigenetics meets metabolism through PHB-mediated histone H3.3 deposition by HIRA  Adams PD, Marmorstein R.  Stem Cell Investig. 2017 May 26;4:46. doi: 10.21037/sci.2017.05.08.

Ronen Marmostein Lab

Locus-specific histone deacetylation using a synthetic CRISPR-Cas9-based HDAC

Locus-specific histone deacetylation using a synthetic CRISPR-Cas9-based HDAC. Kwon DY, Zhao YT, Lamonica JM, Zhou Z.  Nat Commun. 2017 May 12;8:15315. doi: 10.1038/ncomms15315.

Zhaolan Zhou Lab

Cell-Type-Specific Epigenetic Editing at the Fosb Gene Controls Susceptibility to Social Defeat Stress

Cell-Type-Specific Epigenetic Editing at the Fosb Gene Controls Susceptibility to Social Defeat Stress  Hamilton PJ, Burek DJ, Lombroso SI, Neve RL, Robison AJ, Nestler EJ, Heller EA.  Neuropsychopharmacology. 2017 May 2. doi: 10.1038/npp.2017.88

Elizabeth Heller Lab

Meiosis-specific Proteins MEIOB and SPATA22 Cooperatively Associate with the ssDNA-binding RPA Complex and DNA Double-strand Breaks

Meiosis-specific Proteins MEIOB and SPATA22 Cooperatively Associate with the ssDNA-binding RPA Complex and DNA Double-strand Breaks  Xu Y, Schonbrunn E, Wang PJ, Greenberg RA.  Biol Reprod. 2017 Apr 27. doi: 10.1093/biolre/iox040.

Roger Greenberg Lab

DNA Methyltransferases Demonstrate Reduced Activity against Arabinosylcytosine: Implications for Epigenetic Instability in Acute Myeloid Leukemia

DNA Methyltransferases Demonstrate Reduced Activity against Arabinosylcytosine: Implications for Epigenetic Instability in Acute Myeloid Leukemia  Nabel CS, DeNizio JE, Carroll M, Kohli RM.  Biochemistry. 2017 Apr 25;56(16):2166-2169. doi: 10.1021/acs.biochem.7b00208. Epub 2017 Apr 12.

Rahul Kohli Lab

EBF2 transcriptionally regulares brown adipogenesis via the histone reader DPF3 and the BAF chromatin remodeling complex

EBF2 transcriptionally regulares brown adipogenesis via the histone reader DPF3 and the BAF chromatin remodeling complex. Shapira SN, Lim HW, Rajakumari S, Sakers AP, Ishibashia J, Harms MJ, Won KJ, Seale P. Genes Dev. 2017 Apr 1;31(7):660-673. doi: 10.1101/gad.294405.116. Epub 2017 Apr 20. PMID:28428261

Cancer and Metabolism Patrick Seale Lab

Time-resolved Global and Chromatin Proteomics during Herpes Simplex Virus Type 1 (HSV-1) Infection

Time-resolved Global and Chromatin Proteomics during Herpes Simplex Virus Type 1 (HSV-1) Infection  Kulej K, Avgousti DC, Sidoli S, Herrmann C, Della Fera AN, Kim ET, Garcia BA, Weitzman MD.  Mol Cell Proteomics. 2017 Apr;16(4 suppl 1):S92-S107. doi: 10.1074/mcp.M116.065987.

Matt Weitzman Lab

Managing cell and human identity

Managing cell and human identity.  Moreno J, Gearhart J, Zoloth L, Pyeritz R, Zaret KS.  Science. 2017 Apr 14;356(6334):139-140. doi: 10.1126/science.aan2763.

Ken Zaret Lab

Elevating expression of MeCP2 T158M rescues DNA binding and Rett syndrome-like phenotypes

Elevating expression of MeCP2 T158M rescues DNA binding and Rett syndrome-like phenotypes. Lamonica JM, Kwon DY, Goffin D, Fenik P, Johnson BS, Cui Y, Guo H, Veasey S, and Zhou ZJournal of Clinical Investigation 127(5): 1889-1904,2017.

Developmental Zhaolan Zhou Lab

The BET Protein BRD2 Cooperates with CTCF to Enforce Transcriptional and Architectural Boundaries

Hsu SC, Gilgenast TG, Bartman CR, Edwards CR, Stonestrom AJ, Huang P, Emerson DJ, Evans P, Werner MT, Keller CA, Giardine B, Hardison RC, Raj A, Phillips-Cremins JE, Blobel GA.  Mol Cell. 2017 Apr 6;66(1):102-116.e7. doi: 10.1016/j.molcel.2017.02.027.

Gerd Blobel Lab

Maturing of the nuclear receptor family

Maturing of the nuclear receptor family. Lazar MA.  J Clin Invest. 2017 Apr 3;127(4):1123-1125. doi: 10.1172/JCI92949. Epub 2017 Apr 3.

Mitch Lazar Lab

Cell fate conversion: a chromatin remodeling checkpoint revealed

Cell fate conversion: a chromatin remodeling checkpoint revealed.  Zaret KS.  Cell Res. 2017 May;27(5):598-599. doi: 10.1038/cr.2017.44. Epub 2017 Mar 31.

Ken Zaret Lab

Metazoan Nuclear Pores Provide a Scaffold for Poised Genes and Mediate Induced Enhancer-Promoter Contacts

Pascual-Garcia P, Debo B, Aleman JR, Talamas JA, Lan Y, Nguyen NH, Won KJ, Capelson M.  Mol Cell. 2017 Apr 6;66(1):63-76.e6. doi: 10.1016/j.molcel.2017.02.020. Epub 2017 Mar 30.
 

Spatial / Architectural Former Faculty Labs

Differential Salt Fractionation of Nuclei to Analyze Chromatin-associated Proteins from Cultured Mammalian Cells

Differential Salt Fractionation of Nuclei to Analyze Chromatin-associated Proteins from Cultured Mammalian Cells  Herrmann C, Avgousti DC, Weitzman MD.  Bio Protoc. 2017 Mar 20;7(6). pii: e2175.

Matt Weitzman Lab

In Vitro Differentiation of Human Pluripotent Stem Cells into Trophoblastic Cells

In Vitro Differentiation of Human Pluripotent Stem Cells into Trophoblastic Cells  Wang J, Anguera MC.  J Vis Exp.;(121). doi: 10.3791/55268.

Montserrat Anguera Lab

Erratum for Zaret, At the Revolution with Fred Sherman

Erratum for Zaret, At the Revolution with Fred Sherman  Zaret KS. Mol Cell Biol. 2017 Feb 15;37(5). pii: e00671-16. doi: 10.1128/MCB.00671-16. Print 2017 Mar 1.

Ken Zaret Lab

Epicardial YAP/TAZ orchestrate an immunosuppressive response following myocardial infarction

Epicardial YAP/TAZ orchestrate an immunosuppressive response following myocardial infarction Ramjee V, Li D, Manderfield LJ, Liu F, Engleka KA, Aghajanian H, Rodell CB, Lu W, Ho V, Wang T, Li L, Singh A, Cibi DM, Burdick JA, Singh MK, Jain R, Epstein JA.  J Clin Invest. 2017 Mar 1;127(3):899-911. doi: 10.1172/JCI88759.

Jon Epstein Lab

Targeting PPARγ in the epigenome rescues genetic metabolic defects in mice

Targeting PPARγ in the epigenome rescues genetic metabolic defects in mice  Soccio RE, Li Z, Chen ER, Foong YH, Benson KK, Dispirito JR, Mullican SE, Emmett MJ, Briggs ER, Peed LC, Dzeng RK, Medina CJ, Jolivert JF, Kissig M, Rajapurkar SR, Damle M, Lim HW, Won KJ, Seale P, Steger DJ, Lazar MA.  J Clin Invest. 2017 Apr 3;127(4):1451-1462. doi: 10.1172/JCI91211. Epub 2017 Feb 27.

Mitch Lazar Lab

Rapid generation of drug-resistance alleles at endogenous loci using CRISPR-Cas9 indel mutagenesis

Rapid generation of drug-resistance alleles at endogenous loci using CRISPR-Cas9 indel mutagenesis  Ipsaro JJ, Shen C, Arai E, Xu Y, Kinney JB, Joshua-Tor L, Vakoc CR, Shi J.  PLoS One. 2017 Feb 23;12(2):e0172177.

Junwei Shi Lab

A cut above

A cut above. He C, Bonasio R.  Elife. 2017 Feb 15;6. pii: e25000. doi: 10.7554/eLife.25000.

Roberto Bonasio Lab

Bioorthogonal Chemistry for the Isolation and Study of Newly Synthesized Histones and Their Modifications

Bioorthogonal Chemistry for the Isolation and Study of Newly Synthesized Histones and Their Modifications  Arnaudo AM, Link AJ, Garcia BA.  ACS Chem Biol. 2016 Mar 18;11(3):782-91. doi: 10.1021/acschembio.5b00816. Epub 2016 Feb 10.

Former Faculty Labs

Mechanisms for targeted, purposeful mutation revealed in an APOBEC-DNA complex

Mechanisms for targeted, purposeful mutation revealed in an APOBEC-DNA complex  Schutsky EK, Hostetler ZM, Kohli RM.  Nat Struct Mol Biol. 2017 Feb 6;24(2):97-98. doi: 10.1038/nsmb.3373.

Rahul Kohli Lab

Recurrent Innovation at Genes Required for Telomere Integrity in Drosophila

Recurrent Innovation at Genes Required for Telomere Integrity in Drosophila  Lee YC, Leek C, Levine MT.  Mol Biol Evol. 2017 Feb 1;34(2):467-482. doi: 10.1093/molbev/msw248.

Mia Levine Lab

RNA Binding to CBP Stimulates Histone Acetylation and Transcription

RNA Binding to CBP Stimulates Histone Acetylation and Transcription  Bose DA, Donahue G, Reinberg D, Shiekhattar R, Bonasio R, Berger SL.  Cell. 2017 Jan 12;168(1-2):135-149.e22. doi:10.1016/j.cell.2016.12.020. Epub 2017 Jan 12. PMID:28086087

Cancer and Metabolism Shelley Berger Lab

CENP-A Modifications on Ser68 and Lys124 Are Dispensable for Establishment, Maintenance, and Long-Term Function of Human Centromeres

CENP-A Modifications on Ser68 and Lys124 Are Dispensable for Establishment, Maintenance, and Long-Term Function of Human Centromeres  Fachinetti D, Logsdon GA, Abdullah A, Selzer EB, Cleveland DW, Black BE.  Dev Cell. 2017 Jan 9;40(1):104-113. doi: 10.1016/j.devcel.2016.12.014.

Ben Black Lab

The Sustained Impact of Model Organisms-in Genetics and Epigenetics

The Sustained Impact of Model Organisms-in Genetics and Epigenetics  Bonini NM, Berger SL.  Genetics. 2017 Jan;205(1):1-4. doi: 10.1534/genetics.116.187864.

Shelley Berger Lab

Putting PHDs to work: PHF11 clears the way for EXO1 in double-strand break repair

Putting PHDs to work: PHF11 clears the way for EXO1 in double-strand break repair  Zahn KE, Greenberg RA.  Genes Dev. 2017 Jan 1;31(1):3-5. doi: 10.1101/gad.295923.117.

Roger Greenberg Lab

Distinct cellular and molecular environments support aging-related DNA methylation changes in the substantia nigra

Distinct cellular and molecular environments support aging-related DNA methylation changes in the substantia nigra  Fasolino M, Liu S, Wang Y, Zhou Z.  Epigenomics. 2017 Jan;9(1):21-31. doi: 10.2217/epi-2016-0084.

Zhaolan Zhou Lab

The Chromatin Modifier MSK1/2 Suppresses Endocrine Cell Fates during Mouse Pancreatic Development

The Chromatin Modifier MSK1/2 Suppresses Endocrine Cell Fates during Mouse Pancreatic Development. Bhat N, Park J, Zoghbi HY, Arthur JS, Zaret KS. PLoS One. 2019 Dec 14;11(12):e0166703. doi: 10.1371/journal.pone.0166703. eCollection 2016.

Ken Zaret Lab

Genetic and epigenomic mechanisms of mammalian circadian transcription

Genetic and epigenomic mechanisms of mammalian circadian transcription. Dec 6, 2016 Papazyan R, Zhang Y, Lazar MA. Nat Struct Mol Biol. 2016 Dec 6;23(12):1045-1052. doi: 10.1038/nsmb.3324. Review.

Mitch Lazar Lab

Mutations along a TET2 active site scaffold stall oxidation at 5-hydroxymethylcytosine

Mutations along a TET2 active site scaffold stall oxidation at 5-hydroxymethylcytosine.  Liu MY, Torabifard H, Crawford DJ, DeNizio JE, Cao XJ, Garcia BA, Cisneros GA, Kohli RM.  Nat Chem Biol. 2017 Feb;13(2):181-187. doi: 10.1038/nchembio.2250. Epub 2016 Dec 5.

Rahul Kohli Lab

Circadian time signatures of fitness and disease

Circadian time signatures of fitness and disease.  Bass J, Lazar MA.  Science. 2016 Nov 25;354(6315):994-999. Review.

Mitch Lazar Lab

Deletion of histone deacetylase 3 in adult beta cells improves glucose tolerance via increased insulin secretion

Deletion of histone deacetylase 3 in adult beta cells improves glucose tolerance via increased insulin secretion.  Remsberg JR, Ediger BN, Ho WY, Damle M, Li Z, Teng C, Lanzillotta C, Stoffers DA, Lazar MA.  Mol Metab. 2016 Nov 22;6(1):30-37. doi: 10.1016/j.molmet.2016.11.007. eCollection 2017 Jan.

Mitch Lazar Lab

Physiological Suppression of Lipotoxic Liver Damage by Complementary Actions of HDAC3 and SCAP/SREBP

Physiological Suppression of Lipotoxic Liver Damage by Complementary Actions of HDAC3 and SCAP/SREBP.  Papazyan R, Sun Z, Kim YH, Titchenell PM, Hill DA, Lu W, Damle M, Wan M, Zhang Y, Briggs ER, Rabinowitz JD, Lazar MA.  Cell Metab. 2016 Dec 13;24(6):863-874. doi: 10.1016/j.cmet.2016.10.012. Epub 2016 Nov 17.

Mitch Lazar Lab

A New Path through the Nuclear Pore

Gozalo A, Capelson M. Cell. 2016 Nov 17;167(5):1159-1160. doi: 10.1016/j.cell.2016.11.011.

Former Faculty Labs

Epigenetic regulation of intestinal stem cells by Tet 1-mediated DNA hydroxymethylation

Epigenetic regulation of intestinal stem cells by Tet 1-mediated DNA hydroxymethylation. Kim R, Sheaffer KL, Choi I, Won KJ, Kaestner KH. Genes Dev. 2016

Developmental Klaus Kaestner Lab

Molecular Basis for Cohesin Acetylation by Establishment of Sister Chromatid Cohesion N-Acetyltransferase ESCO1

Molecular Basis for Cohesin Acetylation by Establishment of Sister Chromatid Cohesion N-Acetyltransferase ESCO1.  Rivera-Colón Y, Maguire A, Liszczak GP, Olia AS, Marmorstein R.  J Biol Chem. 2016 Dec 16;291(51):26468-26477. Epub 2016 Nov 1.

Ronen Marmostein Lab

A new bookmark of the mitotic genome in embryonic stem cells

A new bookmark of the mitotic genome in embryonic stem cells.  Hsiung CC, Blobel GA.  Nat Cell Biol. 2016 Oct 27;18(11):1124-1125. DOI: 10.1038/ncb3432

 

Gerd Blobel Lab

High-Resolution Mapping of RNA-Binding Regions in the Nuclear Proteome of Embryonic Stem Cells

High-Resolution Mapping of RNA-Binding Regions in the Nuclear Proteome of Embryonic Stem Cells.  He C, Sidoli S, Warneford-Thomson R, Tatomer DC, Wilusz JE, Garcia BA, Bonasio R.  Mol Cell. 2016 Oct 20;64(2):416-430. doi: 10.1016/j.molcel.2016.09.034.

Roberto Bonasio Lab

Break-induced telomere synthesis underlies alternative telomere maintenance

Break-induced telomere synthesis underlies alternative telomere maintenance. Dilley RL, Verma P, Cho NW, Winters HD, Wondisford AR, Greenberg RA. Nature. 2016 Nov 3;539(7627):54-58. doi: 10.1038/nature20099. Epub 2016 Oct 19.

Roger Greenberg Lab

Humanized H19/Igf2 locus reveals diverged imprinting mechanism between mouse and human and reflects Silver-Russell syndrome phenotypes

Humanized H19/Igf2 locus reveals diverged imprinting mechanism between mouse and human and reflects Silver-Russell syndrome phenotypes. Hur SK, Freschi A, Ideraabdullah F, Thorvaldsen JL, Luense LJ, Weller AH, Berger SL, Cerrato F, Riccio A, Bartolomei MS. Proc Natl Acad Sci U S A. 2016 Sep 27;113(39):10938-43. doi: 10.1073/pnas.1603066113. Epub 2016 Sep 12.

Marisa Bartolomei Lab

Chemically Linked Vemurafenib Inhibitors Promote an Inactive BRAFV600E Conformation

Chemically Linked Vemurafenib Inhibitors Promote an Inactive BRAFV600E Conformation. Grasso M, Estrada MA, Ventocilla C, Samanta M, Maksimoska J, Villanueva J, Winkler JD, Marmorstein R. ACS Chem Biol. 2016 Oct 21;11(10):2876-2888. Epub 2016 Sep 6.

Ronen Marmostein Lab

Lysine methylation represses p53 activity in teratocarcinoma cancer cells

Lysine methylation represses p53 activity in teratocarcinoma cancer cells. Zhu J, Dou Z, Sammons MA, Levine AJ, Berger SL. Proc Natl Acad Sci U S A. 2016 Aug 30;113(35):9822-7. doi: 10.1073/pnas.1610387113. Epub 2016 Aug 17.

Shelley Berger Lab

Multiplexed data independent acquisition (MSX-DIA) applied by high resolution mass spectrometry improves quantification quality for the analysis of histone peptides

Multiplexed data independent acquisition (MSX-DIA) applied by high resolution mass spectrometry improves quantification quality for the analysis of histone peptides  Sidoli S, Fujiwara R, Garcia BA.  Proteomics. 2016 Aug;16(15-16):2095-105. doi: 10.1002/pmic.201500527. Epub 2016 Jun 8.

Former Faculty Labs

Morphologic and molecular changes in the placenta: what we can learn from environmental exposures

Morphologic and molecular changes in the placenta: what we can learn from environmental exposures. Vrooman LA, Xin F, Bartolomei MS. Fertil Steril. 2016 Sep 15;106(4):930-40. doi: 10.1016/j.fertnstert.2016.08.016. Epub 2016 Aug 11. Review.

Marisa Bartolomei Lab

Epigenetic Mechanisms of Longevity and Aging

Epigenetic Mechanisms of Longevity and Aging.  Sen P, Shah PP, Nativio R, Berger SL.  Cell. 2016 Aug 11;166(4):822-39. doi: 10.1016/j.cell.2016.07.050.

Shelley Berger Lab

A Chromatin-Focused siRNA Screen for Regulators of p53-Dependent Transcription

A Chromatin-Focused siRNA Screen for Regulators of p53-Dependent Transcription. Sammons MA, Zhu J, Berger SL. G3 (Bethesda). 2016 Aug 9;6(8):2671-8. doi: 10.1534/g3.116.031534.

Shelley Berger Lab

In vivo imaging of DNA double-strand break induced telomere mobility during alternative lengthening of telomeres

In vivo imaging of DNA double-strand break induced telomere mobility during alternative lengthening of telomeres. Cho NW, Lampson MA, Greenberg RA. Methods. 2017 Feb 1;114:54-59. doi: 10.1016/j.ymeth.2016.07.010. Epub 2016 Aug 1.

Roger Greenberg Lab

Systematically Altering Bacterial SOS Activity under Stress Reveals Therapeutic Strategies for Potentiating Antibiotics

Systematically Altering Bacterial SOS Activity under Stress Reveals Therapeutic Strategies for Potentiating Antibiotics. Mo CY, Manning SA, Roggiani M, Culyba MJ, Samuels AN, Sniegowski PD, Goulian M, Kohli RM. mSphere. 2016 Aug 10;1(4). pii: e00163-16. doi: 10.1128/mSphere.00163-16. eCollection 2016 Jul-Aug.

Rahul Kohli Lab

Can assisted reproductive technologies cause adult-onset disease? Evidence from human and mouse

Can assisted reproductive technologies cause adult-onset disease? Evidence from human and mouse. Vrooman LA, Bartolomei MS. Reprod Toxicol. 2017 Mar;68:72-84. doi: 10.1016/j.reprotox.2016.07.015. Epub 2016 Jul 26.

Marisa Bartolomei Lab

HNF6 and Rev-erbα integrate hepatic lipid metabolism by overlapping and distinct transcriptional mechanisms

HNF6 and Rev-erbα integrate hepatic lipid metabolism by overlapping and distinct transcriptional mechanisms.  Zhang Y, Fang B, Damle M, Guan D, Li Z, Kim YH, Gannon M, Lazar MA.  Genes Dev. 2016 Jul 15;30(14):1636-44. doi: 10.1101/gad.281972.116. Epub 2016 Jul 21.

Mitch Lazar Lab

Differential quantification of isobaric phosphopeptides using data-independent acquisition mass spectrometry

Differential quantification of isobaric phosphopeptides using data-independent acquisition mass spectrometry.  Sidoli S, Fujiwara R, Kulej K, Garcia BA.  Mol Biosyst. 2016 Jul 19;12(8):2385-8. doi: 10.1039/c6mb00385k.

Former Faculty Labs

APOBEC3A damages the cellular genome during DNA replication

APOBEC3A damages the cellular genome during DNA replication.  Green AM, Landry S, Budagyan K, Avgousti DC, Shalhout S, Bhagwat AS, Weitzman MD.  Cell Cycle. 2016;15(7):998-1008. doi: 10.1080/15384101.2016.1152426.

Matt Weitzman Lab

Structural and Functional Role of Acetyltransferase hMOF K274 Autoacetylation

Structural and Functional Role of Acetyltransferase hMOF K274 Autoacetylation.  McCullough CE, Song S, Shin MH, Johnson FB, Marmorstein R.  J Biol Chem. 2016 Aug 26;291(35):18190-8. doi: 10.1074/jbc.M116.736264. Epub 2016 Jul 5.

Ronen Marmostein Lab

Coronary vasculature patterning requires a novel endothelial ErbB2 holoreceptor

Coronary vasculature patterning requires a novel endothelial ErbB2 holoreceptor.  Aghajanian H, Cho YK, Manderfield LJ, Herling MR, Gupta M, Ho VC, Li L, Degenhardt K, Aharonov A, Tzahor E, Epstein JA.  Nat Commun. 2016 Jun 30;7:12038. doi: 10.1038/ncomms12038.

Jon Epstein Lab

A core viral protein binds host nucleosomes to sequester immune danger signals

A core viral protein binds host nucleosomes to sequester immune danger signals.  Avgousti DC, Herrmann C, Kulej K, Pancholi NJ, Sekulic N, Petrescu J, Molden RC, Blumenthal D, Paris AJ, Reyes ED, Ostapchuk P, Hearing P, Seeholzer SH, Worthen GS, Black BE, Garcia BA, Weitzman MD.  Nature. 2016 Jul 7;535(7610):173-7. Epub 2016 Jun 29.

Matt Weitzman Lab

Comprehensive analysis of histone post-translational modifications in mouse and human male germ cells

Comprehensive analysis of histone post-translational modifications in mouse and human male germ cells.  Luense LJ, Wang X, Schon SB, Weller AH, Lin Shiao E, Bryant JM, Bartolomei MS, Coutifaris C, Garcia BA, Berger SL.  Epigenetics Chromatin. 2016 Jun 21;9:24. doi: 10.1186/s13072-016-0072-6. eCollection 2016.

Shelley Berger Lab

A hyperactive transcriptional state marks genome reactivation at the mitosis-G1 transition

A hyperactive transcriptional state marks genome reactivation at the mitosis-G1 transition.  Hsiung CC, Bartman CR, Huang P, Ginart P, Stonestrom AJ, Keller CA, Face C, Jahn KS, Evans P, Sankaranarayanan L, Giardine B, Hardison RC, Raj A, Blobel GA.  Genes Dev. 2016 Jun 15;30(12):1423-39. doi: 10.1101/gad.280859.116.

Gerd Blobel Lab

The expanding scope and impact of epigenetic cytosine modifications

The expanding scope and impact of epigenetic cytosine modifications.  Liu MY, DeNizio JE, Schutsky EK, Kohli RM.  Curr Opin Chem Biol. 2016 Aug;33:67-73. doi: 10.1016/j.cbpa.2016.05.029. Epub 2016 Jun 14.

Rahul Kohli Lab

Choreographing the Double Strand Break Response: Ubiquitin and SUMO Control of Nuclear Architecture

Choreographing the Double Strand Break Response: Ubiquitin and SUMO Control of Nuclear Architecture.  Harding SM, Greenberg RA.  Front Genet. 2016 Jun 7;7:103. doi: 10.3389/fgene.2016.00103. eCollection 2016.
 

Roger Greenberg Lab

Cell fate control by pioneer transcription factors

Cell fate control by pioneer transcription factors.  Iwafuchi-Doi M, Zaret KS.  Development. 2016 Jun 1;143(11):1833-7. doi: 10.1242/dev.133900.

Ken Zaret Lab

lncRHOXF1, a Long Noncoding RNA from the X Chromosome That Suppresses Viral Response Genes during Development of the Early Human Placenta

lncRHOXF1, a Long Noncoding RNA from the X Chromosome That Suppresses Viral Response Genes during Development of the Early Human Placenta. Penkala I, Wang J, Syrett CM, Goetzl L, López CB, Anguera MC. Mol Cell Biol. 2016 May 31;36(12):1764-75. doi: 10.1128/MCB.01098-15. Print 2016 Jun 15.

Montserrat Anguera Lab

Preferential Phosphorylation on Old Histones during Early Mitosis in Human Cells

Preferential Phosphorylation on Old Histones during Early Mitosis in Human Cells Lin S, Yuan ZF, Han Y, Marchione DM, Garcia BA.  J Biol Chem. 2016 Jul 15;291(29):15342-57. doi: 10.1074/jbc.M116.726067. Epub 2016 May 19.

Former Faculty Labs

Noncanonical views of homology-directed DNA repair

Noncanonical views of homology-directed DNA repair.  Verma P, Greenberg RA.  Genes Dev. 2016 May 15;30(10):1138-54. doi: 10.1101/gad.280545.116. Review.

Roger Greenberg Lab

Local Genome Topology Can Exhibit an Incompletely Rewired 3D-Folding State during Somatic Cell Reprogramming

Local Genome Topology Can Exhibit an Incompletely Rewired 3D-Folding State during Somatic Cell Reprogramming. Beagan JA1, Gilgenast TG1, Kim J1, Plona Z1, Norton HK1, Hu G1, Hsu SC2, Shields EJ2, Lyu X3, Apostolou E4, Hochedlinger K4, Corces VG3, Dekker J5, Phillips Cremins JE6. Cell Stem Cell. 2016 May 5; 18(5):611-24. doi: 10.1016/j.stem.2016.04.004

Spatial / Architectural Jennifer Phillips-Cremins Lab

A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics

A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.  Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA.  Mol Cell Proteomics. 2016 Jul;15(7):2462-75. doi: 10.1074/mcp.O115.049627. Epub 2016 Apr 25.

Former Faculty Labs

Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping

Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping.  Bartman CR, Hsu SC, Hsiung CC, Raj A, Blobel GA.  Mol Cell. 2016 Apr 21;62(2):237-47. doi: 10.1016/j.molcel.2016.03.007. Epub 2016 Apr 7.

Gerd Blobel Lab

Tagging methyl-CpG-binding domain proteins reveals different spatiotemporal expression and supports distinct functions

Tagging methyl-CpG-binding domain proteins reveals different spatiotemporal expression and supports distinct functions.  Wood KH, Johnson BS, Welsh SA, Lee JY, Cui Y, Krizman E, Brodkin ES, Blendy JA, Robinson MB, Bartolomei MS, Zhou Z.  Epigenomics. 2016 Apr;8(4):455-73. doi: 10.2217/epi-2015-0004. Epub 2016 Apr 12.

Zhaolan Zhou Lab

The Pioneer Transcription Factor FoxA Maintains an Accessible Nucleosome Configuration at Enhancers for Tissue-Specific Gene Activation

The Pioneer Transcription Factor FoxA Maintains an Accessible Nucleosome Configuration at Enhancers for Tissue-Specific Gene Activation.  Iwafuchi-Doi M, Donahue G, Kakumanu A, Watts JA, Mahony S, Pugh BF, Lee D, Kaestner KH, Zaret KS.  Mol Cell. 2016 Apr 7;62(1):79-91. doi: 10.1016/j.molcel.2016.03.001.

Ken Zaret Lab

Long-Term Retention of CENP-A Nucleosomes in Mammalian Oocytes Underpins Transgenerational Inheritance of Centromere Identity

Long-Term Retention of CENP-A Nucleosomes in Mammalian Oocytes Underpins Transgenerational Inheritance of Centromere Identity.  Smoak EM, Stein P, Schultz RM, Lampson MA, Black BE.  Curr Biol. 2016 Apr 25;26(8):1110-6. doi: 10.1016/j.cub.2016.02.061. Epub 2016 Mar 31.

Ben Black Lab

CENP-C directs a structural transition of CENP-A nucleosomes mainly through sliding of DNA gyres

CENP-C directs a structural transition of CENP-A nucleosomes mainly through sliding of DNA gyres.  Falk SJ, Lee J, Sekulic N, Sennett MA, Lee TH, Black BE.  Nat Struct Mol Biol. 2016 Mar;23(3):204-208. doi: 10.1038/nsmb.3175. Epub 2016 Feb 15.

Spatial / Architectural Ben Black Lab

Unusual maintenance of X chromosome inactivation predisposes female lymphocytes for increased expression from the inactive X

Unusual maintenance of X chromosome inactivation predisposes female lymphocytes for increased expression from the inactive X.  Wang J, Syrett CM, Kramer MC, Basu A, Atchison ML, Anguera MC.  Proc Natl Acad Sci U S A. 2016 Apr 5;113(14):E2029-38. doi: 10.1073/pnas.1520113113. Epub 2016 Mar 21.

Montserrat Anguera Lab

The Nuclear Receptor Rev-erbα Regulates Adipose Tissue-specific FGF21 Signaling

The Nuclear Receptor Rev-erbα Regulates Adipose Tissue-specific FGF21 Signaling.  Jager J, Wang F, Fang B, Lim HW, Peed LC, Steger DJ, Won KJ, Kharitonenkov A, Adams AC, Lazar MA.  J Biol Chem. 2016 May 13;291(20):10867-75. doi: 10.1074/jbc.M116.719120. Epub 2016 Mar 21.

Mitch Lazar Lab

A dynamic intron retention program in the mammalian megakaryocyte and erythrocyte lineages

A dynamic intron retention program in the mammalian megakaryocyte and erythrocyte lineages.  Edwards CR, Ritchie W, Wong JJ, Schmitz U, Middleton R, An X, Mohandas N, Rasko JE, Blobel GA.  Blood. 2016 Mar 9. pii: blood-2016-01-692764

Gerd Blobel Lab

Visualizing allele-specific expression in single cells reveals epigenetic mosaicism in an H19 loss of imprinting mutant

Visualizing allele-specific expression in single cells reveals epigenetic mosaicism in an H19 loss of imprinting mutant. Ginard, P., Kalish, J.M., Jiang, C.L., Yu, A.C., Bartolomei, M.S.* and A. Raj*. (2016). Genes and Development, 30:567-578

Developmental Spatial / Architectural Arjun Raj Lab

Histone H4 acetylation and the epigenetic reader Brd4 are critical regulators of pluripotency in embryonic stem cells

Histone H4 acetylation and the epigenetic reader Brd4 are critical regulators of pluripotency in embryonic stem cells.  Gonzales-Cope M, Sidoli S, Bhanu NV, Won KJ, Garcia BA.  BMC Genomics. 2016 Feb 4;17:95. doi: 10.1186/s12864-016-2414-y.

Former Faculty Labs

MLL1 is essential for the senescence-associated secretory phenotype

MLL1 is essential for the senescence-associated secretory phenotype.  Capell BC, Drake AM, Zhu J, Shah PP, Dou Z, Dorsey J, Simola DF, Donahue G, Sammons M, Rai TS, Natale C, Ridky TW, Adams PD, Berger SL.  Genes Dev. 2016 Feb 1;30(3):321-36. doi: 10.1101/gad.271882.115.

Shelley Berger Lab

Histone modification profiling reveals differential signatures associated with human embryonic stem cell self-renewal and differentiation

Histone modification profiling reveals differential signatures associated with human embryonic stem cell self-renewal and differentiation.  Bhanu NV, Sidoli S, Garcia BA.  Proteomics. 2016 Feb;16(3):448-58. doi: 10.1002/pmic.201500231. Epub 2016 Jan 28.

Former Faculty Labs

From Endoderm to Liver Bud: Paradigms of Cell Type Specification and Tissue Morphogenesis

From Endoderm to Liver Bud: Paradigms of Cell Type Specification and Tissue Morphogenesis. Ken Zaret. Curr Top Dev Biol. 2016;117:647-69. doi: 10.1016/bs.ctdb.2015.12.015. Epub 2016 Jan 21.

Ken Zaret Lab

Tet2 Catalyzes Stepwise 5-Methlycytosine Oxidation by an Iterative and de novo Mechanism

Tet2 Catalyzes Stepwise 5-Methlycytosine Oxidation by an Iterative and de novo Mechanism.  Crawford DJ, Liu MY, Nabel CS, Cao XJ, Garcia BA, Kohli RM.  J Am Chem Soc. 2016 Jan 27;138(3):730-3. doi: 10.1021/jacs.5b10554. Epub 2016 Jan 13.

Rahul Kohli Lab

The N-terminal Acetyltransferase Naa10/ARD1 Does Not Acetylate Lysine Residues

The N-terminal Acetyltransferase Naa10/ARD1 Does Not Acetylate Lysine Residues.  Magin RS, March ZM, Marmorstein R.  J Biol Chem. 2016 Mar 4;291(10):5270-7. doi: 10.1074/jbc.M115.709428. Epub 2016 Jan 11.

Ronen Marmostein Lab

Epigenetic (re)programming of caste-specific behavior in the ant Camponotus floridanus

Epigenetic (re)programming of caste-specific behavior in the ant Camponotus floridanus.  Simola DF, Graham RJ, Brady CM, Enzmann BL, Desplan C, Ray A, Zwiebel LJ, Bonasio R, Reinberg D, Liebig J, Berger SL.  Science. 2016 Jan 1;351(6268):aac6633. doi: 10.1126/science.aac6633.

Shelley Berger Lab

Mammalian autophagy degrades nuclear constituents in response to tumorigenic stress

Mammalian autophagy degrades nuclear constituents in response to tumorigenic stress.  Dou Z, Ivanov A, Adams PD, Berger SL.  Autophagy. 2016 Aug 2;12(8):1416-7. doi: 10.1080/15548627.2015.1127465. Epub 2015 Dec 10.

Shelley Berger Lab

H3K9me3-Dependent Heterochromatin: Barrier to Cell Fate Changes

H3K9me3-Dependent Heterochromatin: Barrier to Cell Fate Changes.  Becker JS, Nicetto D, Zaret KS.  Trends Genet. 2016 Jan;32(1):29-41. doi: 10.1016/j.tig.2015.11.001. Epub 2015 Dec 8. Review.

Ken Zaret Lab

Autophagy mediates degradation of nuclear lamina

Autophagy mediates degradation of nuclear lamina. Dou Z, Xu C, Donahue G, Shimi T, Pan JA, Zhu J, Ivanov A, Capell BC, Drake AM, Shah PP, Catanzaro JM, Daniel Ricketts M, Lamark T, Adam SA, Marmorstein R, Zong WX, Johansen T, Goldman RD, Adams PD, Berger SL. Nature. 2015 Nov 5;527(7576):105-9. doi: 10.1038/nature15548. Epub 2015 Oct 28.
PMID: 26524528

Shelley Berger Lab

AINTEGUMENTA and AINTEGUMENTA-LIKE6/PLETHORA3 Induce LEAFY Expression in Response to Auxin to Promote the Onset of Flower Formation in Arabidopsis

AINTEGUMENTA and AINTEGUMENTA-LIKE6/PLETHORA3 Induce LEAFY Expression in Response to Auxin to Promote the Onset of Flower Formation in Arabidopsis.  Yamaguchi N, Jeong CW, Nole-Wilson S, Krizek BA, Wagner D.  Plant Physiol. 2016 Jan;170(1):283-93. doi: 10.1104/pp.15.00969. Epub 2015 Nov 4.

Doris Wagner Lab

Optical Measurement of Cell Cycle Dependent Growth.

Optical Measurement of Cell Cycle Dependent Growth. M. Mir, Z. Wang, Z. Shen, M. Bednarz, R. Bashir, I. Golding and G. Popescu. Proceedings of the National Academies of Sciences (PNAS) 108 (32): 13124-13129, 2011.

Mustafa Mir Lab

MERIT40 controls BRCA1-Rap80 complex integrity and recruitment to DNA double-strand breaks

MERIT40 controls BRCA1-Rap80 complex integrity and recruitment to DNA double-strand breaks. Shao G, Patterson-Fortin J, Messick TE, Feng D, Shanbhag N, Wang Y, Greenberg RA. Genes Dev. 2009 Mar 15;23(6):740-54. doi: 10.1101/gad.1739609. Epub 2009 Mar 4. PMID: 19261746

Roger Greenberg Lab

The Rap80-BRCC36 de-ubiquitinating enzyme complex antagonizes RNF8-Ubc13-dependent ubiquitination events at DNA double strand breaks

The Rap80-BRCC36 de-ubiquitinating enzyme complex antagonizes RNF8-Ubc13-dependent ubiquitination events at DNA double strand breaks. Shao G, Lilli DR, Patterson-Fortin J, Coleman KA, Morrissey DE, Greenberg RA. Proc Natl Acad Sci U S A. 2009 Mar 3;106(9):3166-71. doi: 10.1073/pnas.0807485106. Epub 2009 Feb 6. PMID: 19202061

Roger Greenberg Lab