Hongjun Song, Ph.D.

Mechanisms regulating adult hippocampal neural stem cells and neurogenesis.
Adult hippocampal neurogenesis reflects a remarkable form of structural plasticity in the mature mammalian brain. Fully characterizing this phenomenon could have far-reaching implications for understanding hippocampal function and revealing fundamental properties of neural development and the regenerative capacity of the central nervous system. Over the past 14 years, my laboratory has systemically investigated adult hippocampal neurogenesis at the molecular, cellular, and circuit levels and reported a number of key findings that have influenced the field. Via genetic clonal analysis, we conclusively demonstrated, for the first time, the existence of bona fide neural stem cells in the adult mammalian hippocampus, capable of both self-renewal and multipotent fate specification of progeny (Bonaguidi et al., Cell 2011). We also revealed how neural activity and experience can regulate the behavior of these stem cells (Song et al., Nature 2012; Jang et al. Cell Stem Cell 2013). We provided the first detailed characterization of newborn neuron integration into the existing neuronal circuitry and its underlying molecular, cellular and circuitry mechanisms (Ge et al., Nature 2006; Faulkner et al. PNAS 2009; Kang et al. Neuron 2011; Kim et al. Cell 2012; Sun et al. J Neurosci. 2013; Song et al. Nat. Neurosci. 2013). In collaboration with Dr. Guo-li Ming, we have discovered critical roles of DISC1, a psychiatric disorder risk gene, in regulating the development of newborn neurons during adult hippocampal neurogenesis (Duan et al. Cell 2007; Faulkner et al. PNAS 2008, Kim et al Neuron 2009; Kim et al. Cell 2012; Zhou et al. Neuron 2013). We discovered novel circuitry mechanisms whereby local neural activity influences the proliferation and development of newborn neurons in the hippocampus (Ma et al., Science 2009; Song et al., Nature 2012; Song et al., Nat Neurosci 2013).

Duan, X., Chang, J.H., Ge, S-y., Faulkner, R.L., Kim, J.Y., Kitabatake, Y., Liu, X-b., Yang, C-h., Jordan, J.D., Ma, D.K., Liu, C.Y., Ganesan, S., Cheng, H.J., Ming, G-l.*, Lu, B.* and Song, H-j.* (2007). Disrupted-In-Schizophrenia 1 regulates integration of new neurons in the adult brain. Cell 130, 1146-1158.
Bonaguidi, M.A., Wheeler, M., Shapiro, J.S., Stadel, R., Sun, G.J., Ming, G-l.*, and Song, H*. (2011). In vivo clonal analysis reveals self-renew and multipotent adult neural stem cell characteristics. Cell 145, 1142-55.
Song, J., Zhong, C., Bonaguidi, M.A., Sun, G.J., Hsu1, D., Gu, Y., Meletis, K., Huang, Z.J., Ge, S., Enikolopov, G., Deisseroth, K., Luscher, B., Christian, K., Ming, G-l., and Song, H. (2012). Neuronal circuitry mechanism regulating adult quiescent neural stem cell fate decision. Nature 489, 150-4.
Sun, G.J., Zhou, Y., Ito, S., Bonaguidi, M.A., Stein-O’Brien, G., Kawasaki, N., Modak, N., Zhu, Y., Ming, G-l., and Song, H. (2015). Latent tri-lineage potential of adult neural stem cells in the hippocampus revealed by Nf1 inactivation. Nature Neuroscience 18, 1722-4.

Neuroepigenetics and Neuroepitranscriptomics. Contrary to the long-held dogma that DNA methylation is a stable epigenetic mark in post-mitotic neurons, it is now recognized to be a robust form of plasticity in the adult nervous system. We have made significant contributions to the current understanding of epigenetic DNA modifications in the adult nervous system. My laboratory identified the first molecular mechanism regulating active DNA demethylation in mature neurons in vivo (Ma et al. Science 2009) and subsequently delineated molecular pathways mediating this process (Guo et al. Cell 2011). More recently, we showed that the neuronal DNA demethylation pathway plays fundamental roles in neuronal function, including regulation of basal levels of synaptic transmission and homeostatic synaptic plasticity (Yu et al. Nat. Neurosci. 2015). My laboratory has established a pipeline for high-throughput sequencing analysis, including RNA-seq, Chip-seq, Bisulfite-seq, ATAC-seq and single-cell RNA-seq and we have designed custom software programs for bioinformatic analyses. We published the first single-base resolution genome-wide DNA methylation profiles in neurons in vivo and showed large scale neuronal activity-induced dynamic methylation changes (Guo et al. Nat. Neurosci, 2011). Via single-base methylome analysis, we also demonstrated the presence of prominent nonCpG methylation in mature neurons in vivo and identified MeCP2 as the first nonCpG DNA methylation binding protein in the field (Guo et al. Nat. Neurosci. 2014). More recently, we have started to explore how methylation of mRNA can affect neurogenesis, axon regeneration and plasticity (Yoon et al. Cell 2017; Weng et al. Neuron 2018).

Ma, D.K., Jang, M.H., Guo, J.U., Kitabatake, Y., Chang, M.L., Pow-Anpongkul, N., Flavell, R.A., Lu, B., Ming, G.L., and Song, H-j. (2009). Neuronal activity-induced Gadd45b promotes epigenetic DNA demethylation and adult neurogenesis. Science 323, 1074-7.
Guo, J.U., Su, Y., Zhong, C., Ming, G.L., and Song, H. (2011). Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain. Cell 145, 423-34.
Yu, H., Su, Y., Shin, J., Zhong, C., Guo, J.U., Weng, Y-l., Gao, F., Geschwind, D.H., Coppola, G., Ming, G-l., and Song, H. (2015). Tet3 regulates synaptic transmission and homeostatic plasticity via DNA oxidation and repair. Nature Neuroscience 18, 836-843.
Yoon, K.J., Ringeling, F.R., Vissers, C., Jacob, F., Pokrass, M., Jimenez-Cyrus, D., Su, Y., Kim, N.S., Zhu, Y., Zheng, L., Kim, S., Wang, X., Doré, L.C., Jin, P., Regot, S., Zhuang, X., Canzar, S., He, C., Ming, G.L., and Song, H. (2017). Temporal control of mammalian cortical neurogenesis by m6A methylation. Cell 171(4):877-889.

Single-cell biology. A complete understanding of the structure and function of neural systems will require integrated analyses at multiple levels. A daunting obstacles to reaching this goal is the technical challenge of characterizing the behavior of single cells in vivo. Many neural processes can be described at the population level, but there are several domains where it is critical to identify molecular and functional properties at the single cell level. My laboratory has developed a “single cell genetic” approach to manipulate target genes in newborn neurons using retroviruses that led to a number of critical discoveries (Ge et al. Nature 2006; Duan et al, Cell 2007; Kim et al. Neuron 2009; Kang et al. Neuron 2011; Kim et al. Cell 2011; Jang et al. Cell Stem Cell 2013; Song et al. Nat. Neurosci. 2013). Our identification of bona fide neural stem cells in the adult brain required clonal analysis to determine whether radial glial-like cells were capable of both self-renewal and giving rise to multiple cell types, thus settling a debate in the field over whether neurons and glia were generated from lineage-restricted progenitors, as opposed to true stem cells (Bonaguidi et al. Cell 2011). To visualize dendritic and axonal growth over development, we devised a new strategy to allow us to reconstruct complete cellular processes of individual cells, revealing a stereotyped pattern of axonal targeting that further suggests the existence of guidance cues in the adult hippocampus (Sun et al., J Neurosci 2013). We have recent developed a single-cell RNA-seq technology and a bioinformatics pipeline to investigate transcriptomes of hundreds to thousands of heterogeneous cell types (Shin et al. Cell Stem Cell, 2015).

Ge, S-y., Goh. E.L.K., Sailor, K.A., Kitabatake, Y., Ming, G-l*. and Song, H-j*. (2006). GABA regulates synaptic integration of newly generated neurons in the adult brain. Nature 439, 589-593.
Bonaguidi, M.A., Wheeler, M., Shapiro, J.S., Stadel, R., Sun, G.J., Ming, G-l.*, and Song, H*. (2011). In vivo clonal analysis reveals self-renew and multipotent adult neural stem cell characteristics. Cell 145, 1142-55.
Jang, M., Bonaguidi, M.A., Kitabatake, Y., Sun, J., Song, J., Kang, E., Jun, H., Zhong, C., Su, Y., Guo, J.U., Wang, M.X., Sailor, K.A., Kim, J.Y., Gao, Y., Christian, K.M., Ming, G-l., and Song, H. (2013). Secreted frizzled-related protein 3 regulates activity-dependent adult hippocampal neurogenesis. Cell Stem Cell 12, 215-23.
Shin, J., Berg, D.A., Zhu, Y., Shin, J.Y., Song, J., Bonaguidi, M.A., Enikolopov, G., Nauen, D.W., Christian, K.M., Ming, G-l., and Song, H. (2015). Single-cell RNA-seq with Waterfall reveals molecular cascades underlying adult neurogenesis. Cell Stem Cell 17, 360-72.

Research Interest

Research in Dr. Hongjun Song’s laboratory focuses on two core topics: (1) neural stem cell regulation and neurogenesis in the developing and adult mammalian brain and how these processes affect neural function; (2) epigenetic and epitranscriptomic mechanisms and their functions in the mammalian nervous system. The lab is also interested in addressing how dysfunction of these mechanisms may be involved in brain disorders.

Erica Korb, Ph.D

The role of chromatin in neurological disorders.
Disruption of epigenetic mechanisms can lead to a wide range of disorders. Neurons appear to be particularly sensitive to these changes and epigenetic misregulation contributes to many neurological disorders, from autism to chronic pain. We demonstrated that Fragile X syndrome (FXS), the most common genetic cause of intellectual disability and autism, results in part from changes to the epigenome. Furthermore, targeting the resulting transcriptional deficits can successfully reverse phenotypes in a mouse model of the disease. We also contributed to work on chronic pain and depression that explore how underlying mechanisms are linked to epigenetic disruption.
Korb, E.,Herre, M., Zucker-Scharff, I., Allis, C.D., Darnell, RB. 2017. Excess translation of epigenetic regulators contributes to Fragile X Syndrome and is alleviated by Bd4 inhibition. Cell. (PMID: 28823556)
Inquimbert, P., Moll, M., Latremoliere, A., Tong, C.K., Wang, J., Sheehan, G.F., Smith, B.M., Korb, E.,Athie, M.C.P., Babaniyi, O., Ghasemlou, N., Yanagawa, Y., Allis, C.D., Hof, P.R., Scholz, J. 2018. NMDA Receptor activation underlies the loss of spinal dorsal horm neurons and the transition to persistent pain after peripheral nerve injury. Cell Rep.(PMID: 29847798)
Sun, H., Damez-Werno, D.M., Scobie, K.M., Shao, N., Dias, C., Rabkin, J., Koo, J.W., Korb, E.,Bagot, R.C., Ahn, F.H., Cahill, M., Labonte, B., Mouzon, E., Heller, E.A., Cates, H., Golden, S.A., Gleason, K., Russo, S.J., Andrews, S., Neve, R., Kennedy, P.J., Maze, I., Dietz, D.M., Allis, C.D., Turecki, G., Varga-Weisz, P., Tamminga, C., Shen, L., Nestler. E.J. 2015. ACF chromatin remodeling complex mediates stress-induced depressive-like behavior. Nat. Med. (PMID: 26390241)
Epigenetic regulation in information storage in the brain
Epigenetic regulation of transcription in neurons is crucial for the mechanisms underlying memory formation and the response to an ever-changing environment. Such cellular responses occur in part through regulation of the chromatin landscape, such as through modifications to the histone proteins that regulate gene activation. However, the link between neuronal stimulation and the resulting changes in histone modifications that activate transcription in neurons is not fully understood. We worked on elucidating mechanisms of epigenetic regulation of transcription that link neuronal inputs to behavioral responses. These projects help advance our understanding of how the brain uses the epigenome to continually adapt to its environment throughout the lifetime of an animal.
Korb, E.,Herre, M., Zucker-Scharff, I., Darnell, RB., Allis, C.D. 2015. BET protein Brd4 activates transcription in neurons and BET inhibitor Jq1 blocks memory in mice. Nat. Neuro. (PMID: 26301327)
Korb, E., Wilkinson, C. L., Delgado, R.N., Lovero, K.L., Finkbeiner, S. 2013. Arc in the nucleus regulates PML-dependent GluA1 transcription and homeostatic plasticity. Nat. Neuro. 16(7), 874-83. (PMID: 23749147)
Korb, E., Finkbeiner, S. 2011. Arc in synaptic plasticity: from gene to behavior. Trends Neurosci. 34, 591-8. (PMID: 21963089)
Korb, E., Finkbeiner, S. 2013. PML in the Brain: From Development to Degeneration. Frontiers in Molecular and Cellular Oncology. 17, 242. (PMID: 2406991)

Research Interest

The Korb lab works at the intersection of neuroscience and epigenetics. Epigenetic regulation is extremely important in neuronal function and contributes to the creation of new memories, our ability to adapt to our environment, and numerous neurological disorders. We try to understand how the world around us can influence gene expression in our neurons to allow us to learn, adapt, and become the people we are today.
In the lab, we focus on chromatin and its role in neuronal function. Chromatin is the complex of DNA and proteins called histones, which package our DNA into complex structures and control access to our genes. To study the role of histones in neuronal function and in disorders such as autism, we combine methods such as microscopy, bioinformatics, biochemistry, behavioral testing, and more. We have multiple areas of research in the lab, all focused on the study of chromatin and how it regulates neuronal function and neurodevelopmental disorders.

Kavitha Sarma, Ph.D.

Research Interest

The Sarma laboratory is interested in the mechanisms of epigenetic gene regulation, or how the dynamic modifications of the architecture of chromatin, the complex of DNA, RNA, and proteins within the nucleus of our cells, impacts gene expression and cellular function. The lab investigates consequences of epigenetic alterations in neuronal cancers and neurodegenerative diseases using a combination of biochemistry, cell and molecular biology, and functional genomics approaches to gain mechanistic insight into how chromatin architecture is modified in disease. Our goal is to identify new pathways and interactions that can be targeted to correct these epigenetic perturbations.

Shelley L. Berger, Ph.D.

1.  Identification of transcriptional adaptors/coactivators Gcn5/Ada2/Ada3 and discovery of novel histone modifications and mechanisms in transcription and sperm genome opening.
We discovered transcriptional “adaptors”, which we showed associate with DNA binding activators, a groundbreaking new model for transcriptional activation, to reveal how histone enzymatic modifiers are recruited to genes. We revealed the importance of adaptor Gcn5 acetyltransferase activity in transcriptional activation (1998), to unify understanding of transcription and chromatin regulation. We discovered numerous novel histone modifications, modification cross-talk, and sequential histone modifications in transcription, including histone phosphorylation/acetylation (2001) and ubiquitylation/deubiquitylation. In 2017, we discovered that enhancer RNAs bind directly to CBP, the key metazoan acetyltransferase, to stimulate HAT activity in vitro and at enhancers and promoters in vivo.  We recently showed (2019) that Gcn5 provides key histone acetylation to broadly open the mouse genome during spermatogenesis for broad chromatin restructuring.

  • Wang L, Liu L. and Berger SL. (1998) Critical residues for histone acetylation by GCN5, functioning in Ada and SAGA complexes, are also required for transcriptional function in vivo. Genes & Development 12: 640-653. PMCID: PMC316586
  • Lo W-S, Duggan L, Belotserkovskya R, Emre T, Lane W, Shiekhattar R, and Berger SL.  (2001) Snf1 is a histone kinase which works in concert with the histone acetyltransferase Gcn5 to regulate transcription.  Science 293:1142-6. PMID:11498592
  • Bose DA, Donahue G, Reinberg D, Shiekhattar R, Bonasio R, Berger SL. (2017)  RNA binding to CBP stimulates histone acetylation and transcription. Cell 168,135-149. PMCID: PMC5325706.
  • Luense LJ, Donahue G, Lin-Shiao E….Bartolomei M, Berger SL. (2019) Gcn5-mediated histone acetylation governs nucleosome dynamics in spermiogenesis. Developmental Cell 51:745-758.

2. Discovery of chromatin mechanisms controlling aging and senescence in yeast and mammals.
Our work uncovered chromatin changes involved in aging and cellular senescence, indicating broad dysregulation of the epigenome. These include pioneering studies demonstrating that histone acetylation drives aging in yeast (2009) and disruption of the nuclear lamina with its associated chromatin domains in mammals.  We showed these disruptions trigger both homeostatic genomic protection and cellular damage, and discovery of nuclear autophagy pathways in senescence leading to inflammation in aging and cancer (2015, 2017, 2019, 2020). Our findings suggest potential epigenetic therapeutics to ameliorate age-associated disease.

  • Dang W…Kaeberlein M, Kennedy BK, and Berger SL. (2009) Histone H4 lysine-16 acetylation regulates cellular lifespan. Nature 459:802-7. PMCID: PMC2702157.
  • Dou Z…^Adams PD, and ^Berger SL. (2015) Autophagy mediates degradation of nuclear lamina. Nature 527:105-9. PMCID: PMC4824414.   (2017) Cytoplasmic chromatin triggers inflammation in senescence and cancer. Nature, 550:402-406.  PMID:28976970.
  • Sen P, Lan Y…Adams PD, Schultz DC, Berger SL. (2019) Histone acetyltransferase p300 induces de novo super-enhancers to drive cellular senescence. Molecular Cell, 73:684-698. PMID:30773298.
  • Xu C, Wang L…Adams PA, Ott M, Tong W, Johansen T, Dou Z^, and Berger SL^.  (2020)  SIRT1 is downregulated by autophagy in senescence and aging.  Nature Cell Biology, Oct 9..

3. Demonstration of chromatin mechanisms controlling memory and behavior. 
Our studies in mouse brain and memory show a pivotal role of the metabolic enzyme, ACSS2, in fueling “on-site” acetyl-CoA generation on chromatin for neuronal histone acetylation and gene expression in normal memory and in alcohol-fueled addiction memory (2017/19). Our work in human Alzheimer’s disease reveals that the cognitively normal aging brain is epigenetically protected compared to the AD brain (2018/20). In other research on brain, we pioneered investigation of eusocial ant caste-specific behavior for organismal-level chromatin regulation and epigenetics, owing to the remarkable fact that female ants of distinct social castes (such as queen, soldier, and forager) share an identical genome. We sequenced the first ant genomes and then profiled the first histone modification epigenomes (2013). Groundbreaking results indicate a critical role of histone modifications in altering ant brain function to instruct complex social behavior; we identified a “window”, early after hatching, to behavioral reprogramming via epigenetic manipulation (2016).  We pioneered Crisper genetics in ants (2017).

  • Simola DF…^Reinberg D, ^Liebig J, ^Berger SL.  (2016)  Epigenetic (re)programming of caste-specific behavior in the ant C. floridanus. Science 351:aac6633. PMID: 26722000, PMCID: PMC5057185.
  • Mews, P, Donahue G… Berger SL. (2017) Acetyl-CoA metabolism by ACSS2 regulates neuronal histone acetylation and hippocampal memory. Nature 546,381-386. PMCID: PMC5505514.  Mews P, ^Egervari G…Garcia, B, ^Berger SL. (2019) Alcohol metabolism contributes to brain histone acetylation. Nature 574: 717-721.
  • Glastad K, Graham RJ, Ju L, Rossler J, Brady CM, and Berger SL (2019) Epigenetic regulator CoRest controls social behavior in ants.  Molecular Cell 77:338-351.
  • Nativio R, Lan Y…Garcia BA, Trojanowski JQ, Bonini NM^, Berger SL^.  (2020) An integrated multi-omics approach identifies epigenetic drivers associated with Alzheimer’s disease.  Nature Genetics 52:1024-1035.

4. Discovery of tumor suppressor p53 factor and histone modifications and their mechanisms including activating p53 acetylation, repressive p53 methylation, and novel chromatin pathways in p53-mediated transcriptional activation.
Our work revealed new enzyme modifiers and post-translational modifications of p53 (including acetylation, methylation, and demethylation, 2006/7/10)) regulating p53 activity. Our findings spurred broad efforts to discover novel transcription factor modifications. We showed p53 methylation is generally repressive to its function, and showed repressive p53 methylation occurring in certain cancers bearing high levels of wild type p53. We discovered novel epigenetic pathways used by wild type and mutant p53 in regulating chromatin structure/function in normal and cancer cells, such as gain-of-function p53 mutants driving transcriptional activating and growth promoting histone modifications (2015).  We showed that p53 and p63 (2019) establish new enhancers during stress and development.

  • Huang J…Jenuwein T, and Berger SL. (2006) Repression of p53 activity by Smyd2-mediated methylation.  Nature 444:629-32. PMID:17108971.
  • Bungard D…Thompson CB, Jones RG and Berger SL. (2010) Signaling kinase AMPK activates stress-promoted transcription via histone H2B phosphorylation. Science 329: 1201-5. PMCID: PMC3922052.
  • Zhu J, Sammons MA, Donahue G, Dou Z…Arrowsmith CH, and Berger SL. (2015) Gain-of-function p53 mutants co-opt epigenetic pathways to drive cancer growth. Nature 525:206-11. PMCID: PMC4568559
  • Lin-Shiao E, Lan Y…Sammons M, Ludwig K, and Berger SL. (2019) p63 establishes epithelial enhancers at critical craniofacial development genes. Science Advances, May 1; 5:eaaw0946.

5. Investigation of epigenetic mechanisms affecting cancer immunotherapy.
We established collaborations with Carl June (pioneered CAR T cell therapy in cancer) and John Wherry (discovered key aspects of T cell exhaustion).  We investigate epigenetic regulation in patient response to immunotherapy, and controlling T cell exhaustion.

  • Pauken KE…Berger SL, and Wherry EJ.  (2016) Epigenetic stability of exhausted T cells limits durability of reinvigoration by PD-1 blockade. Science 354,1160-1165.
  •  Fraietta JA…Berger SL, Bushman FD, June CH, and Melenhorst JJ. (2018) Disruption of TET2 promotes the therapeutic efficacy of CD19-targeted T-cells. Nature 555, 307-312.
  • Khan O…Berger SL, and Wherry EJ.  (2019) TOX transcriptionally and epigenetically programs CD8+ T cell exhaustion.  Nature 571, 211-218.

Research Interest

Our lab focuses on mechanisms that regulate gene expression with a special emphasis on how the DNA-packaging structure of chromatin is manipulated during genomic processes. Our findings inform the study of cancer and other diseases, and ultimately drug discovery.

Marisa Bartolomei, Ph.D.

Mechanism of Genomic Imprinting: As a postdoctoral fellow in the laboratory of Dr. Shirley Tilghman, I identified the one of the first imprinted genes—the H19 gene and also determined that this gene was adjacent to the imprinted Igf2 gene, representing the first evidence of imprinted gene clusters. In my own laboratory, we study the mechanisms governing imprinted gene expression and have determined that imprinted genes and clusters are regulated by differentially methylated imprinting control regions [ICRs]. In the case of H19 and Igf2, the ICR is a paternally methylated CTCF-dependent insulator. Through the use of cis-acting mutations we have characterized imprinting at the H19 locus and have elucidated elements that are important for setting the DNA methylation imprint in the germline and maintaining imprinting in the embryo after fertilization. Our mouse models contributed to the discovery that epigenetic mutations in the H19 ICR caused Silver-Russell Syndrome in a subset of patients. Additionally, microdeletions in the H19 ICR have been identified in Beckwith-Wiedemann Syndrome. We are generating mouse models as well as using iPS cells to study patient-derived mutations. 

  • Bartolomei, M.S., Zemel, S. and S.M. Tilghman. (1991). Parental imprinting of the mouse H19Nature 351:153-155.
  • Thorvaldsen, J.L., Duran, K.L. and M.S. Bartolomei. (1998). The H19differentially methylated domain provides multiple regulatory functions in H19 and Igf2 reciprocal imprinting. Genes & Development12:3693-3702.
  • Engel, N., West, A.G., Felsenfeld, G., and M.S. Bartolomei. (2004). Antagonism between DNA hypermethylation and enhancer-blocking activity at the H19DMD is uncovered by CpG mutations. Nature Genetics36:883-888.
  • Ideraabdullah, F.Y., Thorvaldsen, J.L., Myers, J.A. and M.S. Bartolomei. (2014). Tissue specific insulator function at H19/Igf2 revealed by deletions at the imprinting control region. Human Molecular Genetics23:6246-6259. PMCID: PMC4222363

Discovery that mouse models epigenetic perturbations identified in Assisted Reproductive Technologies (ART): In the imprinting field, experiments performed in the 1990’s were aimed at elucidating when monoallelic expression was initially set for imprinted genes. Two studies in our laboratory and in the Surani laboratory gave contrasting results for the H19 gene, with our lab showing maternal-specific expression when the gene was activated in the blastocyst and the Surani lab describing biallelic expression at this time. We subsequently determined that culturing mouse preimplantation embryos was associated with loss of imprinted gene expression. It was later shown that ART was associated with a higher than expected number of imprinting syndromes, including Beckwith-Wiedemann Syndrome and Angelman Syndrome, with almost all documented cases caused by loss of DNA methylation of the ICR. The mouse, which has the added benefit of normal fertility, has proven a valuable model to address these observations and determine mechanisms with the eventual goal of improving ART outcomes. We have shown that in vitro culture, embryo transfer, in vitro fertilization and hormonal hyperstimulation contribute to errors in epigenetic gene regulation. We have also determined that placental tissues are especially sensitive to the manipulations involved in ART.

  • Doherty, A.S., Mann, M.R.W., Tremblay, K.D., Bartolomei, M.S. and R.M. Schultz. (2000). Differential effects of culture on imprinted H19 expression in the preimplantation mouse embryo. Biology of Reproduction62:1526-1535.
  • Mann, M.R.W., Lee, S.S., Doherty, A.S., Verona, R.I., Nolen, L.D., Schultz, R.M., and M.S. Bartolomei. (2004). Selective loss of imprinting in the placenta following preimplantation development in culture. Development,131:3727-3735.
  • Rivera, R.M., Stein, P., Weaver, J.R., Mager, J., Schultz, R.M. and M.S. Bartolomei. (2008). Manipulations of mouse embryos prior to implantation result in aberrant expression of imprinted genes on day 9.5 of development. Human Molecular Genetics17:1-14.
  • deWaal, E., Mak, W., Calhoun, S., Stein, P., Ord, T., Krapp, C., Coutifaris, C., Schultz, R.M. and M.S. Bartolomei. (2014). In vitro culture increases the frequency of stochastic epigenetic errors at imprinted genes in placental tissues from mouse concepti produced through assisted reproductive technologies, Biology of Reproduction90:1-12. PMCID: PMC4076403

Generation of a mouse model to study endocrine disrupting compounds (EDCs): Numerous experiments in mouse model systems as well as human studies have suggested that exposure to EDCs is associated with aberrant DNA methylation. Because imprinted genes are regulated by DNA methylation, we tested whether imprinting could be disrupted when pregnant dams were exposed to levels of BPA that are comparable to human exposure. We demonstrated that genomic imprinting and DNA methylation of ICRs and repetitive DNA were perturbed in offspring exposed in utero, with a pronounced effect in placenta. We have also shown that metabolic phenotypes observed in F1 offspring exposed in utero were transmitted to their F2 offspring, thus exhibiting multigenerational transmission of the phenotype.

  • Susiarjo, M., Sasson, I., Mesaros, C. and M.S. Bartolomei. (2013). Bisphenol A exposure disrupts genomic imprinting in the mouse. PLOS Genetics9:e1003401. PMCID: PMC3616904
  • Susiarjo, M., Xin, F., Bansal, A., Stefaniak, M., Li, C., Simmons, R.A. and M.S. Bartolomei. (2015). Bisphenol A exposure disrupts metabolic health across multiple generations in the mouse. Endocrinology, Mar 25:en20142027. [Epub ahead of print]. PMCID: In progress

CTCF and insulators: CTCF was initially described as a factor that functioned in transcriptional repression and activation. The first demonstration of its insulator activity was by the Felsenfeld laboratory at the globin locus. It soon became apparent that there were CTCF sites in the H19/Igf2 ICR and that this ICR exhibited insulator activity on the maternal allele. To study the role of CTCF at H19 we generated a knockdown line and showed that in the absence of CTCF, H19 became hypermethylated, and also that embryos died early in development. This study was the first that reported the essential role for CTCF in development. Further experiments demonstrated the extensive role of CTCF in gene activity as well as a role for CTCF interacting with cohesins at a number of developmentally important insulators and regulatory regions. We have also studied CTCF binding in an ES cell differentiation model and elucidated sequence preferences both genomically and biochemically, contributing to the knowledge of the role of CTCF in early developmental decisions, as suggested by the knockdown studies.

  • Fedoriw, A.M, Stein, P., Svoboda, P., Schultz, R.M. and M.S. Bartolomei. (2004). Transgenic RNAi reveals essential function for CTCF in H19gene imprinting. Science303:238-240.
  • Wan, L-B., Pan, H., Hannenhalli, S., Cheng, Y., Ma, J., Fedoriw, A., Lobanenkov, V., Latham, K.E., Schultz, R.M. and M.S. Bartolomei. (2008). Maternal depletion of CTCF reveals multiple functions during ooycte and preimplantation embryo development. Development135:2729-2738. PMCID: PMC2596970
  • Stedman, W., Kang, H., Lin, S., Kissil, J.L., Bartolomei, M.S. and P.M. Lieberman. (2008). Cohesins localize with CTCF at the KSHV latency control region and at cellular c-Myc and H19/IGF2 insulators, EMBO Journal27:654-666. PMCID: PMC2262040
  • Plasschaert, R.N., Vigneau, S., Tempera, I., Gupta, R., Maksimoska, J., Everett, L., Davuluri, R., Marmorstein, R., Lieberman, P.M., Schultz, D., Hannenhalli, S. and M.S. Bartolomei. (2014). CTCF binding site sequences differences are associated with unique regulatory and functional trends during embryonic stem cell differentiation, Nucleic Acids Research42:774-789. PMCID: PMC3902912

Role of DNA methylation in epigenetic gene regulation in the mouse embryo: In early work as a postdoctoral fellow with Dr. Shirley Tilghman, I demonstrated that DNA methylation was critical for conferring parental identity of imprinted genes. Subsequently, my laboratory demonstrated that DNA methylation was erased in primordial germ cells by the time they enter the gonad and established in a sex-specific manner. We and others have also demonstrated that loss of the maintenance methyltransferase DNMT1 disrupts imprinted gene expression in the embryo as well as the placenta. More recently we have collaborated with a number of groups to understand the mechanism by which DNA methylation imprints are established and erased in the germline, including studies on the role of TDG and unpublished studies on the Tet enzyme family.

  • Bartolomei, M.S., Webber, A.L., Brunkow, M.E. and S. M. Tilghman. (1993). Epigenetic mechanisms underlying the imprinting of the mouse H19Genes and Development7:1663-1673.
  • Davis, T.L., Yang, G.J., McCarrey, J.R. and M.S. Bartolomei. (2000). The H19methylation imprint is erased and reestablished differentially on the parental alleles during male germ cell development. Human Molecular Genetics9:2885-2894.
  • Weaver, J.R., Sarkisian, G., Krapp, C., Mager, J., Mann, M.R. and M.S. Bartolomei. (2010). Domain-specific response of imprinted genes to reduced DNMT1. Molecular and Cellular Biology30: 3916-3928. PMCID: PMC2916450
  • Cortellino, S., Xu, J., Sannai, M., Moore, R., Caretti, E., Cigliano, A., Le Coz, M., Devarajan, K., Wessels, A., Soprano, D., Abramowitz, L.K., Bartolomei, M.S., Rambow, F., Bassi, M.R., Bruno, T., Fanciulli, M., Renner, C., Klein-Szanto, A.J., Matsumoto, Y., Kobi, D., Davidson, I., Alberti, C., Larue, L. and A. Bellacosa. (2011). Thymine DNA glycosylase is essential for active DNA demethylation by linked deamination-base excision repair. Cell146: 67-79. PMCID: PMC3230223

Research Interest

The research in the Bartolomei laboratory focuses epigenetic control of genomic imprinting. They also study how the environment can perturb genomic imprinting and other epigenetic processes important in reproduction and health.

Elizabeth Heller, Ph.D.

Proteomic characterization of inhibitory synapses. During doctoral training at The Rockefeller University under the mentorship of Dr. Nathaniel Heintz, I aimed to genetically tag and purify individual synapse types in the mammalian brain, in order to characterize their protein content using an innovative biochemical enrichment strategy coupled with high throughput proteomic analysis. In pursuit of this goal, I developed the first protocol for the specific biochemical isolation and characterization of the elusive inhibitory synapse.  We made a remarkable discovery, namely, that inhibitory synapses consist of structural proteins and ion channels, yet are completely lacking in the signaling molecules that comprise the major component of excitatory synapses.

Selimi F, Cristea IM, Heller E, Chait BT, Heintz N. Proteomic studies of a single CNS synapse type: the parallel fiber/purkinje cell synapse. PLoS Biol. 2009 Apr 14;7(4):e83. PubMed PMID: 19402746; PubMed Central PMCID: PMC2672601.
Heller EA, Zhang W, Selimi F, Earnheart JC, Ślimak MA, Santos-Torres J, Ibañez-Tallon I, Aoki C, Chait BT, Heintz N. The biochemical anatomy of cortical inhibitory synapses. PLoS One. 2012;7(6):e39572. PubMed PMID: 22768092; PubMed Central PMCID: PMC3387162.

Identification of critical period for sleep-consolidated spatial memory. During my undergraduate training I conducted an independent study under Dr. Ted Abel, aimed at elucidating the time course of sleep-induced memory formation in mice by examining memory deficits that result from sleep deprivation during discrete times following learning. We found that fear conditioning is blocked by sleep deprivation during a time period 5-10 hours post training, but unaffected by sleep deprivation for five hours immediately following training. This finding provided critical insights into the time-course of sleep-induced memory consolidation.

Graves LA, Heller EA, Pack AI, Abel T. Sleep deprivation selectively impairs memory consolidation for contextual fear conditioning. Learn Mem. 2003 May-Jun;10(3):168-76. PubMed PMID: 12773581; PubMed Central PMCID: PMC202307.

Locus-specific epigenetic editing for the study of addiction and depression. My postdoctoral research aimed to investigate the causal molecular mechanisms by which chromatin modifications contribute to reward-related pathology in the mammalian brain. There is a preponderance of compelling evidence implicating epigenetic modifications in the pathology of addiction and depression, in both human patients and animal models, yet previous studies have been unable to distinguish between the mere presence and the functional relevance of epigenetic modifications at relevant loci. To elucidate the molecular function of epigenetic regulation relevant to reward pathology, I have developed the use of engineered transcription factors to deliver histone modifications to a specific gene of interest in reward-related regions of the mammalian brain (major publications listed in Personal Statement).
Identification of cellular and molecular mechanisms underlying addiction and stress. In addition to pursuing my main postdoctoral research project, described above, I have also worked with others both inside and outside of the Nestler lab to investigate the molecular basis of drug addiction. For example, I have studied the role of serum- and glucocorticoid-inducible kinase 1 (SGK1) in regulating morphine and cocaine reward, and found that while its transcription and activity are upregulated in vivo by morphine and cocaine, exogenous SGK1 overexpression causes opposite behavioral responses to these two drugs. I have also contributed to several additional studies on the epigenetics of addiction, such as the role of nucleosome remodeling and the Sirtuin family of histone deacetylase.

Ferguson D, Koo JW, Feng J, Heller E, Rabkin J, Heshmati M, Renthal W, Neve R, Liu X, Shao N, Sartorelli V, Shen L, Nestler EJ. Essential role of SIRT1 signaling in the nucleus accumbens in cocaine and morphine action. J Neurosci. 2013 Oct 9;33(41):16088-98. PubMed PMID: 24107942; PubMed Central PMCID: PMC3792451.
Cates HM, Thibault M, Pfau M, Heller E, Eagle A, Gajewski P, Bagot R, Colangelo C, Abbott T, Rudenko G, Neve R, Nestler EJ, Robison AJ. Threonine 149 phosphorylation enhances ΔFosB transcriptional activity to control psychomotor responses to cocaine. J Neurosci. 2014 Aug 20;34(34):11461-9. PubMed PMID: 25143625; PubMed Central PMCID: PMC4138349.
Koo JW, Lobo MK, Chaudhury D, Labonté B, Friedman A, Heller E, Peña CJ, Han MH, Nestler EJ. Loss of BDNF signaling in D1R-expressing NAc neurons enhances morphine reward by reducing GABA inhibition. Neuropsychopharmacology. 2014 Oct;39(11):2646-53. PubMed PMID: 24853771; PubMed Central PMCID: PMC4207344.
Heller EA, Kaska S, Fallon B, Ferguson D, Kennedy PJ, Neve RL, Nestler EJ, Mazei-Robison MS. Morphine and cocaine increase serum- and glucocorticoid-inducible kinase 1 activity in the ventral tegmental area. J Neurochem. 2015 Jan;132(2):243-53. PubMed PMID: 25099208; PubMed Central PMCID: PMC4302038.

Research Interest

The Heller Lab studies the mechanisms by which remodeling of the epigenome leads to aberrant neuronal gene function and behavior.  To approach this problem, we directly manipulate histone and DNA modifications at specific genes in vivo, using viral delivery of epigenetic editing tools.  We focus on uncovering the mechanisms by which chromatin modifications interact with the transcriptional machinery following exposure to psychostimulants, such as drugs of abuse and stress. Because the behavioral disease traits of addiction and depression persist long after cessation of the harmful experience,  stable epigenetic remodeling is an attractive mechanism for such long-lasting effects and presents an intriguing target for therapeutic intervention.

Jennifer E. Phillips-Cremins, Ph.D.

Research Interest

Epigenomics and Systems Neurobiology Lab: The Cremins Lab investigates the link between three-dimensional organization of genomes and the establishment and maintenance of neural cell function. We employ systems level experimental and computational approaches to (1) create high-resolution 3-D genome architecture maps and (2) integrate 3-D architecture maps with genome-wide maps of epigenetic modifications and gene expression. Current work is focused on understanding the role for higher-order chromatin organization during differentiation of embryonic stem cells into neurons, during reprogramming of neurons into induced pluripotent stem cells and in models of neurodegenerative disease.

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