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

Cancer and MetabolismKathryn Wellen Lab

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.

Jennifer Phillips-Cremins LabZhaolan Zhou LabHao Wu Lab

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.

Jennifer Phillips-Cremins Lab Zhaolan Zhou Lab Hao Wu Lab

Controllable genome editing with split-engineered base editors

Junwei Shi LabRahul Kohli Lab

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.

Zhaolan Zhou Lab

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

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

Zhaolan Zhou Lab

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

Gerd Blobel LabGolnaz Vahedi LabEric Joyce LabRajan Jain Lab

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 Golnaz Vahedi Lab Eric Joyce Lab Rajan Jain Lab

Tramtrack acts during late pupal development to direct ant caste identity

Shelley Berger Lab

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

Arjun Raj LabRajan Jain Lab

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.

Arjun Raj Lab Rajan Jain Lab

Testing the super-enhancer concept

Gerd Blobel Lab

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

Gerd Blobel Lab

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

R. Babak Faryabi Lab

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

George Burslem Lab

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

Roberto Bonasio LabFormer Faculty Labs

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

Jon Epstein Lab

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

Shelley Berger LabArjun Raj LabEric Joyce Lab

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

Shelley Berger Lab Arjun Raj Lab Eric Joyce Lab

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

Rajan Jain Lab

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

Irfan Asangani Lab

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

Ben Black Lab

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

Roberto Bonasio LabMarisa Bartolomei LabRahul Kohli Lab

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

Roberto Bonasio Lab Marisa Bartolomei Lab Rahul Kohli Lab

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

Gerd Blobel LabMelike Lakadamyali Lab

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

Ken Zaret LabKlaus Kaestner Lab

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

Ken Zaret Lab Klaus Kaestner Lab

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

Shelley Berger LabJunwei Shi Lab

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

Shelley Berger Lab Junwei Shi Lab

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

Doris Wagner Lab

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

Roger Greenberg LabJunwei Shi LabR. Babak Faryabi Lab

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

Roger Greenberg Lab Junwei Shi Lab R. Babak Faryabi Lab

Genetic screening for single-cell variability modulators driving therapy resistance

Arjun Raj LabJunwei Shi Lab

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

Arjun Raj Lab Junwei Shi Lab

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

Montserrat Anguera Lab
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

Gerd Blobel Lab

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

Jennifer Phillips-Cremins Lab

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

Jennifer Phillips-Cremins Lab

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

Jennifer Phillips-Cremins Lab

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

Klaus Kaestner Lab

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

Klaus Kaestner Lab

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

Kathryn Wellen Lab

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

Matt Weitzman Lab

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

Roger Greenberg LabIrfan Asangani Lab
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
Roger Greenberg Lab Irfan Asangani Lab

Targeting cardiac fibrosis with engineered T cells

Jon Epstein Lab
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

Jon Epstein LabEric Joyce Lab
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

Jon Epstein Lab
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

Jon Epstein Lab

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

Shelley Berger LabRoberto Bonasio LabArjun Raj Lab
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

Roberto Bonasio LabFormer Faculty Labs

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

Gerd Blobel Lab

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

Gerd Blobel Lab
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

Gerd Blobel Lab

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

Shelley Berger LabFormer Faculty Labs
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

Shelley Berger LabFormer Faculty Labs

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

Marisa Bartolomei Lab

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

Marisa Bartolomei Lab
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

Marisa Bartolomei Lab

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

Montserrat Anguera Lab

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

Shelley Berger Lab

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.

Doris Wagner Lab

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.

Hao Wu Lab

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.

Jennifer Phillips-Cremins LabGerd Blobel Lab

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

Jennifer Phillips-Cremins Lab Gerd Blobel Lab

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

Roberto Bonasio LabFormer Faculty LabsKavitha Sarma Lab

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

Roberto Bonasio Lab Former Faculty Labs Kavitha Sarma Lab

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

Ben Black Lab

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.

Ken Zaret Lab

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.

R. Babak Faryabi Lab

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.

Golnaz Vahedi Lab

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.

Arjun Raj LabGolnaz Vahedi LabKlaus Kaestner LabR. Babak Faryabi Lab

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]

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

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

Elizabeth Heller Lab

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

Jennifer Phillips-Cremins Lab

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

Hongjun Song Lab

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.

Gerd Blobel Lab

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

Roger Greenberg Lab

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

Montserrat Anguera Lab
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

Montserrat Anguera Lab

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

Roberto Bonasio LabKavitha Sarma Lab

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

Roberto Bonasio Lab Kavitha Sarma Lab

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

Kavitha Sarma Lab

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.

Ken Zaret Lab

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.

Former Faculty Labs

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.

Irfan Asangani Lab

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.

Mitch Lazar Lab

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.

Brian Capell Lab

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.

Ben Black Lab

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.

Ben Black Lab

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.

Brian Capell Lab

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.

Jennifer Phillips-Cremins Lab

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

Matt Weitzman Lab

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

Jennifer Phillips-Cremins Lab

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.

Zhaolan Zhou Lab

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.

Former Faculty LabsGerd Blobel Lab

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

Former Faculty Labs Gerd Blobel Lab

Diversification and collapse of a telomere elongation mechanism.

Mia Levine Lab

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.

Mitch Lazar Lab

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.

Former Faculty Labs

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.

Shelley Berger Lab

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.

Ronen Marmostein Lab

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.

Elizabeth Heller Lab

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.

Former Faculty LabsGerd Blobel Lab

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

Former Faculty Labs Gerd Blobel Lab

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

Former Faculty Labs

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.

Jennifer Phillips-Cremins Lab

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.

Ronen Marmostein Lab

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.

Klaus Kaestner Lab

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.

Marisa Bartolomei Lab

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.

Doris Wagner Lab

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.

Former Faculty Labs

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.

Shelley Berger LabFormer Faculty Labs

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.

Mitch Lazar Lab

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.

Arjun Raj LabGerd Blobel Lab

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

Arjun Raj Lab Gerd Blobel Lab

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

Jon Epstein Lab

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

Jon Epstein Lab

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.

Jon Epstein Lab

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.

Roger Greenberg Lab

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.

Roberto Bonasio LabFormer Faculty LabsKen Zaret Lab

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

Roberto Bonasio Lab Former Faculty Labs Ken Zaret Lab

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

Arjun Raj Lab

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.

Montserrat Anguera Lab

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

Irfan Asangani Lab

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.

Klaus Kaestner Lab

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.

Mia Levine Lab

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.

Montserrat Anguera Lab

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.

Former Faculty Labs

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

Zhaolan Zhou Lab

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

Gerd Blobel Lab

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

Former Faculty Labs

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

Ronen Marmostein Lab

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

Mia Levine Lab

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

Ronen Marmostein 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. 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

Irfan Asangani Lab

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

Hongjun Song Lab

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

Roberto Bonasio Lab

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

Jennifer Phillips-Cremins Lab

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

Rahul Kohli Lab

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

Mitch Lazar Lab

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

Marisa Bartolomei Lab

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

Jon Epstein Lab

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

Hongjun Song Lab

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

NeuroepigeneticsShelley Berger Lab

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

NeuroepigeneticsShelley Berger Lab

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

Marisa Bartolomei Lab

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

Ronen Marmostein Lab

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

Jennifer Phillips-Cremins Lab

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

Arjun Raj Lab

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

Rahul Kohli Lab

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.

Shelley Berger Lab

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

Ben Black Lab

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

Gerd Blobel Lab

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

Golnaz Vahedi Lab

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

Shelley Berger LabBrian Capell Lab

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

Mitch Lazar Lab

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

Ken Zaret Lab

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

Matt Weitzman Lab

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

NeuroepigeneticsHao Wu Lab

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

Brian Capell Lab

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

Former Faculty Labs

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

NeuroepigeneticsHongjun Song Lab

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

Zhaolan Zhou Lab
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

Former Faculty Labs

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

NeuroepigeneticsZhaolan Zhou Lab

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

Jon Epstein Lab

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

Jennifer Phillips-Cremins Lab

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

Montserrat Anguera 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.  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

Shelley Berger Lab

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

Ronen Marmostein Lab

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

Zhaolan Zhou Lab

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

Mitch Lazar Lab

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

DevelopmentalKen Zaret Lab

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.

Mustafa Mir Lab

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

Rahul Kohli Lab

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

Cancer and MetabolismFormer Faculty Labs

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

DevelopmentalRoberto Bonasio LabDoris Wagner Lab

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 Roberto Bonasio Lab Doris Wagner Lab

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

Gerd Blobel Lab

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

DevelopmentalRoberto Bonasio Lab

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

Matt Weitzman Lab

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

Ben Black Lab

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

Marisa Bartolomei Lab

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

Roger Greenberg Lab

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

Cancer and MetabolismRoger Greenberg Lab

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

Spatial / ArchitecturalJennifer Phillips-Cremins Lab

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

Rahul Kohli Lab

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

Mitch Lazar Lab

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

Ken Zaret Lab

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

Former Faculty Labs

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

Cancer and MetabolismKathryn Wellen Lab

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

Zhaolan Zhou Lab

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

Ronen Marmostein Lab

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

Matt Weitzman Lab

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

Roberto Bonasio Lab

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

Shelley Berger Lab

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

Cancer and MetabolismMitch Lazar Lab

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

Elizabeth Heller Lab

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

Faster and less phototoxic 3D fluorescence microscopy using a versatile compressed sensing scheme.

Mustafa Mir Lab

Faster and less phototoxic 3D fluorescence microscopy using a versatile compressed sensing scheme. M. Woringer, X. Darzacq, C. Zimmer, and M. Mir. Optics Express 25(12): 13668-13683, 2017.

Mustafa Mir Lab

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

Arjun Raj Lab

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

Shelley Berger Lab

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

Ronen Marmostein Lab

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

Zhaolan Zhou Lab

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

Elizabeth Heller Lab

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

Roger Greenberg Lab

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

Rahul Kohli Lab

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

Cancer and MetabolismPatrick Seale Lab

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

Matt Weitzman Lab

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

Ken Zaret Lab

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

DevelopmentalZhaolan Zhou Lab

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

Gerd Blobel Lab

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

Mitch Lazar Lab

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

Ken Zaret Lab

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

Spatial / ArchitecturalFormer Faculty Labs

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

Matt Weitzman Lab

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

Montserrat Anguera Lab

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

Ken Zaret Lab

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

Jon Epstein Lab

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

Mitch Lazar Lab

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

Junwei Shi Lab

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

Roberto Bonasio Lab

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

Former Faculty Labs

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

Rahul Kohli Lab

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

Mia Levine Lab

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

Cancer and MetabolismShelley Berger Lab

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

Ben Black Lab

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

Shelley Berger Lab

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

Roger Greenberg Lab

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

Zhaolan Zhou Lab

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

Ken Zaret Lab

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

Mitch Lazar Lab

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

Rahul Kohli Lab

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

Mitch Lazar Lab

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

Mitch Lazar Lab

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

Mitch Lazar Lab

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

Former Faculty Labs

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

DevelopmentalKlaus Kaestner Lab

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

Ronen Marmostein Lab

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

Gerd Blobel Lab
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

Roberto Bonasio Lab

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

Roger Greenberg Lab

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

Marisa Bartolomei Lab

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

Ronen Marmostein Lab

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

Shelley Berger Lab

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

Former Faculty Labs

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

Marisa Bartolomei Lab

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

Shelley Berger Lab

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

Shelley Berger Lab

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

Roger Greenberg Lab

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

Rahul Kohli Lab

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

Marisa Bartolomei Lab

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

Mitch Lazar Lab

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

Former Faculty Labs

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

Matt Weitzman Lab

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

Ronen Marmostein Lab

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

Jon Epstein Lab

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

Matt Weitzman Lab

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

Shelley Berger Lab

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

Gerd Blobel Lab

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

Rahul Kohli Lab

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

Roger Greenberg Lab

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

Ken Zaret Lab

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

Montserrat Anguera Lab

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

Former Faculty Labs

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

Roger Greenberg Lab

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

Spatial / ArchitecturalJennifer Phillips-Cremins Lab

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

Former Faculty Labs

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

Gerd Blobel Lab

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

Zhaolan Zhou Lab

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

Ken Zaret Lab

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

Ben Black Lab

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

Spatial / ArchitecturalBen Black Lab

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

Montserrat Anguera Lab

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

Mitch Lazar Lab

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

Gerd Blobel Lab

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

Spatial / ArchitecturalDevelopmentalArjun Raj Lab

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

Spatial / Architectural Developmental Arjun Raj Lab

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

Former Faculty Labs

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

Shelley Berger Lab

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

Former Faculty Labs

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

Ken Zaret Lab

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

Rahul Kohli Lab

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

Ronen Marmostein Lab

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

Shelley Berger Lab

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

Shelley Berger Lab

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

Ken Zaret Lab

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

Shelley Berger Lab

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

Doris Wagner Lab

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.

Mustafa Mir Lab

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

Roger Greenberg Lab

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

Roger Greenberg Lab

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
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