Publication Highlights

  • 2019

    • Interrogating Histone Acetylation and BRD4 as Mitotic Bookmarks of Transcription. Behera V, Stonestrom AJ, Hamagami N, Hsiung CC, Keller CA, Giardine B, Sidoli S, Yuan Z-F, Bhanu NV, Werner MT, Wang H, Garcia BA, Hardison RC, Blobel GA. Cell Rep. 2019 Apr 9;27(2):400-415.e5. doi: 10.1016/j.celrep.2019.03.057. PMID: 30970245

    • Allele-specific RNA imaging shows that allelic imbalances can arise in tissues through transcriptional bursting.
      Symmons O, Chang M, Mellis IA, Kalish JM, Park J, Suszták K, Bartolomei MS, Raj A.
      PLoS Genet. 2019 Jan 9;15(1):e1007874. doi: 10.1371/journal.pgen.1007874. eCollection 2019 Jan.

    • Auxin Response Factors promote organogenesis by chromatin-mediated repression of the pluripotency gene SHOOTMERISTEMLESS. Chung Y, Zhu Y, Wu MF, Simonini S, Kuhn A, Armenta-Medina A, Jin R, Østergaard L, Gillmor CS, Wagner D. Nat Commun. 2019 Feb 21;10(1):886. doi: 10.1038/s41467-019-08861-3. PMID:30792395

    • Histone Acetyltransferase p300 Induces De Novo Super-Enhancers to Drive Cellular Senescence.
      Sen P, Lan Y, Li CY, Sidoli S, Donahue G, Dou Z, Frederick B, Chen Q, Luense LJ, Garcia BA, Dang W, Johnson FB, Adams PD, Schultz DC, Berger SL. Mol Cell. 2019 Feb 8. pii: S1097-2765(19)30041-3. doi: 10.1016/j.molcel.2019.01.021. [Epub ahead of print]

    • Coordination between TGF-β cellular signaling and epigenetic regulation during epithelial to mesenchymal transition. Lu C, Sidoli S, Kulej K, Ross K, Wu CH, Garcia BA. Epigenetics Chromatin. 2019 Feb 8;12(1):11. doi: 10.1186/s13072-019-0256-y. PMID:30736855

    • Transcriptional Burst Initiation and Polymerase Pause Release Are Key Control Points of Transcriptional Regulation.
      Bartman CR, Hamagami N, Keller CA, Giardine B, Hardison RC, Blobel GA, Raj A. Mol Cell. 2019 Feb 7;73(3):519-532.e4. doi: 10.1016/j.molcel.2018.11.004. Epub 2018 Dec 13.

    • Patient Adipose Stem Cell-Derived Adipocytes Reveal Genetic Variation that Predicts Antidiabetic Drug Response. Hu W, Jiang C, Guan D, Dierickx P, Zhang R, Moscati A, Nadkarni GN, Steger DJ, Loos RJF, Hu C, Jia W, Soccio RE, Lazar MA. Cell Stem Cell. 2019 Feb 7;24(2):299-308.e6. doi: 10.1016/j.stem.2018.11.018. Epub 2019 Jan 10. PMID:30639037

    • Lineage-specific reorganization of nuclear peripheral heterochromatin and H3K9me2 domains. See K, Lan Y, Rhoades J, Jain R, Smith CL, Epstein JA. Development. 2019 Feb 5;146(3). pii: dev174078. doi: 10.1242/dev.174078. PMID:30723106

    • RAD52 and SLX4 act nonepistatically to ensure telomere stability during alternative telomere lengthening. Verma P, Dilley RL, Zhang T, Gyparaki MT, Li Y, Greenberg RA. Genes Dev. 2019 Feb 1;33(3-4):221-235. doi: 10.1101/gad.319723.118. Epub 2019 Jan 28. PMID:30692206

    • H3K9me3-heterochromatin loss at protein-coding genes enables developmental lineage specification. Nicetto D, Donahue G, Jain T, Peng T, Sidoli S, Sheng L, Montavon T, Becker JS, Grindheim JM, Blahnik K, Garcia BA, Tan K, Bonasio R, Jenuwein T, Zaret KS. Science. 2019 Jan 18;363(6424):294-297. doi: 10.1126/science.aau0583. Epub 2019 Jan 3. PMID:30606806

    • Diversity of Epigenetic Features of the Inactive X-Chromosome in NK Cells, Dendritic Cells, and Macrophages. Syrett CM, Sindhava V, Sierra I, Dubin AH, Atchison M, Anguera MC. Front Immunol. 2019 Jan 8;9:3087. doi: 10.3389/fimmu.2018.03087. eCollection 2018.

  • 2018

    • Exploiting Substrate Promiscuity to Develop Activity-Based Probes for TET Family Enzymes. Ghanty U, DeNizio JE, Liu MY, Kohli RM. J Am Chem Soc. 2018 Dec 6. doi: 10.1021/jacs.8b04722. PMID:30518204

    • Sex-Specific Regulation of Fear Memory by Targeted Epigenetic Editing of Cdk5.
      Sase AS, Lombroso SI, Santhumayor BA, Wood RR, Lim CJ, Neve RL, Heller EA. Biol Psychiatry. 2018 Dec 5. pii: S0006-3223(18)32054-7. doi: 10.1016/j.biopsych.2018.11.022. [Epub ahead of print] PMID:30661667

    • ClampFISH detects individual nucleic acid molecules using click chemistry-based amplification.
      Rouhanifard SH, Mellis IA, Dunagin M, Bayatpour S, Jiang CL, Dardani I, Symmons O, Emert B, Torre E, Cote A, Sullivan A, Stamatoyannopoulos JA, Raj A. Nat Biotechnol. 2018 Nov 12. doi: 10.1038/nbt.4286. [Epub ahead of print]

    • A changing paradigm of transcriptional memory propagation through mitosis. Katherine C. Palozola, Jonathan Lerner, Kenneth S. ZaretNature Reviews Molecular Cell Biology (2018) s41580-018-0077-z

    • Targeted demethylation at the CDKN1C/p57 induces human β cell replication. Ou K, Yu M, Moss NG, Wang YJ, Wang AW, Nguyen SC, Jiang C, Feleke E, Kameswaran V, Joyce EF, Naji A, Glaser B, Avrahami D, Kaestner KHJ Clin Invest. 2018 Oct 23. pii: 99170. doi: 10.1172/JCI99170.

    • Systematic Evaluation of Soluble Protein Expression Using a Fluorescent Unnatural Amino Acid Reveals No Reliable Predictors of Tolerability.
      Hostetler ZM, Ferrie JJ, Bornstein MR, Sungwienwong I, Petersson EJ, Kohli RM.
      ACS Chem Biol. 2018 Oct 19;13(10):2855-2861. doi: 10.1021/acschembio.8b00696. Epub 2018 Sep 20.
      PMID: 30216041

    • Phosphorylation of TIP60 suppresses 53BP1 localization at DNA damage sites.
      Li ML, Jiang Q, Bhanu NV, Wu J, Li W, Garcia BA, Greenberg RA. Mol Cell Biol. 2018 Oct 8. pii: MCB.00209-18. doi: 10.1128/MCB.00209-18. [Epub ahead of print]
      PMID: 30297459

    • Nondestructive, base-resolution sequencing of 5-hydroxymethylcytosine using a DNA deaminase.
      Schutsky EK, DeNizio JE, Hu P, Liu MY, Nabel CS, Fabyanic EB, Hwang Y, Bushman FD, Wu H, Kohli RM.Nat Biotechnol. 2018 Oct 8. doi: 10.1038/nbt.4204. [Epub ahead of print] PMID: 30295673

    • Single-nucleus transcriptomic survey of cell diversity and functional maturation in postnatal mammalian hearts.
      Hu P, Liu J, Zhao J, Wilkins BJ, Lupino K, Wu H, Pei L. Genes Dev. 2018 Oct 1;32(19-20):1344-1357. doi: 10.1101/gad.316802.118. Epub 2018 Sep 25. PMID: 30254108;

    • Recurrent Amplification of the Heterochromatin Protein 1 (HP1) Gene Family across Diptera.
      Helleu Q, Levine MT. Mol Biol Evol. 2018 Oct 1;35(10):2375-2389. doi: 10.1093/molbev/msy128. PMID: 29924345

    • Sex-Specific Gene Expression Differences Are Evident in Human Embryonic Stem Cells and During In Vitro Differentiation of Human Placental Progenitor Cells.
      Syrett CM, Sierra I, Berry CL, Beiting D, Anguera MC. Stem Cells Dev. 2018 Oct 1;27(19):1360-1375. doi: 10.1089/scd.2018.0081. Epub 2018 Aug 21. PMID: 29993333

    • Disease-Associated Short Tandem Repeats Co-localize with Chromatin Domain Boundaries. Sun JH, Zhou L, Emerson DJ, Phyo SA, Titus KR, Gong W, Gilgenast TG, Beagan JA, Davidson BL, Tassone F, Phillips-Cremins JE. Cell. 2018 Sep 20;175(1):224-238.e15. doi: 10.1016/j.cell.2018.08.005. Epub 2018 Aug 30. PMID: 30173918

    • Autocrine Mfge8 Signaling Prevents Developmental Exhaustion of the Adult Neural Stem Cell Pool. Zhou Y, Bond AM, Shade JE, Zhu Y, Davis CO, Wang X, Su Y, Yoon KJ, Phan AT, Chen WJ, Oh JH, Marsh-Armstrong N, Atabai K, Ming GL, Song H. Cell Stem Cell. 2018 Sep 6;23(3):444-452.e4. doi: 10.1016/j.stem.2018.08.005. Epub 2018 Aug 30. PMID: 30174295

    • Hydrogen-Deuterium Exchange Coupled to Top- and Middle-Down Mass Spectrometry Reveals Histone Tail Dynamics before and after Nucleosome Assembly. Karch KR, Coradin M, Zandarashvili L, Kan ZY, Gerace M, Englander SW, Black BE, Garcia BA. Structure. 2018 Aug 25. pii: S0969-2126(18)30294-6. doi: 10.1016/j.str.2018.08.006. [Epub ahead of print] PMID: 30293810

    • EWS/ETS-Driven Ewing Sarcoma Requires BET Bromodomain Proteins. Gollavilli PN, Pawar A, Wilder-Romans K, Natesan R, Engelke CG, Dommeti VL, Krishnamurthy PM, Nallasivam A, Apel IJ, Xu T, Qin ZS, Feng FY, Asangani IA. Cancer Res. 2018 Aug 15;78(16):4760-4773. doi: 10.1158/0008-5472.CAN-18-0484. Epub 2018 Jun 13. PMID: 29898995

    • A Cosine Similarity-Based Method to Infer Variability of Chromatin Accessibility at the Single-Cell Level. Cai S, Georgakilas GK, Johnson JL, Vahedi G. Front Genet. 2018 Aug 15;9:319. doi: 10.3389/fgene.2018.00319. eCollection 2018. PMID: 30158954

    • 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 Aug 15. pii: canres.0484.2018. doi: 10.1158/0008-5472.CAN-18-0484. Epub 2018 Jun 13.

    • Diet-Induced Circadian Enhancer Remodeling Synchronizes Opposing Hepatic Lipid Metabolic Processes.
      Guan D, Xiong Y, Borck PC, Jang C, Doulias PT, Papazyan R, Fang B, Jiang C, Zhang Y, Briggs ER, Hu W, Steger D, Ischiropoulos H, Rabinowitz JD, Lazar MA.
      Cell. 2018 Aug 9;174(4):831-842.e12. doi: 10.1016/j.cell.2018.06.031. Epub 2018 Jul 26.
      PMID: 30057115

    • Structural Basis for MARK1 Kinase Autoinhibition by Its KA1 Domain. Emptage RP, Lemmon MA, Ferguson KM, Marmorstein R. Structure. 2018 Aug 7;26(8):1137-1143.e3. doi: 10.1016/j.str.2018.05.008. Epub 2018 Jun 28. PMID: 30099988

    • 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.

    • 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 GA. Science. 2018 Jul 20;361(6399):285-290. doi: 10.1126/science.aao0932. PMID: 30026227

    • PPARγ is a nexus controlling alternative activation of macrophages via glutamine metabolism.
      Nelson VL, Nguyen HCB, Garcìa-Cañaveras JC, Briggs ER, Ho WY, DiSpirito JR, Marinis JM, Hill DA, Lazar MA.
      Genes Dev. 2018 Aug 1;32(15-16):1035-1044. doi: 10.1101/gad.312355.118. Epub 2018 Jul 13.

    • Condensin II drives large-scale folding and spatial partitioning of interphase chromosomes in Drosophila nuclei. Rosin LF, Nguyen SC, Joyce EF. PLoS Genet. 2018 Jul 12;14(7):e1007393. doi: 10.1371/journal.pgen.1007393. eCollection 2018 Jul. PMID: 30001329

    • 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 BA. J Proteome Res. 2018 Jul 6;17(7):2533-2541. doi: 10.1021/acs.jproteome.8b00133. Epub 2018 May 30. PMID: 29790754

    • 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.

    • 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]

    • 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.

    • 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. PMID: 29872540

    • 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.

    • 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.

    • 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.

    • 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.

    • 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.

    • 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

    • 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.

    • 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

    • 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.

    • 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.

    • 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

    • 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

    • 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.

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

    • Resistance to BET Inhibitor Leads to Alternative Therapeutic Vulnerabilities in Castration-Resistant Prostate Cancer. Pawar A, Gollavilli PN, Wang S, Asangani IA. Cell Rep. 2018 Feb 27;22(9):2236-2245. doi: 10.1016/j.celrep.2018.02.011.

    • 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

    • Lineage-determining transcription factor TCF-1 initiates the epigenetic identity of T cells. Johnson, J.L., Georgakilas, G., Petrovic, J., Kurachi, M., Cai, S., Harly, C., Pear, W.S., Bhandoola, A., Wherry, E., Vahedi G. Immunity. Cell Press, 48(2): 243-257, February 2018.

    • 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

    • 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.

    • 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 Feb 8. pii: eaao6891. doi: 10.1126/science.aao6891.

    • 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 Jan 15. doi: 10.1038/nmeth.4560.

  • 2017

    • Genomic and Proteomic Resolution of Heterochromatin and Its Restriction of Alternate Fate Genes. Becker JS, McCarthy RL, Sidoli S, Donahue G, Kaeding KE, He Z, Lin S, Garcia BA, Zaret KS. Mol Cell. 2017 Dec 21;68(6):1023-1037.e15. doi: 10.1016/j.molcel.2017.11.030.

    • 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.

    • 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.

    • 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):

    • 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.

    • 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.

    • The Crucial Role of DNA Methylation and MeCP2 in Neuronal Function. Fasolino M, Zhou Z.  Genes. 8(5) pii: E141, 2017.
    • Temporal Control of Mammalian Cortical Neurogenesis by m6A Methylation. Yoon KJ, Ringeling FR, Vissers C, Jacob F, Pokrass M, Jimenez-Cyrus D, Su Y, Kim NS, Zhu Y, Zheng L, Kim S, Wang X, Doré LC, Jin P, Regot S, Zhuang X, Canzar S, He C, Ming GL, Song H.Cell. 2017 Nov 2;171(4):877-889.e17

    • 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.

    • 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. doi: 10.1038/nm.4406.

    • 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.

    • 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

    • 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

    • 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.

    • 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.

    • 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

    • 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.

    • Mitotic transcription and waves of gene reactivation during mitotic exit. Palozola KC, Donahue G, Liu H, Grant GR, Becker JS, Cote A, Yu H, Raj A, Zaret KS.  Science. 2017 Oct 6;358(6359):119-122. doi: 10.1126/science.aal4671. Epub 2017 Sep 14.

    • 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.

    • 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.

    • 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.

    • 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.

    • 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.

    • 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.

    • 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.


    • 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.

    • 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.

    • 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.

    • 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.

    • 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.

    • 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.

    • 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.

    • 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.

    • 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.

    • 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.

    • 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.

    • 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.

    • 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.

    • 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.

    • 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

    • 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.

    • 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.

    • 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.

    • 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.

    • 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, Zhou Z.  J Clin Invest. 2017 May 1;127(5):1889-1904. doi: 10.1172/JCI90967. Epub 2017 Apr 10.

    • The BET Protein BRD2 Cooperates with CTCF to Enforce Transcriptional and Architectural Boundaries  Hsu SC, Gilgenast TG, Bartman CR, Edwards CR, Stonestrom AJ, Huang P, Emerson DJ, Evans P, Werner MT, Keller CA, Giardine B, Hardison RC, Raj A, Phillips-Cremins JE, Blobel GA.  Mol Cell. 2017 Apr 6;66(1):102-116.e7. doi: 10.1016/j.molcel.2017.02.027.

    • 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.

    • 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.

    • Metazoan Nuclear Pores Provide a Scaffold for Poised Genes and Mediate Induced Enhancer-Promoter Contacts  Pascual-Garcia P, Debo B, Aleman JR, Talamas JA, Lan Y, Nguyen NH, Won KJ, Capelson M.  Mol Cell. 2017 Apr 6;66(1):63-76.e6. doi: 10.1016/j.molcel.2017.02.020. Epub 2017 Mar 30.



    • 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.

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

    • 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.

    • 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.

    • 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.

    • 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.

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

    • 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.

    • 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.

    • 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.

    • 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.

    • 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.


    • 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.

  • 2016

    • 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.

    • 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.

    • 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.

    • 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.

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

    • 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.

    • A New Path through the Nuclear Pore.  Gozalo A, Capelson M.  Cell. 2016 Nov 17;167(5):1159-1160. doi: 10.1016/j.cell.2016.11.011.

    • 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.

    • 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


    • 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.

    • 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.

    • 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.

    • 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.

    • 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.

    • 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.

    • 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.

    • 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.

    • 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.

    • 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.

    • 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.

    • 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.

    • 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.

    • 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.

    • 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.

    • 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.

    • 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.


    • 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.

    • 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.

    • 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.

    • 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.

    • 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.


    • 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.


    • IncRHOXF1, 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, Lopez CB, Anguera MC.  Mol Cell Biol. 2016 May 31;36(12):1764-75. doi: 10.1128/MCB.01098-15. Print 2016 Jun 15.

    • 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.

    • 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.

    • 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.

    • 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.

    • 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.

    • 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.

    • 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.

    • 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.

    • 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.

    • 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

    • Visualizing allele-specific expression in single cells reveals epigenetic mosaicism in an H19 loss-of-imprinting mutant.  Ginart P, Kalish JM, Jiang CL, Yu AC, Bartolomei MS, Raj A.  Genes Dev. 2016 Mar 1;30(5):567-78. doi: 10.1101/gad.275958.115.

    • 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.

    • 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.

    • 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.

    • 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.

    • 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.

    • 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.

    • 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.