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Mutant NPM1 hijacks transcriptional hub to maintain pathogenic gene programs in acute myeloid leukemia.Wang X*, Fan D*, Han Q*, Liu Y*, Miao H, Wang X, Li Q, Chen D, Gore H, Himadewi P, Pfeifer GP, Cierpicki T, Grembecka J, Su J, Chong S#, Wan L#, Zhang X#. Cancer Discovery https://doi.org/10.1158/2159-8290.CD-22-0424. (*co-first; #co-corresponding)
A pioneer factor locally opens compacted chromatin to enable targeted ATP-dependent nucleosome remodeling Frederick MA, Williamson KE, Garcia MF, Ferretti MB, McCarthy RL, Donahue G, Monteiro EL, Takenaka N, Reynaga J, Kadoch C, Zaret KS. Nat Struct Mol Biol. 2022 Dec 19; doi: 10.1038/s41594-022-00886-5
CTCF blocks antisense transcription initiation at divergent promoters.
Luan J, Vermunt MW, Syrett CM, Coté A, Tome JM, Zhang H, Huang A, Luppino JM, Keller CA, Giardine BM, Zhang S, Dunagin MC, Zhang Z, Joyce EF, Lis JT, Raj A, Hardison RC, Blobel GA. Nat Struct Mol Biol. 2022 Nov;29(11):1136-1144. doi: 10.1038/s41594-022-00855-y. Epub 2022 Nov 11. PMID: 36369346
Hotspot mutations in the structured ENL YEATS domain link aberrant transcriptional condensates and cancer. Song L*, Yao X*, Li H, Peng B, Boka AP, Liu Y, Chen G, Liu Z, Mathias KM, Xia L, Li Q, Mir M, Li Y#, Li H#, Wan L#. Molecular Cell, 2022 Nov 3;82(21):4080-4098.e12. (featured in cover) PMID:36272410 (*co-first;#co-corresponding)
Small-molecule inhibition of the acyl-lysine reader ENL as a strategy against acute myeloid leukemia
Small-molecule inhibition of the acyl-lysine reader ENL as a strategy against acute myeloid leukemia. Liu Y, Li H, Alikarami F, Barrett DR, Khan TA, Michino M, Hill C, Mahdavi L, Song L, Tang S, Yang L, Li Y, Pokharel SP, Li Q, Stamford AW, Liverton N, Renzetti LM, Taylor S, Watt GF, Ladduwahetty T, Kargman S, Meinke PT, Foley MA, Shi J, Li H, Chen CW, Gardini A, Huggins DJ, Bernt KM#, Wan L#. Cancer Discovery, September 2022.
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
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.
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.
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.
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.
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.
Glastad KM, Ju L, Berger SL. PLoS Genet. 2021 Sep 22;17(9):e1009801. doi: 10.1371/journal.pgen.1009801. PMID: 34550980; PMCID: PMC8489709.
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.
Single-molecule tracking technologies for quantifying the dynamics of gene regulation in cells, tissue, and embryos.
A.P. Boka, A. Mukherjee, M. Mir. Development 148(18): dev199744, September 2021.
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.
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.
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.
Green A and Burslem GM. RSC Med Chem. 2021; Accepted Manuscript. doi: 10.1039/D1MD00193K
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.
Smith CL, Poleshko A, Epstein JA. Nucleic Acids Res. 2021 May 22:gkab392. doi: 10.1093/nar/gkab392. Epub ahead of print. PMID: 34023908
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Fernandez LR, Gilgenast TG, Phillips-Cremins JE. Genome Biology. 2020;21(1):219. doi: 10.1186/s13059-020-02061-9. PMID: 32859248
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
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
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
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
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
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
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
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
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
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
Bartolomei MS, Oakey RJ, Wutz A. PLoS Genet. 2020 Aug 6;16(8):e1008970. doi: 10.1371/journal.pgen.1008970. PMID: 32760145
Syrett CM, Sierra I, Beethem ZT, Dubin AH, Anguera MC. J Autoimmun. 2020;107:102357. doi: 10.1016/j.jaut.2019.102357. PMID: 31780316
Egervari G, Glastad KM, Berger SL. Science. 2020;370(657):660-662. doi: 10.1126/science.abb4367.
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
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
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
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
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
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
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
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;201919259. doi: 10.1073/pnas.1919259117.
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 RB, Vahedi G. Immunity. 2020. pii: S1074-7613(20)30030-3. doi: 10.1016/j.immuni.2020.01.003. [Epub ahead of print]
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.
Beagan J, Phillips-Cremins JE. Nat Genet. 2020;52(1):8-16. doi: 10.1038/s41588-019-0561-1. PMID: 31925403
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
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
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
Sierra I, Anguera MC. Curr Opin Genet Dev. 2019;55:26-31. doi: 10.1016/j.gde.2019.04.012. PMID: 31108425
Yan et al., 2019, Cell Reports29, 1369–1380 October 29, 2019ª2019 The Author(s).https://doi.org/10.1016/j.celrep.2019.09.052
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
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
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
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
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
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
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
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
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
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
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
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
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.
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Epstein JA. JAMA Cardiol. 2019 Feb 1;4(2):95-96. doi: 10.1001/jamacardio.2018.4435. No abstract available. PMID:30480702
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
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
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
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.
Dynamic Multifactor hubs transiently interact with sites of active transcription in Drospophila embryos. M. Mir, M. R. Stadler, S.A. Ortiz, X. Darzacq, M. B. Eisen. eLife 7(e40497 ), 2018.
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
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 KH. J Clin Invest. 2018 Oct 23. pii: 99170. doi: 10.1172/JCI99170.
Helleu Q, Levine MT. Mol Biol Evol. 2018 Oct 1;35(10):2375-2389. doi: 10.1093/molbev/msy128. PMID: 29924345
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
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
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 Z. Genome 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
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
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.
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.
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 IA. Cancer Res. 2018 Jun 13. pii: canres.0484.2018. doi: 10.1158/0008-5472.CAN-18-0484
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.
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. doi: 10.1038/s41593-018-0101-9.
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.
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.
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
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
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
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.
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 Mar 16;359(6381):1274-1277. doi: 10.1126/science.aao6891. Epub 2018 Feb 8.
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
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.
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.
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. 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
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.
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.
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.
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.
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
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.
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
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.
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.
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
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 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.
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.
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.
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.
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
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, and Zhou Z. Journal of Clinical Investigation 127(5): 1889-1904,2017.
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.
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.
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
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.
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.
Physiological Suppression of Lipotoxic Liver Damage by Complementary Actions of HDAC3 and SCAP/SREBP
Physiological Suppression of Lipotoxic Liver Damage by Complementary Actions of HDAC3 and SCAP/SREBP. Papazyan R, Sun Z, Kim YH, Titchenell PM, Hill DA, Lu W, Damle M, Wan M, Zhang Y, Briggs ER, Rabinowitz JD, Lazar MA. Cell Metab. 2016 Dec 13;24(6):863-874. doi: 10.1016/j.cmet.2016.10.012. Epub 2016 Nov 17.
Gozalo A, Capelson M. Cell. 2016 Nov 17;167(5):1159-1160. doi: 10.1016/j.cell.2016.11.011.
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
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.
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.
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.
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.
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
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.
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.
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. Ginard, P., Kalish, J.M., Jiang, C.L., Yu, A.C., Bartolomei, M.S.* and A. Raj*. (2016). Genes and Development, 30:567-578
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.
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.
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.
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
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.
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.
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
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