Selected Publications
2022
Fu R, He W, Dou J, Villarreal OD, Bedford E, Wang H, Hou C, Zhang L, Wang Y, Ma D, Chen Y, Gao X, Depken M, Xu H. Systematic decomposition of sequence determinants governing CRISPR/Cas9 specificity. Nat Commun. 2022 Jan 25;13(1):474.
Ma MCJ, Tadros S, Bouska A, Heavican T, Yang H, Deng Q, Moore D, Akhter A, Hartert K, Jain N, Showell J, Ghosh S, Street L, Davidson M, Carey C, Tobin J, Perumal D, Vose JM, Lunning MA, Sohani AR, Chen BJ, Buckley S, Nastoupil LJ, Davis RE, Westin JR, Fowler NH, Parekh S, Gandhi M, Neelapu S, Stewart D, Bhalla K, Iqbal J, Greiner T, Rodig SJ, Mansoor A, Green MR. Subtype-specific and co-occurring genetic alterations in B-cell non-Hodgkin lymphoma. Haematologica. 2022 Mar 1;107(3):690-701.
Orouji E, Raman AT, Singh AK, Sorokin A, Arslan E, Ghosh AK, Schulz J, Terranova C, Jiang S, Tang M, Maitituoheti M, Callahan SC, Barrodia P, Tomczak K, Jiang Y, Jiang Z, Davis JS, Ghosh S, Lee HM, Reyes-Uribe L, Chang K, Liu Y, Chen H, Azhdarinia A, Morris J, Vilar E, Carmon KS, Kopetz SE, Rai K. Chromatin state dynamics confers specific therapeutic strategies in enhancer subtypes of colorectal cancer. Gut. 2022 May;71(5):938-949.
Van HT, Harkins PR, Patel A, Jain AK, Lu Y, Bedford MT, Santos MA. Methyl-lysine readers PHF20 and PHF20L1 define two distinct gene expression-regulating NSL complexes. J Biol Chem. 2022 Mar;298(3):101588.
2021
Cermakova K, Demeulemeester J, Lux V, Nedomova M, Goldman SR, Smith EA, Srb P, Hexnerova R, Fabry M, Madlikova M, Horejsi M, De Rijck J, Debyser Z, Adelman K, Hodges HC, Veverka V. A ubiquitous disordered protein interaction module orchestrates transcription elongation. Science. 2021 Nov 26;374(6571):1113-1121.
Maron MI, Lehman SM, Gayatri S, DeAngelo JD, Hegde S, Lorton BM, Sun Y, Bai DL, Sidoli S, Gupta V, Marunde MR, Bone JR, Sun ZW, Bedford MT, Shabanowitz J, Chen H, Hunt DF, Shechter D. Independent transcriptomic and proteomic regulation by type I and II protein arginine methyltransferases. iScience. 2021 Aug 11;24(9):102971.
Morales F, Corrales E, Zhang B, Vásquez M, Santamaría-Ulloa C, Quesada H, Sirito M, Estecio MR, Monckton DG, Krahe R. Myotonic dystrophy type 1 (DM1) clinical subtypes and CTCF site methylation status flanking the CTG expansion are mutant allele length-dependent. Hum Mol Genet. 2021 Dec 27;31(2):262-274.
Shah VV, Duncan AD, Jiang S, Stratton SA, Allton KL, Yam C, Jain A, Krause PM, Lu Y, Cai S, Tu Y, Zhou X, Zhang X, Jiang Y, Carroll CL, Kang Z, Liu B, Shen J, Gagea M, Manu SM, Huo L, Gilcrease M, Powell RT, Guo L, Stephan C, Davies PJ, Parker-Thornburg J, Lozano G, Behringer RR, Piwnica-Worms H, Chang JT, Moulder SL, Barton MC. Mammary-specific expression of Trim24 establishes a mouse model of human metaplastic breast cancer. Nat Commun. 2021 Sep 10;12(1):5389.
Shaik S, Maegawa S, Haltom AR, Wang F, Xiao X, Dobson T, Sharma A, Yang Y, Swaminathan J, Kundra V, Li XN, Schadler K, Harmanci A, Xu L, Gopalakrishnan V. REST promotes ETS1-dependent vascular growth in medulloblastoma. Mol Oncol. 2021 May;15(5):1486-1506.
Yang J, Horton JR, Akdemir KC, Li J, Huang Y, Kumar J, Blumenthal RM, Zhang X, Cheng X. Preferential CEBP binding to T:G mismatches and increased C-to-T human somatic mutations. Nucleic Acids Res. 2021 May 21;49(9):5084-5094.
Yu D, Horton JR, Yang J, Hajian T, Vedadi M, Sagum CA, Bedford MT, Blumenthal RM, Zhang X, Cheng X. Human MettL3-MettL14 RNA adenine methyltransferase complex is active on double-stranded DNA containing lesions. Nucleic Acids Res. 2021 Nov 18;49(20):11629-11642.
2020
Alam H*, Tang M*, Maitituoheti M, Dhar SS, Kumar M, Han CY, Ambati CSR, Amin S, Gu B, Chen T-Y, Lin Y-H, Chen J, Muller F, Putluri N, Flores ER, DeMayo FJ, Baseler L, Rai K#, Lee MG# KMT2D deficiency impairs super-enhancers to confer a glycolytic vulnerability in lung cancer. Cancer Cell. 2020 Apr 13;37(4):599-617.e7. (*equal contribution, #o-corresponding authors)
Bailey CP, Figueroa M, Gangadharan A, Yang Y, Romero MM, Kennis BA, Yadavilli S, Henry V, Collier T, Monje M, Lee DA, Wang L, Nazarian J, Gopalakrishnan V, Zaky W, Becher OJ, Chandra J. Pharmacologic inhibition of lysine-specific demethylase 1 as a therapeutic and immune-sensitization strategy in pediatric high-grade glioma. Neuro Oncol. 2020 Sep 29;22(9):1302-1314.
Bhardwaj SK, Hailu SG, Olufemi L, Brahma S, Kundu S, Hota SK, Persinger J, Bartholomew B. Dinucleosome specificity and allosteric switch of the ISW1a ATP-dependent chromatin remodeler in transcription regulation. Nat Commun. 2020 Nov 20;11(1):5913.
Farria AT, Plummer JB, Salinger AP, Shen J, Lin K, Lu Y, McBride KM, Koutelou E, Dent SYR. Transcriptional Activation of MYC-Induced Genes by GCN5 Promotes B-cell Lymphomagenesis. Cancer Res. 2020 Dec 15;80(24):5543-5553.
Maitituoheti M, Keung EZ, Tang M, Yan L, Alam H, Han G, Singh AK, Raman AT, Terranova C, Sarkar S, Orouji E, Amin SB, Sharma S, Williams M, Samant NS, Dhamdhere M, Zheng N, Shah T, Shah A, Axelrad JB, Anvar NE, Lin YH, Jiang S, Chang EQ, Ingram DR, Wang WL, Lazar A, Lee MG, Muller F, Wang L, Ying H, Rai K. Enhancer Reprogramming Confers Dependence on Glycolysis and IGF Signaling in KMT2D Mutant Melanoma. Cell Rep. 2020 Oct 20;33(3):108293.
Mondello P, Tadros S, Teater M, Fontan L, Chang AY, Jain N, Yang H, Singh S, Ying HY, Chu CS, Ma MCJ, Toska E, Alig S, Durant M, de Stanchina E, Ghosh S, Mottok A, Nastoupil L, Neelapu SS, Weigert O, Inghirami G, Baselga J, Younes A, Yee C, Dogan A, Scheinberg DA, Roeder RG, Melnick AM, Green MR. Selective Inhibition of HDAC3 Targets Synthetic Vulnerabilities and Activates Immune Surveillance in Lymphoma. Cancer Discov. 2020 Mar;10(3):440-459.
Veazey KJ, Cheng D, Lin K, Villarreal OD, Gao G, Perez-Oquendo M, Van HT, Stratton SA, Green M, Xu H, Lu Y, Bedford MT, Santos MA. CARM1 inhibition reduces histone acetyltransferase activity causing synthetic lethality in CREBBP/EP300-mutated lymphomas. Leukemia. 2020 Dec;34(12):3269-3285.
Zeng Y, Ren R, Kaur G, Hardikar S, Ying Z, Babcock L, Gupta E, Zhang X, Chen T, Cheng X. The inactive Dnmt3b3 isoform preferentially enhances Dnmt3b-mediated DNA methylation. Genes Dev. 2020 Nov 1;34(21-22):1546-1558.
2019
Liu Y, Qin S, Chen T, Lei M, Dhar SS, Ho J, Dong A, Loppnau P, Li Y, Lee MG, Min J (2019) Structural insights into trans-histone regulation of H3K4 methylation by unique histone H4 binding of MLL3/4. Nature Commun 2019 Jan 3;10(1):36.
He W, Zhang L, Villarreal OD, Fu R, Bedford E, Dou J, Patel AY, Bedford MT, Shi X, Chen T, Bartholomew B, Xu H. De novo identification of essential protein domains from CRISPR-Cas9 tiling-sgRNA knockout screens. Nat Commun 10(1):4541, 10/2019. PMCID: PMC6778102.
Manickavinayaham S, Vélez-Cruz R, Biswas AK, Bedford E, Klein BJ, Kutateladze TG, Liu B, Bedford MT, Johnson DG. E2F1 acetylation directs p300/CBP-mediated histone acetylation at DNA double-strand breaks to facilitate repair. Nat Commun 10(1):4951, 10/2019. PMCID: PMC6821830.
Wu X, Liu S, Sagum C, Chen J, Singh R, Chaturvedi A, Horton JR, Kashyap TR, Fushman D, Cheng X, Bedford MT, Wang B. Crosstalk between Lys63- and Lys11-polyubiquitin signaling at DNA damage sites is driven by Cezanne. Genes Dev 33(23-24):1702-1717, 2019.
Jain N, Hartert K, Tadros S, Fiskus W, Havranek O, Ma MCJ, Bouska A, Heavican T, Kumar D, Deng Q, Moore D, Pak C, Liu CL, Gentles AJ, Hartmann E, Kridel R, Smedby KE, Juliusson G, Rosenquist R, Gascoyne RD, Rosenwald A, Giancotti F, Neelapu SS, Westin J, Vose JM, Lunning MA, Greiner T, Rodig S, Iqbal J, Alizadeh AA, Davis RE, Bhalla K, Green MR. Targetable genetic alterations of TCF4 (E2-2) drive immunoglobulin expression in diffuse large B cell lymphoma. Sci Transl Med 11(497), 6/2019/ PMID: 31217338
Ren R, Hardikar S, Horton JR, Lu Y, Zeng Y, Singh AK, Lin K, Della Coletta L, Shen J, Zhang X, Chen T*, Cheng X*. (2019) Structural basis of specific DNA binding by the transcription factor ZBTB24. Nucleic Acids Res 47 (16), 8388-8398. doi: 10.1093/nar/gkz557. (*Co-corresponding authors).
Veland N, Lu Y, Hardikar S, Gaddis S, Zeng Y, Liu B, Estecio M, Takata Y, Lin K, Tomida MW, Shen J, Saha D, Gowher H, Zhao H, Chen T. (2019) DNMT3L facilitates DNA methylation partly by maintaining DNMT3A stability in mouse embryonic stem cells. Nucleic Acids Res 47(1):152-167. doi: 10.1093/nar/gky947.
Koutelou E, Wang L, Schibler AC, Chao HP, Kuang X, Lin K, Lu Y, Shen J, Jeter CR, Salinger A, Wilson M, Chen YC, Atanassov BS, Tang DG, Dent SYR. USP22 controls multiple signaling pathways that are essential for vasculature formation in the mouse placenta. Development 146(4), 2/2019. e-Pub 2/2019. PMCID: PMC6398448.
2018
Alam H, Li N, Dhar SS, Wu SJ, Lv J, Chen K, Flores ER, Baseler L, Lee MG (2018) HP1γ promotes lung adenocarcinoma by downregulating the transcription-repressive regulators NCOR2 and ZBTB7A. Cancer Res. May 15. pii: canres.3571.2017. doi: 10.1158/0008-5472.CAN-17-3571.
Chen T-Y, Lee S-H, Dhar SS, Lee MG (2018) Protein arginine methyltransferase 7-mediated miR-221 repression maintains Oct4, Nanog and Sox2 levels in mouse embryonic stem cells. J Biol Chem 293: 3925-3936 PMCID:PMC5857983
Koppula P, Zhang Y, Zhuang L, Gan B. Amino acid transporter SLC7A11/xCT at the crossroads of regulating redox homeostasis and nutrient dependency of cancer. Cancer Communications. 2018 Apr 25; 38(1):12. PMID: 29764521 (invited review).
Zhang Y, Shi J, Liu X, Feng L, Gong Z, Koppula P, Sirohi K, Li X, Wei Y, Lee H, Zhuang L, Chen G, Xiao Z, Jung M, Chen J, Huang P, Gan B. BAP1 links metabolic regulation of ferroptosis to tumor suppression. Nature Cell Biology, 2018 Oct; 20(10):1181-1192. PMCID: PMC6170713.
Hamidi T, Singh AK, Veland N, Vemulapalli V, Chen J, Hardikar S, Bao J, Fry CJ, Yang V, Lee KA, Guo A, Arrowsmith CH, Bedford MT, Chen T. (2018) Identification of Rpl29 as a major substrate of the lysine methyltransferase Set7/9. J Biol Chem 293, 12770-12780.
Veland N, Lu Y, Hardikar S, Gaddis S, Zeng Y, Liu B, Estecio M, Takata Y, Lin K, Tomida MW, Shen J, Saha D, Gowher H, Zhao H, Chen T. (2018) DNMT3L facilitates DNA methylation partly by maintaining DNMT3A stability in mouse embryonic stem cells. Nucleic Acids Res2018 Oct 13. doi: 10.1093/nar/gky947. [Epub ahead of print].
Bailey CP, Figueroa M, Mohiuddin S, Zaky W, Chandra J. Cutting Edge Therapeutic Insight Derived from Molecular Biology of Pediatric Highr-Grade Glioma and Deffuse Intrinsic Pontine Glioma. Bioengineering. 2018
Bao J, Perez C, Kim J, Zhang H, Murphy CJ, Hamidi T, Jaubert J, Platt CD, Chou J, Deng M, Zhou MH, Huang Y, Gaitán-Peñas H, Guénet JL, Lin K, Lu Y, Chen T, Bedford MT, Dent SY, Richburg JH, Estévez R, Pan HL, Geha RS, Shi Q, Benavides F. Deficient LRRC8A-dependent volume-regulated anion channel activity is associated with male infertility in mice. JCI Insight 3(16). e-Pub 8/2018. PMCID: PMC6141173.
Bao J, Di Lorenzo A, Lin K, Lu Y, Zhong Y, Sebastian MM, Muller WJ, Yang Y, Bedford MT. Mouse models of overexpression reveal distinct oncogenic roles for different type I protein arginine methyltransferases. Cancer Res. e-Pub 10/2018.
Bao J, Rousseaux S, Shen J, Lin K, Lu Y, Bedford MT. The arginine methyltransferase CARM1 represses p300•ACT•CREMτ activity and is required for spermiogenesis. Nucleic Acids Res 46(9):4327-4343, 5/2018. PMCID: PMC5961101.
Brahma S, Ngubo M, Paul S, Udugama M, Bartholomew B. The Arp8 and Arp4 module acts as a DNA sensorcontrolling INO80 Chromatin remodeling. Nat Commun. 2018 Aug 17;9(1):3309. doi: 10.1038/s41467-018-05710-7.
Zhang Y, Shi J, Liu X, Feng L, Gong Z, Koppula P, Sirohi K, Li X, Wei Y, Lee H, Zhuang L, Chen G, Xiao ZD, Hung MC, Chen J, Huang P, Li W, Gan B. BAP1 links metabolic regulation of ferroptosis to tumour suppression. Nat Cell Biol. 2018 Sep 10. doi: 10.1038/s41556-018-0178-0. [Epub ahead of print]
Dhar SS, Zhao D, Lin T, Gu B, Pal K, Wu SJ, Alam H, Lv J, Yun K, Gopalakrishnan V, Flores ER, Northcott PA, Rajaram V, Li W, Shilatifard A, Sillitoe RV, Chen K, Lee MG. MLL4 Is Required to Maintain Broad H3K4me3 Peaks and Super-Enhancers at Tumor Suppressor Genes. Mol Cell. 2018 Jun 7;70(5):825-841
Horton JR, Liu X, Wu L, Zhang K, Shanks J, Zhang X, Rai G, Mott BT, Jansen DJ, Kales SC, Henderson MJ, Pohida K, Fang Y, Hu X, Jadhav A, Maloney DJ, Hall MD, Simeonov A, Fu H, Vertino PM, Yan Q, Cheng X. Insights into the Action of Inhibitor Enantiomers against Histone Lysine Demethylase 5A. J Med Chem. 2018 Apr 12;61(7):3193-3208.
Zhang H, Li HS, Hillmer EJ, Zhao Y, Chrisikos TT, Hu H, Wu X, Thompson EJ, Clise-Dwyer K, Millerchip KA, Wei Y, Puebla-Osorio N, Kaushik S, Santos MA, Wang B, Garcia-Manero G, Wang J, Sun SC, Watowich SS. Genetic rescue of lineage-balanced blood cell production reveals a crucial role for STAT3 antiinflammatory activity in hematopoiesis. Proc Natl Acad Sci U S A. 2018 Mar 6;115(10):E2311-E2319.
Patel A, Yang P, Tinkham M, Pradhan M, Sun MA, Wang Y, Hoang D, Wolf G, Horton JR, Zhang X, Macfarlan T, Cheng X. DNA Conformation Induces Adaptable Binding by Tandem Zinc Finger Proteins. Cell. 2018 Mar 22;173(1):221-233
2017
Koppula P, Zhang Y, Shi J, Li W, Gan B. The glutamate/cystine antiporter SLC7A11/xCT enhances cancer cell dependency on glucose by exporting glutamate. J Biol Chem. 2017 Aug 25; 292(34):14240-14249. PMCID: PMC5572906.
Xiao ZD, Han L, Lee H, Zhuang L, Zhang Y, Baddour J, Nagrath D, Wood CG, Gu J, Wu X, Liang H, Gan B. Energy stress-inducing lncRNA FILNC1 represses c-Myc-mediated energy metabolism and inhibits renal tumor development. Nature Communications, 2017, 2017, Oct 4; 8(1):783. PMCID: PMC5627275.
Dai F, Lee H, Zhang Y, Zhuang L, Yao H, Xi Y, Xiao ZD, You MJ, Li W, Su X, Gan B. BAP1 inhibits the ER stress gene regulatory network and modulates metabolic stress response. Proc Natl Acad Sci U S A. 2017 Mar 21;114(12):3192-3197. PMCID: PMC5373337.
Espejo AB, Black K, Veland N, Kim J, Chen T, Sudo M, Walker C, Bedford MT. (2017). PRMT5 C- terminal phosphorylation modulates a 14-3-3/PDZ interaction switch. J Biol Chem 292, 2255-2265.
Veland N, Chen T. (2017) Mechanisms of DNA methylation and demethylation during mammalian development. In: Handbook of Epigenetics, 2nd edition (ed. Tollefsbol T), Academic Press, pp11-24.
Dan J, Rousseau P, Hardikar S, Veland N, Wong J, Autexier C, Chen T. (2017) Zscan4 inhibits maintenance DNA methylation to facilitate telomere elongation in mouse embryonic stem cells. Cell Rep 20, 1936-1949.
Veland N, Hardikar S, Zhong Y, Gayatri S, Dan J, Strahl BD, Rothbart SB, Bedford MT, Chen T. (2017) The arginine methyltransferase PRMT6 regulates DNA methylation and contributes to global DNA hypomethylation in cancer. Cell Rep 21, 3390-3397.
Paul A, Wang B. RNF8- and Ube2S-Dependent Ubiquitin Lysine 11-Linkage Modification in Response to DNA Damage. Mol Cell. 2017 May 18;66(4):458-472.e5.
Brahma S, Udugama MI, Kim J, Hada A, Bhardwaj SK, Hailu SG, Lee TH, Bartholomew B. INO80 exchanges H2A.Z for H2A by translocating on DNA proximal to histone dimers. Nat Commun. 2017 Jun 12;8:15616.
Johnson GS, Li J, Beaver LM, Dashwood WM, Sun D, Rajendran P, Williams DE, Ho E, Dashwood RH. A functional pseudogene, NMRAL2P, is regulated by Nrf2 and serves as a coactivator of NQO1 in sulforaphane-treated colon cancer cells. Mol Nutr Food Res. 2017 Apr;61(4).
Fiziev P, Akdemir KC, Miller JP, Keung EZ, Samant NS, Sharma S, Natale CA, Terranova CJ, Maitituoheti M, Amin SB, Martinez-Ledesma E, Dhamdhere M, Axelrad JB, Shah A, Cheng CS, Mahadeshwar H, Seth S, Barton MC, Protopopov A, Tsai KY, Davies MA, Garcia BA, Amit I, Chin L, Ernst J, Rai K. Systematic Epigenomic Analysis Reveals Chromatin States Associated with Melanoma Progression. Cell Rep. 2017 Apr 25;19(4):875-889
Bae N, Viviano M, Su X, Lv J, Cheng D, Sagum C, Castellano S, Bai X, Johnson C, Khalil MI, Shen J, Chen K, Li H, Sbardella G, Bedford MT. Developing Spindlin1 small-molecule inhibitors by using protein microarrays. Nat Chem Biol. 2017 Jul;13(7):750-756.
Wan L, Wen H, Li Y, Lyu J, Xi Y, Hoshii T, Joseph JK, Wang X, Loh YE, Erb MA, Souza AL, Bradner JE, Shen L, Li W, Li H, Allis CD, Armstrong SA, Shi X. ENL links histone acetylation to oncogenic gene expression in acute myeloid leukaemia. Nature. 2017 Mar 9;543(7644):265-269.
2016
Carugo A, Genovese G, Seth S, Nezi L, Rose JL, Bossi D, Cicalese A, Shah PK, Viale A, Pettazzoni PF, Akdemir KC, Bristow CA, Robinson FS, Tepper J, Sanchez N, Gupta S, Estecio MR, Giuliani V, Dellino GI, Riva L, Yao W, Di Francesco ME, Green T, D'Alesio C, Corti D, Kang Y, Jones P, Wang H, Fleming JB, Maitra A, Pelicci PG, Chin L, DePinho RA, Lanfrancone L, Heffernan TP, Draetta GF. In Vivo Functional Platform Targeting Patient-Derived Xenografts Identifies WDR5-Myc Association as a Critical Determinant of Pancreatic Cancer. Cell Rep 16(1):133-47, 2016.
Li N, Dhar SS, Chen TY, Kan PY, Wei Y, Kim JH, Chan CH, Lin HK, Hung MC, Lee MG. JARID1D Is a Suppressor and Prognostic Marker of Prostate Cancer Invasion and Metastasis. Cancer Res 15;76(4):831-43, 2016
Snee MJ, Wilson WC, Zhu Y, Chen SY, Wilson BA, Kseib C, O'Neal J, Mahajan N, Tomasson MH, Arur S, Skeath JB. Collaborative Control of Cell Cycle Progression by the RNA Exonuclease Dis3 and Ras Is Conserved Across Species. Genetics 203(2):749-62, 2016
Liu X, Xiao ZD, Han L, Zhang J, Lee SW, Wang W, Lee H, Zhuang L, Chen J, Lin HK, Wang J, Liang H, Gan B. LncRNA NBR2 engages a metabolic checkpoint by regulating AMPK under energy stress. Nat Cell Biol 18(4):431-42, 2016.
Wu Q, Paul A, Su D, Mehmood S, Foo TK, Ochi T, Bunting EL, Xia B, Robinson CV, Wang B, Blundell TL. Structure of BRCA1-BRCT/Abraxas Complex Reveals Phosphorylation-Dependent BRCT Dimerization at DNA Damage Sites. Mol Cell 61(3):434-48, 2016.
2015
Hirsch CL, Coban Akdemir Z, Wang L, Jayakumaran G, Trcka D, Weiss A, Hernandez JJ, Pan Q, Han H, Xu X, Xia Z, Salinger AP, Wilson M, Vizeacoumar F, Datti A, Li W, Cooney AJ, Barton MC, Blencowe BJ, Wrana JL, Dent SY. Myc and SAGA rewire an alternative splicing network during early somatic cell reprogramming. Genes Dev.29(8):803-16, 2015.
Yang Y, Hadjikyriacou A, Xia Z, Gayatri S, Kim D, Zurita-Lopez C, Kelly R, Guo A, Li W, Clarke SG, Bedford MT. PRMT9 is a type II methyltransferase that methylates the splicing factor SAP145. Nat Commun. 6:6428, 2015.
Kapoor P, Bao Y, Xiao J, Luo J, Shen J, Persinger J, Peng G, Ranish J, Bartholomew B, Shen X. 2015 Regulation of Mec1 kinase activity by the SWI/SNF chromatin remodeling complex. Genes Dev. 29(6):591-602, 2015.
Zhan Y, Kost-Alimova M, Shi X, Leo E, Bardenhagen JP, Shepard HE, Appikonda S, Vangamudi B, Zhao S, Tieu TN, Jiang S, Heffernan TP, Marszalek JR, Toniatti C, Draetta G, Tyler J, Barton M, Jones P, Palmer WS, Geck Do MK, Andersen JN. Development of novel cellular histone-binding and chromatin-displacement assays for bromodomain drug discovery. Epigenetics Chromatin 8:37, 2015
2014
Wen H, Li Y, Xi Y, Jiang S, Stratton S, Peng D, Tanaka K, Ren Y, Xia Z, Wu J, Li B, Barton MC, Li W, Li H, Shi X ZMYND11 links histone H3.3K36me3 to transcription elongation and tumour suppression. Nature 508(7495):263-8, 2014.
Yang Y, McBride KM, Hensley S, Lu Y, Chedin F, Bedford MT Arginine methylation facilitates the recruitment of TOP3B to chromatin to prevent R loop accumulation. Mol Cell 53(3):484-97, 2014.
Li Y, Wen H, Xi Y, Tanaka K, Wang H, Peng D, Ren Y, Jin Q, Dent SYR., Li W, Li H, Shi X. AF9 YEATS Domain Links Histone Acetylation to DOT1L-Mediated H3K79 Methylation. Cell 159(3):558-71, 2014
2013
Johnson DG, Dent SY. Chromatin: receiver and quarterback for cellular signals. Cell 152(4):685-9, 2013
Yang Y, Bedford MT. Protein arginine methyltransferases and cancer. Nat Rev Cancer 13(1):37-50, 2013
Kapoor P, Chen M, Winkler DD, Luger K, Shen X. Evidence for monomeric actin function in INO80 chromatin remodeling. Nat Struct Mol Biol 20(4):426-32, 2013
James LI, Barsyte-Lovejoy D, Zhong N, Krichevsky L, Korboukh VK, Herold JM, MacNevin CJ, Norris JL et al. Discovery of a chemical probe for the L3MBTL3 methyllysine reader domain. Nat Chem Biol 9(3):184-91, 2013
Yuan J, Chen J. FIGNL1-containing protein complex is required for efficient homologous recombination repair. Proc Natl Acad Sci U S A 110(26):10640-5, 2013
Nishida N, Mimori K, Mori M, Calin GA. EGFR gets in the way of microRNA biogenesis. Cell Res 23(10):1157-8, 2013
Ling H, Spizzo R, Atlasi Y, Nicoloso M, Shimizu M, Redis RS, Nishida N, Gafà R et al. CCAT2, a novel noncoding RNA mapping to 8q24, underlies metastatic progression and chromosomal instability in colon cancer. Genome Res 23(9):1446-61, 2013.
Chen K, Xi Y, Pan X, Li Z, Kaestner K, Tyler J, Dent S, He X, Li W. DANPOS: dynamic analysis of nucleosome position and occupancy by sequencing. Genome Res 23(2):341-51, 2013
Chen K, Wilson MA, Hirsch C, Watson A, Liang S, Lu Y, Li W, Dent SY. Stabilization of the promoter nucleosomes in nucleosome-free regions by the yeast Cyc8-Tup1 corepressor. Genome Res 23(2):312-22, 2013
Garcia-Manero G, Jabbour E, Borthakur G, Faderl S, Estrov Z, Yang H, Maddipoti S, Godley LA et al. Randomized Open-Label Phase II Study of Decitabine in Patients With Low- or Intermediate-Risk Myelodysplastic Syndromes. J Clin Oncol 31(20):2548-53, 2013
Suen KM, Lin CC, George R, Melo FA, Biggs ER, Ahmed Z, Drake MN, Arur S et al. Interaction with Shc prevents aberrant Erk activation in the absence of extracellular stimuli. Nat Struct Mol Biol 20(5):620-7, 2013
Stratton SA, Barton MC. The hierarchy of a regenerative cell cycle: Cyclin E1 multi-tasks. Hepatology 59(2):370-1, 2013
Kurinna S, Stratton SA, Coban Z, Schumacher JM, Grompe M, Duncan AW, Barton MC. p53 regulates a mitotic transcription program and determines ploidy in normal mouse liver. Hepatology 57(5):2004-13, 2013