Selected Publications
Faculty in the Department of Epigenetics and Molecular Carcinogenesis have authored more than 350 peer-reviewed publications over the past five years. A small selection of our publications is highlighted below.
2020
Abba MC, Canzoneri R, Gurruchaga A, Lee J, Tatineni P, Kil H, Lacunza E, Aldaz CM. LINC00885 a Novel Oncogenic Long Non-Coding RNA Associated with Early Stage Breast Cancer Progression. Int J Mol Sci. 2020 Oct 8;21(19):7407.
Benavides F, Rülicke T, Prins JB, Bussell J, Scavizzi F, Cinelli P, Herault Y, Wedekind D. Genetic quality assurance and genetic monitoring of laboratory mice and rats: FELASA Working Group Report. Lab Anim. 2020 Apr;54(2):135-148.
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.
Hardikar S, Ying Z, Zeng Y, Zhao H, Liu B, Veland N, McBride K, Cheng X, Chen T. The ZBTB24-CDCA7 axis regulates HELLS enrichment at centromeric satellite repeats to facilitate DNA methylation. Protein Cell. 2020 Mar;11(3):214-218.
Helmink BA, Reddy SM, Gao J, Zhang S, Basar R, Thakur R, Yizhak K, Sade-Feldman M, Blando J, Han G, Gopalakrishnan V, Xi Y, Zhao H, Amaria RN, Tawbi HA, Cogdill AP, Liu W, LeBleu VS, Kugeratski FG, Patel S, Davies MA, Hwu P, Lee JE, Gershenwald JE, Lucci A, Arora R, Woodman S, Keung EZ, Gaudreau PO, Reuben A, Spencer CN, Burton EM, Haydu LE, Lazar AJ, Zapassodi R, Hudgens CW, Ledesma DA, Ong S, Bailey M, Warren S, Rao D, Krijgsman O, Rozeman EA, Peeper D, Blank CU, Schumacher TN, Butterfield LH, Zelazowska MA, McBride KM, Kalluri R, Allison J, Petitprez F, Fridman WH, Sautès-Fridman C, Hacohen N, Rezvani K, Sharma P, Tetzlaff MT, Wang L, Wargo JA. B cells and tertiary lymphoid structures promote immunotherapy response. Nature. 2020 Jan;577(7791):549-555.
Hwang T, Reh S, Dunbayev Y, Zhong Y, Takata Y, Shen J, McBride KM, Murnane JP, Bhak J, Lee S, Wood RD, Takata KI. Defining the mutation signatures of DNA polymerase θ in cancer genomes. NAR Cancer. 2020 Sep;2(3):zcaa017.
Jain K, Fraser CS, Marunde MR, Parker MM, Sagum C, Burg JM, Hall N, Popova IK, Rodriguez KL, Vaidya A, Krajewski K, Keogh MC, Bedford MT*, Strahl BD.* Characterization of the plant homeodomain (PHD) reader family for their histone tail interactions. Epigenetics Chromatin. 2020 Jan 24;13(1):3 (*Co-corresponding authors)
Jung YS, Stratton SA, Lee SH, Kim MJ, Jun S, Zhang J, Zheng B, Cervantes CL, Cha JH, Barton MC, Park JI. TMEM9-v-ATPase Activates Wnt/β-Catenin Signaling via APC Lysosomal Degradation for Liver Regeneration and Tumorigenesis. Hepatology. 2020 May 7. doi: 10.1002/hep.31305.
Koutelou E, Farria AT, Dent SYR. Complex functions of Gcn5 and Pcaf in development and disease. Biochim Biophys Acta Gene Regul Mech. 2020 Jul 28:194609.
Kumar A, Zhong Y, Albrecht A, Sang PB, Maples A, Liu Z, Vinayachandran V, Reja R, Lee CF, Kumar A, Chen J, Xiao J, Park B, Shen J, Liu B, Person MD, Trybus KM, Zhang KYJ, Pugh BF, Kamm KE, Milewicz DM, Shen X*, Kapoor P*. Actin R256 Mono-methylation Is a Conserved Post-translational Modification Involved in Transcription. Cell Rep. 2020 Sep 29;32(13):108172. (*co-corresponding authors)
Kumar J, Kaur G, Ren R, Lu Y, Lin K, Li J, Huang Y, Patel A, Barton MC, Macfarlan T, Zhang X, Cheng X. KRAB domain of ZFP568 disrupts TRIM28-mediated abnormal interactions in cancer cells. NAR Cancer. 2020 Jun;2(2):zcaa007.
McGrail DJ, Garnett J, Yin J, Dai H, Shih DJH, Lam TNA, Li Y, Sun C, Li Y, Schmandt R, Wu JY, Hu L, Liang Y, Peng G, Jonasch E, Menter D, Yates MS, Kopetz S, Lu KH, Broaddus R, Mills GB, Sahni N,* Lin SY.* Proteome Instability Is a Therapeutic Vulnerability in Mismatch Repair-Deficient Cancer. Cancer Cell. 2020 Mar 16;37(3):371-386.e12. (*Co-corresponding authors)
Shen Y, Gao G, Yu X, Kim H, Wang L, Xie L, Schwarz M, Chen X, Guccione E, Liu J*, Bedford MT*, Jin J*. Discovery of First-in-Class Protein Arginine Methyltransferase 5 (PRMT5) Degraders. J Med Chem. 2020 Sep 10;63(17):9977-9989. (*Co-corresponding authors)
Turner OC, Aeffner F, Bangari DS, High W, Knight B, Forest T, Cossic B, Himmel LE, Rudmann DG, Bawa B, Muthuswamy A, Aina OH, Edmondson EF, Saravanan C, Brown DL, Sing T, Sebastian MM. Society of Toxicologic Pathology Digital Pathology and Image Analysis Special Interest Group Article*: Opinion on the Application of Artificial Intelligence and Machine Learning to Digital Toxicologic Pathology. Toxicol Pathol. 2020 Feb;48(2):277-294.
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 Jun 24. doi: 10.1038/s41375-020-0908-8.
Woodcock CB, Horton JR, Zhou J, Bedford MT, Blumenthal RM, Zhang X, Cheng X. Biochemical and structural basis for YTH domain of human YTHDC1 binding to methylated adenine in DNA. Nucleic Acids Res. 2020 Oct 9;48(18):10329-10341.
Zelazowska MA, Dong Q, Plummer JB, Zhong Y, Liu B, Krug LT, McBride KM. Gammaherpesvirus-infected germinal center cells express a distinct immunoglobulin repertoire. Life Sci Alliance. 2020 Feb 6;3(3):e201900526.
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 Oct 1;34(21-22):1546-58. (*co-first authors, #co-corresponding authors)
2019
Bao J, Di Lorenzo A, Lin K, Lu Y, Zhong Y, Sebastian MM, Muller WJ, Yang Y, Bedford MT. (2019) Mouse models of overexpression reveal distinct oncogenic roles for different type I protein arginine methyltransferases. Cancer Res. 79(1):21-32.
Gao G, Zhang L, Villarreal OD, He W, Su D, Bedford E, Moh P, Shen J, Shi X, Bedford MT, Xu H. (2019) PRMT1 loss sensitizes cells to PRMT5 inhibition. Nucleic Acids Res. 47(10):5038-5048.
He W, Zhang L, Villarreal OD, Fu R, Bedford E, Dou J, Patel AY, Bedford MT, Shi X, Chen T, Bartholomew B, Xu H. (2019) De novo identification of essential protein domains from CRISPR-Cas9 tiling-sgRNA knockout screens. Nat Commun. 10(1):4541.
Hussain T, Kil H, Hattiangady B, Lee J, Kodali M, Shuai B, Attaluri S, Takata Y, Shen J, Abba MC, Shetty AK, Aldaz CM. (2019) Wwox deletion leads to reduced GABA-ergic inhibitory interneuron numbers and activation of microglia and astrocytes in mouse hippocampus. Neurobiol Dis. 121:163-176.
Koutelou E, Wang L, Schibler A, Chao HP, Kuang X, Lin K, Lu Y, Shen J, Jeter CR, Salinger A, Wilson M, Chen YC, Atanassov BS, Tang DG, Dent SY. (2019) Usp22 controls multiple signaling pathways that are essential for vasculature formation in the mouse placenta. Development. Feb 22;146(4). pii: dev174037. ]
Manickavinayaham S, Vélez-Cruz R, Biswas AK, Bedford E, Klein BJ, Kutateladze TG, Liu B, Bedford MT, Johnson DG. (2019) E2F1 acetylation directs p300/CBP-mediated histone acetylation at DNA double-strand breaks to facilitate repair. Nat Commun. 10(1):4951.
McBride KM, Kil H, Mu Y, Plummer JB, Lee J, Zelazowski MJ, Sebastian M, Abba MC, Aldaz CM. (2019) Wwox Deletion in Mouse B Cells Leads to Genomic Instability, Neoplastic Transformation, and Monoclonal Gammopathies. Front Oncol. 9:517.
Patel L, Kang R, Rosenberg SC, Qiu Y, Raviram R, Chee S, Hu R, Ren B, Cole F,* Corbett KD*. (2019) Dynamic reorganization of the genome shapes the recombination landscape in meiotic prophase. Nat Struct Mol Biol. 26(3):164-174. (*co-corresponding authors)
Ren R, Hardikar S, Horton JR, Lu Y, Zeng Y, Singh AK, Lin K, Coletta LD, Shen J, Lin Kong CS, Hashimoto H, 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.
Wible DJ, Chao HP, Tang DG, Bratton SB. (2019) ATG5 cancer mutations and alternative mRNA splicing reveal a conjugation switch that regulates ATG12-ATG5-ATG16L1 complex assembly and autophagy. Cell Discov. 5:42.
Veland N, Lu Y, Hardikar S, Gaddis S, Zeng Y, Liu B, Estecio MR, 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.
2018
Appikonda S, Thakkar KN, Shah PK, Dent SYR, Andersen JN, Barton MC. (2018) Cross-talk between chromatin acetylation and SUMOylation of tripartite motif-containing protein 24 (TRIM24) impacts cell adhesion. J Biol Chem. 293(19):7476-7485.
Bao J, Perez CJ, 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. (2018) Deficient LRRC8A-dependent volume-regulated anion channel activity is associated with male infertility in mice. JCI Insight. pii: 99767. doi: 10.1172/jci.insight.99767.
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. (2018) Nucleic Acids Res. 46(9):4327-4343.
Brahma S, Ngubo M, Paul S, Udugama M, Bartholomew B. (2018) The Arp8 and Arp4 module acts as a DNA sensor controlling INO80 chromatin remodeling. Nat Commun. 90(1):3309
Cheng D, Vemulapalli V, Lu Y, Shen J, Aoyagi S, Fry CJ, Yang Y, Foulds CE, Stossi F, Treviño LS, Mancini MA, O’Malley BW, Walker CL, Boyer TG, Bedford MT. (2018) CARM1 methylates MED12 to regulate its RNA binding ability. Life Sci Alliance. 1(5):e201800117.
Das P, Veazey KJ, Van HT, Kaushik S, Lin K, Lu Y, Ishii M, Kikuta J, Ge K, Nussenzweig A, Santos MA. (2018) Histone methylation regulator PTIP is required to maintain normal and leukemic bone marrow niches. Proc Natl Acad Sci U S A. 2018 Oct 23;115(43):E10137-E10146. pii: 201806019.
Franco HL, Nagari A, Malladi V, Li W, Xi Y, Richardson D, Allton KL, Tanaka K, Li J, Murakami S, Keyomarsi K, Bedford MT, Shi X, Li W, Barton MC, Dent SYR, Kraus WL. (2018) Enhancer transcription reveals subtype-specific gene expression programs controlling breast cancer pathogenesis. Genome Res. 28(2):159-170.
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(33):12770-12780.
Jain AK, Barton MC. (2018) p53: emerging roles in stem cells, development and beyond. Development. 145(8)
Kaushik S, Liu F, Veazey KJ, Gao G, Das P, Neves LF, Lin K, Zhong Y, Lu Y, Giuliani V, Bedford MT, Nimer SD, Santos MA. (2018) Genetic deletion or small-molecule inhibition of the arginine methyltransferase PRMT5 exhibit anti-tumoral activity in mouse models of MLL-rearranged AML. Leukemia. 32(2):499-509.
Kang R, Zelazowski MJ, Cole F. (2018) Missing the Mark: PRDM9-dependent methylation is required for meiotic DSB targeting. Mol Cell. 69(5):725-727.
Singarapu N, Ma K, Reeh KAG, Shen J, Lancaster JN, Yi S, Xie H, Orkin SH, Manley NR, Ehrlich LIR, Jiang N, Richie ER. (2018) Polycomb repressive complex 2 is essential for development and maintenance of a functional TEC compartment. Sci Rep. 8(1):14335.
Wang L, Koutelou E, Hirsch C, McCarthy R, Schibler A, Lin K, Lu Y, Jeter C, Shen J, Barton MC, Dent SYR. (2018) GCN5 regulates FGF signaling and activates selective MYC target tenes during early embryoid body differentiation. Stem Cell Reports. 10(1):287-299
Wible DJ, Bratton SB. (2018) Reciprocity in ROS and autophagic signaling. Curr Opin Toxicol. 7:28-36.
2017
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. (2017) Developing Spindlin1 small-molecule inhibitors by using protein microarrays. Nat Chem Biol. 13(7):750-756.
Brahma S, Udugama MI, Kim J, Hada A, Bhardwaj SK, Hailu SG, Lee TH, Bartholomew B. (2017) INO80 exchanges H2A.Z for H2A by translocating on DNA proximal to histone dimers. Nat Commun. 8:15616.
Carr SM, Munro S, Sagum CA, Fedorov O, Bedford MT, La Thangue NB. (2017) Tudor-domain protein PHF20L1 reads lysine methylated retinoblastoma tumour suppressor protein. Cell Death Differ. 24(12):2139-2149.
Dan J, Rousseau P, Hardikar S, Veland N, Wong J, Autexier C, Chen T. (2017) Zscan4 inhibits maintenance DNA methylation to facilitate telomere Eeongation in mouse embryonic stem cells. Cell Rep. 20(8):1936-1949.
Espejo AB, Gao G, Black K, Gayatri S, Veland N, Kim J, Chen T, Sudol M, Walker C, Bedford MT. (2017) PRMT5 C-terminal phosphorylation modulates a 14-3-3/PDZ interaction switch. J Biol Chem. 292(6):2255-2265.
Li J, Xi Y, Li W, McCarthy RL, Stratton SA, Zou W, Li W, Dent SY, Jain AK, Barton MC. (2017) TRIM28 interacts with EZH2 and SWI/SNF to activate genes that promote mammosphere formation. Oncogene. 36(21):2991-3001.
Manandhar M, Lowery MG, Boulware KS, Lin KH, Lu Y, Wood RD. (2017) Transcriptional consequences of XPA disruption in human cell lines. DNA Repair (Amst). 57:76-90.
Mi W, Guan H, Lyu J, Zhao D, Xi Y, Jiang S, Andrews FH, Wang X, Gagea M, Wen H, Tora L, Dent SYR, Kutateladze TG, Li W, Li H, Shi X. (2017) YEATS2 links histone acetylation to tumorigenesis of non-small cell lung cancer. Nat Commun. 8(1):1088
Mu Y, Zelazowska MA, McBride KM. (2017) Phosphorylation promotes activation-induced cytidine deaminase activity at the Myc oncogene. J Exp Med. 214(12):3543-3552.
Ortiz GJ, Li Y, Post SM, Pant V, Xiong S, Larsson CA, El-Naggar AK, Johnson DG, Lozano G. (2017) Contrasting effects of an Mdm2 functional polymorphism on tumor phenotypes. Oncogene. Sep 18. doi: 10.1038/onc.2017.344. [Epub ahead of print]
Takata KI, Reh S, Yousefzadeh MJ, Zelazowski MJ, Bhetawal S, Trono D, Lowery MG, Sandoval M, Takata Y, Lu Y, Lin K, Shen J, Kusewitt DF, McBride KM, Cole F, Wood RD. (2017) Analysis of DNA polymerase ν function in meiotic recombination, immunoglobulin class-switching, and DNA damage tolerance. PLoS Genet. 13(6):e1006818.
Schrock MS, Batar B, Lee J, Druck T, Ferguson B, Cho JH, Akakpo K, Hagrass H, Heerema NA, Xia F, Parvin JD, Aldaz CM, Huebner K. (2017) Wwox-Brca1 interaction: role in DNA repair pathway choice. Oncogene. 2017 Apr 20;36(16):2215-2227.
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(12):3390-3397
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, Allis CD, Armstrong SA, Shi X. (2017) ENL links histone acetylation to oncogeneic gene expression in acute myeloid leukaemia. Nature. 543(7644):265-269 (*equal contribution)
Zelazowski MJ, Sandoval M, Paniker L, Hamilton HM, Han J, Gribbell MA, Kang R, Cole F. (2017) Age-dependent alterations in meiotic recombination cause chromosome segregation errors in spermatocytes. Cell. 171(3):601-614.e13.
Zhu F, Willette-Brown J, Song NY, Lomada D, Song Y, Xue L, Gray Z, Zhao Z, Davis SR, Sun Z, Zhang P, Wu X, Zhan Q, Richie ER, Hu Y. (2017) Autoreactive T cells and chronic fungal infection drive esophageal carcinogenesis. Cell Host Microbe. 21(4):478-493.
2016
Atanassov BS, Mohan RD, Lan X, Kuang X, Lu Y, Lin K, McIvor E, Li W, Zhang Y, Florens L, Byrum SD, Mackintosh SG, Calhoun-Davis T, Koutelou E, Wang L, Tang DG, Tackett AJ, Washburn MP, Workman JL, Dent SY. (2016) ATXN7L3 and ENY2 coordinate activity of multiple H2B deubiquitinases important for cellular proliferation and tumor growth. Mol Cell. 62(4):558-71.
Bain VE, Gordon J, O’Neil JD, Ramos I, Richie ER, Manley NR. (2016) Tissue-specific roles for sonic hedgehog signaling in establishing thymus and parathyroid organ fate. Development. 143(21):4027-4037.
Jain AK, Xi Y, McCarthy R, Allton K, Akdemir KC, Patel LR, Aronow B, Lin C, Li W, Yang L, Barton MC. (2016) LncPRESS1 is a p53-regulated LncRNA that safeguards pluripotency by disrupting SIRT6-mediated de-acetylation of histone H3K56. Mol Cell. 64(5):967-981
Lange SS, Tomida J, Boulware KS, Bhetawal S, Wood RD. (2016) The polymerase activity of mammalian DNA Pol ζ Is specifically required for cell and embryonic viability. PLoS Genet. 12(1):e1005759.
Li Y, Sabari BR, Panchenko T, Wen H, Zhao D, Guan H, Wan L, Huang H, Tang Z, Zhao Y, Roeder RG, Shi X, Allis CD, Li H. (2016) Molecular coupling of histone crotonylation and active transcription by AF9 YEATS domain. Mol Cell. 62(2):181-93.
Stuckey JI, Dickson BM, Cheng N, Liu Y, Norris JL, Cholensky SH, Tempel W, Qin S, Huber KG, Sagum C, Black K, Li F, Huang XP, Roth BL, Baughman BM, Senisterra G, Pattenden SG, Vedadi M, Brown PJ, Bedford MT, Min J, Arrowsmith CH, James LI, Frye SV. (2016) A cellular chemical probe targeting the chromodomains of Polycomb repressive complex 1. Nat Chem Biol. 12(3):180-7.
Vélez-Cruz R, Manickavinayaham S, Biswas AK, Clary RW, Premkumar T, Cole F, Johnson DG. (2016) RB localizes to DNA double-strand breaks and promotes DNA end resection and homologous recombination through the recruitment of BRG1. Genes Dev. 2016 Nov 15;30(22):2500-2512.
Wu CC, Lee S, Malladi S, Chen MD, Mastrandrea NJ, Zhang Z, Bratton SB. (2016) The Apaf-1 apoptosome induces formation of caspase-9 homo- and heterodimers with distinct activities. Nat Commun. 2016 Nov 24;7:13565
Zhang D, Park D, Zhong Y, Lu Y, Rycaj K, Gong S, Chen X, Liu X, Chao HP, Whitney P, Calhoun-Davis T, Takata Y, Shen J, Iyer VR, Tang DG. (2016) Stem cell and neurogenic gene-expression profiles link prostate basal cells to aggressive prostate cancer. Nat Commun. 7:10798.
Zhang X, Peng D, Xi Y, Yuan C, Sagum CA, Klein BJ, Tanaka K, Wen H, Kutateladze TG, Li W, Bedford MT, Shi X. (2016) G9a-mediated methylation of ERα links the PHF20/MOF histone acetyltransferase complex to hormonal gene expression. Nat Commun. 7:10810.
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. (2015) Myc and SAGA rewire an alternative splicing network during early somatic cell reprogramming. Genes Dev.29(8):803-16.
Hu SB, Xiang JF, Li X, Xu Y, Xue W, Huang M, Wong CC, Sagum CA, Bedford MT, Yang L, Cheng D, Chen LL. (2015) Protein arginine methyltransferase CARM1 attenuates the paraspeckle-mediated nuclear retention of mRNAs containing inverted repeat Alus. Genes Dev. 29(6):630-45.
Kapoor P, Bao Y, Xiao J, Espejo A, Yang L, Bedford MT, Peng G, Shen X. (2015) Phosphorylation-Dependent Enhancement of Rad53 Kinase Activity through the INO80 Chromatin Remodeling Complex. Mol Cell. 58(5):863-9.
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.
Li M, Hada A, Sen P, Olufemi L, Hall MA, Smith BY, Forth S, McKnight JN, Patel A, Bowman GD, Bartholomew B, Wang MD. (2015) Dynamic regulation of transcription factors by nucleosome remodeling. Elife. 4. doi: 10.7554/eLife.06249.
Pathiraja TN, Thakkar KN, Jiang S, Stratton S, Liu Z, Gagea M, Shi X, Shah PK, Phan L, Lee MH, Andersen J, Stampfer M, Barton MC. (2015) TRIM24 links glucose metabolism with transformation of human mammary epithelial cells. Oncogene. 34(22):2836-45.
Yang Y, Hadjikyriacou A, Xia Z, Gayatri S, Kim D, Zurita-Lopez C, Kelly R, Guo A, Li W, Clarke SG, Bedford MT. (2015) PRMT9 is a type II methyltransferase that methylates the splicing factor SAP145. Nat Commun. 6:6428.
Selected Publications 2009-2014
2014
Biswas AK, Mitchell DL, Johnson DG (2014) E2F1 responds to ultraviolet radiation by directly stimulating DNA repair and suppressing carcinogenesis. Cancer Res. 74(12):3369-77.
Cole F, Baudat F, Grey C, Keeney S, de Massy B, Jasin M (2014) Mouse tetrad analysis provides insights into recombination mechanisms and hotspot evolutionary dynamics. Nat Genet. 46(10):1072-80.
Jin M, Zhang T, Liu C, Badeaux MA, Liu B, Liu R, Jeter C, Chen X, Vlassov AV, Tang DG (2014) miRNA-128 suppresses prostate cancer by inhibiting BMI-1 to inhibit tumor-initiating cells. Cancer Res. 74(15):4183-95.
Li Y, Wen H, Xi Y, Tanaka K, Wang H, Peng D, Ren Y, Jin Q, Dent SYR., Li W, Li H, Shi X (2014) AF9 YEATS Domain Links Histone Acetylation to DOT1L-Mediated H3K79 Methylation. Cell.159(3):558-71.
Reeh KA, Cardenas KT, Bain VE, Liu Z, Laurent M, Manley NR, Richie, ER (2014) Ectopic TBX1 suppresses thymic epithelial cell differentiation and proliferation during thymus organogenesis. Development. 141(15):2950-8.
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 (2014) ZMYND11 links histone H3.3K36me3 to transcription elongation and tumour suppression. Nature. 508(7495):263-8.
Yang Y, McBride KM, Hensley S, Lu Y, Chedin F, Bedford MT (2014) Arginine methylation facilitates the recruitment of TOP3B to chromatin to prevent R loop accumulation. Mol Cell. 53(3):484-97.
Yousefzadeh MJ, Wyatt DW, Takata K, Mu Y, Hensley SC, Tomida J, Bylund, GO, Doublie S, Johansson E, Ramsden DA, McBride KM and Wood, RD (2014) Mechanism of Suppression of Chromosomal Instability by DNA Polymerase POLQ. PLoS Genet. 10(10):e1004654.
2013
Badeaux MA, Jeter CR, Gong S, Liu B, Suraneni MV, Rundhaug J, Fischer SM, Yang T, Kusewitt D, Tang DG. (2013) In vivo functional studies of tumor-specific retrogene NanogP8 in transgenic animals. Cell Cycle. 12(15):2395-408.
Chen K, Wilson MA, Hirsch C, Watson A, Liang S, Lu Y, Li W, Dent SY (2013) Stabilization of the promoter nucleosomes in nucleosome-free regions by the yeast Cyc8-Tup1 corepressor. Genome Res. 23:312-22.
Johnson DG, Dent SY (2013) Chromatin: receiver and quarterback for cellular signals. Cell. 152(4):685-9.
Kapoor P, Chen M, Winkler DD, Luger K, Shen X (2013) Evidence for monomeric actin function in INO80 chromatin remodeling. Nat Struct Mol Biol. 20(4):426-32.
Kim SJ, Wong PK. (2013) ROS upregulation during the early phase of retroviral infection plays an important role in viral establishment in the host cell. J Gen Virol. 94(Pt 10):2309-17.
Kim SJ, Zhao H, Hardikar S, Singh AK, Goodell MA, Chen T. (2013) A DNMT3A mutation common in AML exhibits dominant-negative effects in murine ES cells. Blood. 2013 Dec 12;122(25):4086-9.
Lange SS, Bedford E, Reh S, Wittschieben JP, Carbajal S, Kusewitt DF, DiGiovanni J, Wood RD (2013) Dual role for mammalian DNA polymerase zeta in maintaining genome stability and proliferative responses. Proc Natl Acad Sci U S A. 110(8):E687-96.
Li J, Zhao Z, Carter C, Ehrlich LI, Bedford MT, Richie ER (2013) Coactivator-associated arginine methyltransferase 1 regulates fetal hematopoiesis and thymocyte development. J Immunol. 190(2):597-604.
Mikulec CD, Rundhaug JE, Simper MS, Lubet RA, Fischer SM. (2013) The chemopreventive efficacies of nonsteroidal anti-inflammatory drugs: the relationship of short-term biomarkers to long-term skin tumor outcome. Cancer Prev Res (Phila). 6(7):675-85.
Perez CJ, Dumas A, Vallières L, Guénet JL, Benavides F. (2013) Several classical mouse inbred strains, including DBA/2, NOD/Lt, FVB/N, and SJL/J, carry a putative loss-of-function allele of Gpr84. J Hered. 2013 Jul-Aug;104(4):565-71.
Takata K, Reh S, Tomida J, Person MD, Wood RD. (2013) Human DNA helicase HELQ participates in DNA interstrand crosslink tolerance with ATR and RAD51 paralogs. Nat Commun. 2013;4:2338.
Yeh TC, Bratton SB (2013) Caspase-dependent regulation of the ubiquitin-proteasome system through direct substrate targeting. Proc Natl Acad Sci U S A. 110(35):14284-9.
Zhao H, Chen T. (2013) Tet family of 5-methylcytosine dioxygenases in mammalian development. J Hum Genet. 58(7):421-7.
2012
Badeaux AI, Yang Y, Cardenas K, Vemulapalli V, Chen K, Kusewitt D, Richie E, Li W, Bedford MT (2012). Loss of the methyl lysine effector protein PHF20 impacts the expression of genes regulated by the lysine acetyltransferase MOF. J Biol Chem. 287(1):429-37.
Biswas AK, Johnson DG. (2012) Transcriptional and nontranscriptional functions of E2F1 in response to DNA damage. Cancer Res. 72(1):13-7.
Chen YC, Gatchel JR, Lewis RW, Mao CA, Grant PA, Zoghbi HY, Dent SY (2012) Gcn5 loss-of-function accelerates cerebellar and retinal degeneration in a SCA7 mouse model. Hum Mol Genet. 21(2):394-405.
Ferguson BW, Gao X, Kil H, Lee J, Benavides F, Abba MC, Aldaz CM (2012) Conditional Wwox deletion in mouse mammary gland by means of two Cre recombinase approaches. PLoS One. 7(5):e36618.
Lange SS, Wittschieben JP, Wood RD (2012) DNA polymerase zeta is required for proliferation of normal mammalian cells. Nucleic Acids Res. 40 (10):4473-82.
Lu M, Liu Z, Yu H, Wang LE, Li G, Sturgis EM, Johnson DG, Wei Q (2012) Combined effects of E2F1 and E2F2 polymorphisms on risk and early onset of squamous cell carcinoma of the head and neck. Mol Carcinog. 51 Suppl 1:E132-41.
Mitchell D, Paniker L, Godar D (2012) Nucleotide excision repair is reduced in oral epithelial tissues compared with skin. Photochem Photobiol. 88(4):1027-32.
Qin J, Liu X, Laffin B, Chen X, Choy G, Jeter CR, Calhoun-Davis T, Li H, Palapattu GS, Pang S, Lin K, Huang J, Ivanov I, Li W, Suraneni MV, Tang DG (2012) The PSA(-/lo) prostate cancer cell population harbors self-renewing long-term tumor-propagating cells that resist castration. Cell Stem Cell. 10(5):556-69.
Regunathan R, Woo J, Pierce MC, Polydorides AD, Raoufi M, Roayaie S, Schwartz M, Labow D, Shin D, Suzuki R, Bhutani MS, Coghlan LG, Richards-Kortum R, Anandasabapathy S, Kim MK. (2012) Feasibility and preliminary accuracy of high-resolution imaging of the liver and pancreas using FNA compatible microendoscopy (with video). Gastrointest Endosc. 76(2):293-300.
2011
Atanassov BS, Dent SY. (2011) USP22 regulates cell proliferation by deubiquitinating the transcriptional regulator FBP1. EMBO Rep. 12(9):924-30.
Atanassov BS, Koutelou E, Dent SY. The role of deubiquitinating enzymes in chromatin regulation. FEBS Lett. 2011;585(13):2016-23.
Benavides F, Perez C, Blando J, Contreras O, Shen J, Coussens LM, Fischer SM, Kusewitt DF, DiGiovanni J, Conti CJ. (2011) Protective role of cathepsin L in mouse skin carcinogenesis. Mol Carcinog. 51(4):352-61.
Butler JS, Zurita-Lopez CI, Clarke SG, Bedford MT, Dent SY. (2011) Protein-arginine methyltransferase 1 (PRMT1) methylates Ash2L, a shared component of mammalian histone H3K4 methyltransferase complexes. J Biol Chem. 286(14):12234-44.
Chen J, Zhu F, Weaks RL, Biswas AK, Guo R, Li Y, Johnson DG. (2011) E2F1 promotes the recruitment of DNA repair factors to sites of DNA double-strand breaks. Cell Cycle. 10(8):1287-94.
Fernandez AA, Garcia R, Paniker L, Trono D, Mitchell DL. (2011) An experimental population study of nucleotide excision repair as a risk factor for UVB-induced melanoma. Photochem Photobiol. 87(2):335-41.
Fischer SM, Hawk ET, Lubet RA. (2011) Coxibs and other nonsteroidal anti-inflammatory drugs in animal models of cancer chemoprevention. Cancer Prev Res (Phila). 4(11):1728-35.
Guo R, Chen J, Mitchell DL, Johnson DG (2011) GCN5 and E2F1 stimulate nucleotide excision repair by promoting H3K9 acetylation at sites of damage. Nucleic Acids Res. 39(4):1390-7.
Jeter CR, Liu B, Liu X, Chen X, Liu C, Calhoun-Davis T, Repass J, Zaehres H, Shen JJ, Tang DG. (2011) NANOG promotes cancer stem cell characteristics and prostate cancer resistance to androgen deprivation. Oncogene. 30(36):3833-45.
Kim J, Hwangbo J, Wong PK. (2011) p38 MAPK-Mediated Bmi-1 down-regulation and defective proliferation in ATM-deficient neural stem cells can be restored by Akt activation. PLoS One. 2011 Jan 28;6(1):e16615
Lashinger LM, Malone LM, Brown GW, Daniels EA, Goldberg JA, Otto G, Fischer SM, Hursting SD. (2011) Rapamycin partially mimics the anticancer effects of calorie restriction in a murine model of pancreatic cancer. Cancer Prev Res (Phila). 4(7):1041-51.
Latham JA, Chosed RJ, Wang S, Dent SY (2011) Chromatin signaling to kinetochores: transregulation of Dam1 methylation by histone H2B ubiquitination. Cell. 146(5):709-19.
Li H, Tang DG. (2011) Prostate cancer stem cells and their potential roles in metastasis. J Surg Oncol. 103(6):558-62.
Liu C, Kelnar K, Liu B, Chen X, Calhoun-Davis T, Li H, Patrawala L, Yan H, Jeter C, Honorio S, Wiggins JF, Bader AG, Fagin R, Brown D, Tang DG (2011) The microRNA miR-34a inhibits prostate cancer stem cells and metastasis by directly repressing CD44. Nat Med. 17(2):211-5.
Perez C, Parker-Thornburg J, Mikulec C, Kusewitt DF, Fischer SM, Digiovanni J, Conti CJ, Benavides F. (2011) SKHIN/Sprd, a new genetically defined inbred hairless mouse strain for UV-induced skin carcinogenesis studies. Exp Dermatol. 21(3):217-20.
Rahn JJ, Rowley B, Lowery MP, Coletta LD, Limanni T, Nairn RS, Adair GM. (2011) Effects of varying gene targeting parameters on processing of recombination intermediates by ERCC1-XPF. DNA Repair (Amst). 10(2):188-98.
Spannhoff A, Kim YK, Raynal NJ, Gharibyan V, Su MB, Zhou YY, Li J, Castellano S, Sbardella G, Issa JP, Bedford MT (2011) Histone deacetylase inhibitor activity in royal jelly might facilitate caste switching in bees. EMBO Reports. 12(3):238-43.
Surh I, Rundhaug J, Pavone A, Mikulec C, Abel E, Fischer SM. (2011) Upregulation of the EP1 receptor for prostaglandin E2 promotes skin tumor progression. Mol Carcinog. 50(6):458-68.
Yan L, Della Coletta L, Powell KL, Shen J, Thames H, Aldaz CM, MacLeod MC. (2011) Activation of the canonical Wnt/beta-catenin pathway in ATF3-induced mammary tumors. PLoS One. 6(1):e16515.
2010
Alexander A, Cai SL, Kim J, Nanez A, Sahin M, MacLean KH, Inoki K, Guan KL, Shen J, Person MD, Kusewitt D, Mills GB, Kastan MB, Walker CL (2010) ATM signals to TSC2 in the cytoplasm to regulate mTORC1 in response to ROS. Proc Natl Acad Sci U S A.107:4153-8.
Bredfeldt TG, Greathouse KL, Safe SH, Hung MC, Bedford MT, Walker CL. (2010) Xenoestrogen-induced regulation of EZH2 and histone methylation via estrogen receptor signaling to PI3K/AKT. Mol Endocrinol. 24(5):993-1006
Jain A, Bacolla A, Chakraborty P, Grosse F, Vasquez KM. (2010) Human DHX9 helicase unwinds triple-helical DNA structures. Biochemistry. 49(33):6992-9
Kha DT, Wang G, Natrajan N, Harrison L, Vasquez KM. Pathways for double-strand break repair in genetically unstable Z-DNA-forming sequences. J Mol Biol. 2010 398(4):471-80.
Kim D, Lee J, Cheng D, Li J, Carter C, Richie E, Bedford MT. (2010) Enzymatic activity is required for the in vivo functions of CARM1. J Biol Chem. 285(2):1147-52
Guo R, Chen J, Zhu F, Biswas AK, Berton TR, Mitchell DL, Johnson DG (2010) E2F1 localizes to sites of UV-induced DNA damage to enhance nucleotide excision repair. J Biol Chem. 285:19308-15.
Mitchell DL, Fernandez AA, Nairn RS, Garcia R, Paniker L, Trono D, Thames HD, Gimenez-Conti I (2010) Ultraviolet A does not induce melanomas in a Xiphophorus hybrid fish model. Proc Natl Acad Sci U S A. 107(20):9329-34.
Perez CJ, Jaubert J, Guénet JL, Barnhart KF, Ross-Inta CM, Quintanilla VC, Aubin I, Brandon JL, Otto NW, DiGiovanni J, Gimenez-Conti I, Giulivi C, Kusewitt DF, Conti CJ, Benavides F. (2010) Two hypomorphic alleles of mouse argininosuccinate synthetase as a new animal model of citrullinemia type I and other hyperammonemic syndromes. Am J Pathol. 177(4):1958-68.
Pusapati RV, Weaks RL, Rounbehler RJ, McArthur MJ, Johnson DG. (2010) E2F2 suppresses Myc-induced proliferation and tumorigenesis. Mol Carcinog. 49(2):152-6.
Rundhaug JE, Fischer SM. (2010) Molecular mechanisms of mouse skin tumor promotion. Cancers (Basel). 2(2):436-82
Short JD, Dere R, Houston KD, Cai SL, Kim J, Bergeron JM, Shen J, Liang J, Bedford MT, Mills GB, Walker CL. (2010) AMPK-mediated phosphorylation of murine p27 at T197 promotes binding of 14-3-3 proteins and increases p27 stability. Mol Carcinog. 49(5):429-39.
Yang Y, Lu Y, Espejo A, Wu J, Xu W, Liang S, Bedford MT (2010) TDRD3 is an effector molecule for arginine-methylated histone marks. Mol Cell. 40(6):1016-23.
Zhu F, Dollé ME, Berton TR, Kuiper RV, Capps C, Espejo A, McArthur MJ, Bedford MT, van Steeg H, de Vries A, Johnson DG (2010) Mouse models for the p53 R72P polymorphism mimic human phenotypes. Cancer Res. 70(14):5851-9.
2009
Abba MC, Hu Y, Levy CC, Gaddis S, Kittrell FS, Hill J, Bissonnette RP, Brown PH, Medina D, Aldaz CM. (2009) Identification of modulated genes by three classes of chemopreventive agents at preneoplastic stages in a p53-null mouse mammary tumor model. Cancer Prev Res (Phila). 2(2):175-84.
Blando J, Portis M, Benavides F, Alexander A, Mills G, Dave B, Conti CJ, Kim J, Walker CL. (2009) PTEN deficiency is fully penetrant for prostate adenocarcinoma in C57BL/6 mice via mTOR-dependent growth. Am J Pathol. 174(5):1869-79.
Bua DJ, Kuo AJ, Cheung P, Liu CL, Migliori V, Espejo A, Casadio F, Bassi C, Amati B, Bedford MT, Guccione E, Gozani O. Epigenome microarray platform for proteome-wide dissection of chromatin-signaling networks. (2009) PLoS One. 4(8):e6789.
Chen X, Schneider-Broussard R, Hollowell D, McArthur M, Jeter CR, Benavides F, DiGiovanni J, Tang DG. (2009) Abnormal differentiation, hyperplasia and embryonic/perinatal lethality in BK5-T/t transgenic mice. Differentiation. 77(3):324-34.
Falbo KB, Alabert C, Katou Y, Wu S, Han J, Wehr T, Xiao J, He X, Zhang Z, Shi Y, Shirahige K, Pasero P, and Shen X (2009) Involvement of a chromatin remodeling complex in damage tolerance during DNA replication. Nat Struct Mol Biol. 16(11):1167-72.
Griffith AV, Cardenas K, Carter C, Gordon J, Iberg A, Engleka K, Epstein JA, Manley NR, Richie ER (2009) Increased thymus- and decreased parathyroid-fated organ domains in Splotch mutant embryos. Dev Biol. 327(1):216-27.
Jeter CR, Badeaux M, Choy G, Chandra D, Patrawala L, Liu C, Calhoun-Davis T, Zaehres H, Daley GQ, Tang DG. (2009) Functional evidence that the self-renewal gene NANOG regulates human tumor development. Stem Cells. 2009 May;27(5):993-1005.
Kim DJ, Kataoka K, Sano S, Connolly K, Kiguchi K, DiGiovanni J. (2009) Targeted disruption of Bcl-xL in mouse keratinocytes inhibits both UVB- and chemically induced skin carcinogenesis. Mol Carcinog. 48(10):873-85.
Kuang X, Scofield VL, Yan M, Stoica G, Liu N, Wong PK. (2009) Attenuation of oxidative stress, inflammation and apoptosis by minocycline prevents retrovirus-induced neurodegeneration in mice. Brain Res. 1286:174-84.
Liu B, Zhu F, Xia X, Park E, Hu Y. (2009) A tale of terminal differentiation: IKKalpha, the master keratinocyte regulator. Cell Cycle. 8(4):527-31.
Liu Y, Nairn RS, Vasquez KM. (2009) Targeted gene conversion induced by triplex-directed psoralen interstrand crosslinks in mammalian cells. Nucleic Acids Res. 37(19):6378-88.
Ludes-Meyers JH, Kil H, Parker-Thornburg J, Kusewitt DF, Bedford MT, Aldaz CM. (2009) Generation and characterization of mice carrying a conditional allele of the Wwox tumor suppressor gene. PLoS One. 4(11):e7775.
Repass JF, Laurent MN, Carter C, Reizis B, Bedford MT, Cardenas K, Narang P, Coles M, Richie ER. (2009) IL7-hCD25 and IL7-Cre BAC transgenic mouse lines: new tools for analysis of IL-7 expressing cells. Genesis. 47(4):281-7.
Scofield VL, Yan M, Kuang X, Kim SJ, Crunk D, Wong PK. (2009) The drug monosodium luminol (GVT) preserves thymic epithelial cell cytoarchitecture and allows thymocyte survival in mice infected with the T cell-tropic, cytopathic retrovirus ts1. Immunol Lett. 122(2):159-69.
Shirley SH, Rundhaug JE, Tian J, Cullinan-Ammann N, Lambertz I, Conti CJ, Fuchs-Young R. (2009) Transcriptional regulation of estrogen receptor-alpha by p53 in human breast cancer cells. Cancer Res. 69(8):3405-14.
Zhao J, Jain A, Iyer RR, Modrich PL, Vasquez KM. (2009) Human HMGB1 directly facilitates interactions between nucleotide excision repair proteins on triplex-directed psoralen interstrand crosslinks. DNA Repair (Amst). ;8(7):865-72.