Publications

2023

Dan J, Du Z, Zhang J, Chen T. The interplay between H3K36 methylation and DNA methylation in cancer. Cancer Biol Med. 2023 Aug 18:j.issn.2095-3941.2023.0234. doi: 10.20892/j.issn.2095-3941.2023.0234. Online ahead of print.

Ying Z, Hardikar S, Plummer JB, Hamidi T, Liu B, Chen Y, Shen J, Mu Y, McBride KM, Chen T.  Characterization of a mouse model of ICF syndrome reveals enhanced CD19 activation in inducing hypogammaglobulinemia. bioRxiv. 2023 Mar 11:2023.03.09.531982. doi: 10.1101/2023.03.09.531982. Preprint. PMID: 36945532

2022

Dan J, Chen T. Genetic Studies on Mammalian DNA Methyltransferases. Adv Exp Med Biol. 2022;1389:111-136.

Srour N, Villarreal OD, Hardikar S, Yu Z, Preston S, Miller WH Jr, Szewczyk MM, Barsyte-Lovejoy D, Xu H, Chen T, Del Rincón SV, Richard S. PRMT7 ablation stimulates anti-tumor immunity and sensitizes melanoma to immune checkpoint blockade. Cell Rep. 2022 Mar 29;38(13):110582. 

2021

Cheng EC, Hsieh CL, Liu N, Wang J, Zhong M, Chen T, Li E, Lin H. The Essential Function of SETDB1 in Homologous Chromosome Pairing and Synapsis during Meiosis. Cell Rep. 2021 Jan 5;34(1):108575.

DiNardo CD, Beird HC, Estecio M, Hardikar S, Takahashi K, Bannon SA, Borthakur G, Jabbour E, Gumbs C, Khoury JD, Routbort M, Gong T, Kondo K, Kantarjian H, Garcia-Manero G, Chen T, Futreal PA. Germline DNMT3A mutation in familial acute myeloid leukaemia. Epigenetics. 2021 May;16(5):567-576.

2020

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.

Norvil AB, AlAbdi L, Liu B, Tu YH, Forstoffer NE, Michie AR, Chen T, Gowher H. The acute myeloid leukemia variant DNMT3A Arg882His is a DNMT3B-like enzyme. Nucleic Acids Res. 2020 Apr 17;48(7):3761-3775.

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. 

2019

Li Q, Liu B, Chao HP, Ji Y, Lu Y, Mehmood R, Jeter C, Chen T, Moore JR, Li W, Liu C, Rycaj K, Tracz A, Kirk J, Calhoun-Davis T, Xiong J, Deng Q, Huang J, Foster BA, Gokhale A, Chen X, Tang DG. LRIG1 is a pleiotropic androgen receptor-regulated feedback tumor suppressor in prostate cancer. Nat Commun. 2019 Dec 2;10(1):5494.

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. 2019 Oct 4;10(1):4541.

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. Structural basis of specific DNA binding by the transcription factor ZBTB24. Nucleic Acids Res. 2019 Sep 19;47(16):8388-8398.

Chao HP, Chen Y, Takata Y, Tomida MW, Lin K, Kirk JS, Simper MS, Mikulec CD, Rundhaug JE, Fischer SM, Chen T, Tang DG, Lu Y, Shen J. Systematic evaluation of RNA-Seq preparation protocol performance. BMC Genomics. 2019 Jul 11;20(1):571. 

Zeng Y, Chen T. Genes (Basel). DNA Methylation Reprogramming during Mammalian Development. 2019 Mar 29;10(4). pii: E257. doi: 10.3390/genes10040257. 

Takase R, Hino S, Nagaoka K, Anan K, Kohrogi K, Araki H, Hino Y, Sakamoto A, Nicholson TB, Chen T, Nakao M. Lysine-specific demethylase-2 is distinctively involved in brown and beige adipogenic differentiation. FASEB J. 2019 Apr;33(4):5300-5311.

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. DNMT3L facilitates DNA methylation partly by maintaining DNMT3A stability in mouse embryonic stem cells. Nucleic Acids Res. 2019 Jan 10;47(1):152-167. 

2018

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.  Deficient LRRC8A-dependent volume-regulated anion channel activity is associated with male infertility in mice. JCI Insight.  2018 Aug 23;3(16):e99767.

Gu T, Lin X, Cullen SM, Luo M, Jeong M, Estecio M, Shen J, Hardikar S, Sun D, Su J, Rux D, Guzman A, Lee M, Qi LS, Chen JJ, Kyba M, Huang Y, Chen T, Li W, Goodell MA. DNMT3A and TET1 cooperate to regulate promoter epigenetic landscapes in mouse embryonic stem cells. Genome Biol. 2018 Jul 12;19(1):88.

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. Identification of Rpl29 as a major substrate of the lysine methyltransferase Set7/9. J Biol Chem. 2018 Aug 17;293(33):12770-12780. 

2017

Veland N, Hardikar S, Zhong Y, Gayatri S, Dan J, Strahl BD, Rothbart SB, Bedford MT, Chen T. The Arginine Methyltransferase PRMT6 Regulates DNA Methylation and Contributes to Global DNA Hypomethylation in Cancer. Cell Rep. 2017 Dec 19;21(12):3390-3397. 

Dan J, Rousseau P, Hardikar S, Veland N, Wong J, Autexier C, Chen T.  Zscan4 inhibits maintenance DNA methylation to regulate telomere elongation in mouse embryonic stem cells. Cell Rep. 2017 Aug 22;20(8):1936-1949.

Quek K, Li J, Estecio M, Zhang J, Fujimoto J, Roarty E, Little L, Chow CW, Song X, Behrens C, Chen T, William WN, Swisher S, Heymach J, Wistuba I, Zhang J, Futreal A, Zhang J. DNA methylation intratumor heterogeneity in localized lung adenocarcinomas. Oncotarget. 2017 Mar 28; 8(13): 21994–22002.

Jeziorska DM, Murray RJS, De Gobbi M, Gaentzsch R, Garrick D, Ayyub H, Chen T, Li E, Telenius J, Lynch M, Graham B, Smith AJH, Lund JN, Hughes JR, Higgs DR, Tufarelli C. DNA methylation of intragenic CpG islands depends on their transcriptional activity during differentiation and disease. Proc Natl Acad Sci U S A. 2017 Sep 5;114(36):E7526-E7535.

Gahurova L, Tomizawa SI, Smallwood SA, Stewart-Morgan KR, Saadeh H, Kim J, Andrews SR, Chen T, Kelsey G.  Transcription and chromatin determinants of de novo DNA methylation timing in oocytes. Epigenetics Chromatin.  2017 May 12;10:25.

Espejo AB, Gao G, Black K, Gayatri S, Veland N, Kim J, Chen T, Sudol M, Walker C, Bedford MT.  PRMT5 C-terminal phosphorylation modulates a 14-3-3/PDZ interaction switch. J Biol Chem. 2017 Feb 10;292(6):2255-2265. 

2016

Dan J, Chen T.  Genetic Studies on Mammalian DNA Methyltransferases. Adv Exp Med Biol. 2016;945:123-150.

Chen Y, Kim J, Zhang R, Yang X, Zhang Y, Fang J, Chen Z, Teng L, Chen X, Ge H, Atadja P, Li E, Chen T, Qi W.  Histone Demethylase LSD1 Promotes Adipocyte Differentiation through Repressing Wnt Signaling. Cell Chem Biol.  2016 Oct 20;23(10):1228-1240.

Jia Y, Li P, Fang L, Zhu H, Xu L, Cheng H, Zhang J, Li F, Feng Y, Li Y, Li J, Wang R, Du JX, Li J, Chen T, Ji H, Han J, Yu W, Wu Q, Wong J.   Negative regulation of DNMT3A de novo DNA methylation by frequently overexpressed UHRF family proteins as a mechanism for widespread DNA hypomethylation in cancer. Cell Discov. 2016 Apr 12;2:16007.

Kim J, Zhao H, Dan J, Kim S, Hardikar S, Hollowell D, Lin K, Lu Y, Takata Y, Shen J, Chen T.  Maternal Setdb1 Is Required for Meiotic Progression and Preimplantation Development in Mouse. PLoS Genet. 2016 Apr 12;12(4):e1005970.

Blanc RS, Vogel G, Chen T, Crist C, Richard S.  PRMT7 Preserves Satellite Cell Regenerative Capacity. Cell Rep. 14, 2016 Feb 16;14(6):1528-1539.

2015

Kim J, Singh AK, Takata Y, Lin K, Shen J, Lu Y, Kerenyi MA, Orkin SH, Chen T.  LSD1 is essential for oocyte meiotic progression by regulating CDC25B expression in mice. Nat Commun. 2015 Dec 2;6:10116. 

Stewart KR, Veselovska L, Kim J, Huang J, Saadeh H, Tomizawa S, Smallwood SA, Chen T, Kelsey, G.  Dynamic changes in histone modifications precede de novo DNA methylation in oocytes. Genes Dev. 2015 Dec 1;29(23):2449-62.

Hamidi T, Singh AK, Chen T. Genetic alterations of DNA methylation machinery in human diseases. Epigenomics. 2015;7(2):247-65. 

Fei Q, Yang X, Jiang H, Wang Q, Yu Y, Yu Y, Yi W, Zhou S, Chen T, Lu C, Atadja P, Liu XS, Li E, Zhang Y, Shou J.  SETDB1 modulates PRC2 activity at developmental genes independently of H3K9 trimethylation in mouse ES cells. Genome Res. 2015 Sep;25(9):1325-35.

Martin FJ, Xu Y, Lohmann F, Ciccone DN, Nicholson TB, Loureiro JJ, Chen T, Huang Q. KMT1E-mediated chromatin modifications at the FcyRllb promoter regulate thymocyte development. Genes Immun. 2015 Mar;16(2):162-9. 

2014

Chen, T and Dent SY.  Chromatin modifiers and remodellers: regulators of cellular differentiation. Nat Rev Genet. 2014 Feb;15(2):93-106.

2013

Kim SJ, Zhao H, Hardikar S, Singh AK, Goodell MA, Chen T.  A DNMT3A mutation common in AML exhibits dominant-negative effects in murine ES cells. Blood. 2013 Dec 12;122(25):4086-9.

Zhao H, Chen T.  Tet family of 5-methylcytosine dioxygenases in mammalian development. J. Hum. Genet. 2013 Jul;58(7):421-7.

Nicholson TB, Singh AK, Su H, Hevi S, Wang J, Bajko J, Li M, Valdez R, Goetschkes M, Capodieci P, Loureiro J, Cheng X, Li E, Kinzel B, Labow M, Chen T.  A hypomorphic Lsd1 allele results in heart development defects in mice. PLoS One. 2013 Apr 24;8(4):e60913.

2012

Saferali A, Moussette S, Chan D, Trasler J, Chen T, Rozen R, and Naumova AK.  DNA methyltransferase 1 (Dnmt1) mutation affects Snrpn imprinting in the mouse male germ line. Genome.  2012 Sep;55(9):673-82.

Stadtfeld M, Apostolou E, Ferrari F, Choi J, Walsh RM, Chen T, Ooi S, Kim SY, Bestor TH, Shioda T, Park PJ, and Hochedlinger K.  Ascorbic acid prevents loss of Dlk1-Dio3 imprinting and facilitates generation of all-iPS cell mice from terminally differentiated B cells. Nat Genet. 2012 Mar 4;44(4):398-405, S1-2.

2011

Chen T.  Mechanistic and functional links between histone methylation and DNA methylation. Prog Mol Biol Transl Sci. 2011;101:335-48.

Xu Y, Wu F, Tan L, Kong L, Xiong L, Deng J, Barbera AJ, Zheng L, Zhang H, Huang S, Min J, Nicholson T, Chen T, Xu G, Shi Y, Zhang K, Shi YG.  Genome-wide regulation of 5hmC, 5mC, and gene expression by Tet1 hydroxylase in mouse embryonic stem cells. 2011 May 20;42(4):451-64. 

Nguyen AT, Neppl RL, Kallin EM, Chen T, Wang D-Z, Zhang Y.  DOT1L regulates dystrophin expression and is critical for cardiac function. Genes Dev. 2011 Feb 1;25(3):263-74.

He X.-J, Chen T, and Zhu J-K.  Regulation and function of DNA methylation in plants and animals. Cell Res. 2011 Mar;21(3):442-65.

Cho HS, Suzuki T, Dohmae N, Hayami S, Unoki M, Chen T, Kurash J, Field HI, Ponder BAJ, Nakamura Y, Hamamoto R.  Demethylation of MYPT1 by LSD1 promotes cell cycle progression in cancer cells. Cancer Res. 2011 Feb 1;71(3):655-60.

2010

Singh P, Han L, Rivas GE, Lee D-H, Nicholson TB, Larson GP, Chen T, Szabo PE.  Allele-specific H3K79 di- versus tri-methylation distinguishes opposite parental alleles at imprinted regions. Mol Cell Biol. 2010 Jun;30(11):2693-707.

Lohmann F, Loureiro J, Su H, Fang Q, Lei H, Lewis T, Yang Y, Labow M, Li E, Chen T, Kadam S.  KMT1E mediated H3K9 methylation is required for the maintenance of embryonic stem cells by repressing trophectoderm differentiation. Stem Cells. 2010 Feb;28(2):201-12.

2009

Ciccone DN, Su H, Hevi S, Gay F, Lei H, Bajko J, Xu G, Li E, Chen T.  KDM1B is a histone H3K4 demethylase required to establish maternal genomic imprints. Nature. 2009 Sep 17;461(7262):415-8.

Yu Z, Chen, T, Hebert J, Li E, Richard S.  A mouse PRMT1 null allele defines an essential role for arginine methylation in genome maintenance and cell proliferation. Mol Cell Biol. 2009 Jun;29(11):2982-96.

Wang J, Hevi S, Kurash JK, Lei H, Gay F, Bajko J, Su H, Sun W, Chang H, Xu G, Gaudet F, Li E, Chen T.  The lysine demethylase LSD1 (KDM1) is required for maintenance of global DNA methylation. Nat Genet. 2009 Jan;41(1):125-9. 

Ciccone DN, Chen T.  Histone lysine methylation in genomic imprinting. Epigenetics. 2009 May 16;4(4):216-20.

Nicholson TB, Chen T, Richard S.  The physiological and pathophysiological role of PRMT1-mediated protein arginine methylation. Pharmacol Res. 2009 Dec;60(6):466-74.

Nicholson TB, Chen T.  LSD1 demethylates histone and non-histone proteins. Epigenetics. 2009 Apr 1;4(3):129-32.

2008

Jones B, Su H, Bhat A, Lei H, Bajko J, Hevi S, Baltus GA, Kadam S, Zhai H, Valdez R, Gonzalo S, Zhang Y, Li E, Chen T.  The histone H3K79 methyltransferase Dot1L is essential for mammalian development and heterochromatin structure. PLoS Genet. 2008 Sep 12;4(9):e1000190.

Benetti R, Gonzalo S, Jaco I, Muñoz P, Gonzalez S, Schoeftner S, Murchison E, Andl T, Chen T, Klatt P, Li E, Serrano M, Millar S, Hannon G,  Blasco, MA.  A mammalian microRNA cluster controls DNA methylation and telomere recombination via Rbl2-dependent regulation of DNA methyltransferases. Nat Struct Mol Biol. 2008 Sep;15(9):998.

Hu YG, Hirasawa R, Hu JL, Hata K, Jin Y, Chen T, Li E, Rigolet M, Viegas-Pequigno, E, Sasaki H, Xu, GL.  Regulation of DNA methylation activity through DNMT3L promoter methylation by DNMT3 enzymes in embryonic development. Hum Mol Genet. 2008 Sep 1;17(17):2654-64.

Schmid RS, Tsujimoto N, Qu Q, Lei H, Li E, Chen T, Blaustein C.  A methyl-CpG-binding protein 2-enhanced green fluorescence protein reporter mouse model provides a new tool for studying the neuronal basis of Rett syndrome. Neuroreport. 2008 Mar 5;19(4):393-8.

2007

Li JY, Pu MT, Hirasawa R, Li BZ, Huang YN, Zeng R, Jing NH, Chen T, Li E, Sasaki H, Xu GL.  Synergistic function of DNA methyltransferases Dnmt3a and Dnmt3b in the methylation of Oct4 and Nanog. Mol Cell Biol. 2007 Dec;27(24):8748-59.

Chen T, Hevi S, Gay F, Tsujimoto N, He T, Zhang B, Ueda Y, Li E.  Complete inactivation of DNMT1 leads to mitotic catastrophe in human cancer cells. Nat Genet. 2007 Mar;39(3):391-6.

2006

Zhu H, Geiman TM, Xi S, Jiang Q, Schmidtmann A, Chen T, Li E, Muegge, K. Lsh is involved in de novo methylation of DNA. EMBO J. 2006 Jan 25;25(2):335-45. 

Chen T,  Li, E.  Establishment and maintenance of DNA methylation patterns in mammals. Curr Top Microbiol Immunol. 2006;301:179-201.

Gonzalo S, Fraga MF, Chen T, Li E, Esteller M, Blasco MA.  DNA methyltransferases control telomere length and telomere recombination in mammalian cells. Nat Cell Biol. 2006 Apr;8(4):416-24.

Ueda Y, Okano M, Williams C, Chen T, Georgopoulos K,  Li E.  Roles for Dnmt3b in mammalian development: a mouse model for the ICF syndrome. Development. 2006 Mar;133(6):1183-92.

2005

Chen T and Li E.  DNA methylation regulates genomic imprinting, X inactivation, and gene expression during mammalian development. In: Gene Expression and Regulation (ed. J. Ma), a Current Scientific Frontiers Book, Higher Education Press & Springer, pp 377-391.

Dodge JE, Okano, M, Dick F, Tsujimoto N, Chen T, Wang S, Ueda Y, Dyson N, Li E.  Inactivation of Dnmt3b in mouse embryonic fibroblasts results in hypomethylation, chromosomal instability, and spontaneous immortalization. J Biol Chem. 2005 May 6;280(18):17986-91.

Richard S, Torabi N, Franco GV, Tremblay GA, Chen T, Vogel G, Morel M, Cleroux P, Komarova S, Tremblay ML, Li W, Li A, Gao Y J, Henderson JE.  Ablation of the Sam68 RNA binding protein protects mice from age-related bone loss. PLoS Genet. 2005 Dec;1(6):e74. 

2004

Chen T, Tsujimoto N, Li E.  The PWWP domain of Dnmt3a and Dnmt3b is required for directing DNA methylation to the major satellite repeats at pericentromeric heterochromatin. Mol Cell Biol. 2004 Oct;24(20):9048-58.

Chen T and Li E.  Structure and function of eukaryotic DNA methyltransferases. Curr Top Dev Biol 2004;60:55-89.

Fang J, Chen T, Chadwick B, Li E, Zhang Y.  Ring1b-mediated H2A ubiquitination associates with inactive X chromosomes and is involved in initiation of X inactivation. J Biol Chem. 2004 Dec 17;279(51):52812-5. 

2003

Chen T, Ueda Y, Dodge JE, Wang Z, Li E.  Establishment and maintenance of genomic methylation patterns in mouse embryonic stem cells by Dnmt3a and Dnmt3b. Mol Cell Biol. 2003 Aug;23(16):5594-605.

Lehnertz B, Ueda Y, Derijck AAHA, Braunschweig U, Perez-Burgos L, Kubicek S, Chen T, Li E, Jenuwein T, Peters AHFM.  Suv39h-mediated histone H3 lysine 9 methylation directs DNA methylation to major satellite repeats at pericentric heterochromatin. Curr Biol. 2003 Jul 15;13(14):1192-200.

2002

Chen T, Ueda Y, Xie S, Li E.  A novel Dnmt3a isoform produced from an alternative promoter localizes to euchromatin and its expression correlates with active de novo methylation. J Biol Chem. 2002 Oct 11;277(41):38746-54.

Older Publications

Larocque D, Pilotte J, Chen T, Cloutier F, Massie B, Pedraza L, Couture R, Lasko P, Almazan G, Richard S. (2002) Nuclear retention of MBP mRNAs in the quaking viable mice. Neuron 36, 815-829.

Chen T, Cote J, Richard S. (2001) Identification of Sam68 arginine-rich sequences capable of conferring non-specific RNA binding to the GSG domain. J. Biol. Chem. 276, 30803-30811.

Derry JJ, Richard S, Carvajal HV, Ye X, VasioukhinV, Cochrane AW, Chen T, Tyner A. (2000) Sik (BRK) phosphorylates Sam68 in the nucleus and negatively regulates its RNA binding ability. Mol. Cell. Biol. 20, 6114-6126.

Chen T, Boisvert F-M, Bazett-Jones DP, Richard S. (1999) A role for the GSG domain in localizing Sam68 to novel nuclear structures in cancer cells. Mol. Biol. Cell 10, 3015-3033.

Di Fruscio M, Chen T, Richard S. (1999) Characterization of Sam68-like mammalian proteins SLM-1 and SLM-2: SLM-1 is a Src substrate during mitosis. Proc. Natl. Acad. Sci. USA 96, 2710-2715. (Di Fruscio and Chen contributed equally to this work).

Aarts MM, Levy D, He B, Stregger S, Chen T, Richard S, Henderson JE. (1999) Parathyroid hormone-related protein interacts with RNA. J. Biol. Chem. 274, 4832-4838.

Chen, T, Richard, S. (1998) Structure-function analysis of Qk1: a lethal point mutation in mouse quaking prevents homodimerization.Mol. Cell. Biol. 18, 4863-4871.

Di Fruscio M, Chen T, Bonyadi S, Lasko P, Richard S. (1998) The identification of two Drosophila K homology domain proteins: KEP1 and SAM are members of the Sam68 family of GSG domain proteins. J. Biol. Chem. 273, 30122-30130.

Chen T, Damaj B, Herriera C, Lasko P, Richard S. (1997) Self-association of the single KH domain family members Sam68, GRP-33, GLD-1 and Qk1: role of the KH domain. Mol. Cell. Biol. 17, 5707-5718.

Rael ED, Rivas JZ, Chen T, Maddux N, Huizar E, Lieb CS. (1997) Differences in fibrinolysis and complement inactivation by venom from different northern blacktailed rattlesnakes (Crotalus molossus molossus). Toxicon  35, 505-513.

Chen T, Rael ED. (1997) Purification of M5, a fibrinolytic proteinase from Crotalus molossus molossus venom that attacks complement. Int. J. Biochem. Cell Biol. 29, 789-799.