2019

 

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 Jun 21. pii: gkz557. doi: 10.1093/nar/gkz557. [Epub ahead of print]

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. 3(16). pii: 99767. 

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. 19(1):88. doi: 10.1186/s13059-018-1464-7.

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. 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. 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. 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 intratumore heterogeneity in localized lung adenocarcinomas. Oncotarget 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. 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.  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. 292(6):2255-2265 

2016

Dan J, Chen T.  Genetic Studies on Mammalian DNA Methyltransferases. Adv Exp Med Biol. 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.  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. 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 12(4):e1005970.

Blanc RS, Vogel G, Chen T, Crist C, Richard S.  PRMT7 Preserves Satellite Cell Regenerative Capacity. Cell Rep 14, 1528-39.

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. 6:10116. 

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

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. 25: 1325-35.

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

2014

Chen, T and Dent SY.  Chromatin modifiers and remodellers: regulators of cellular differentiation. Nat. Rev. Genet. 15, 93-106.

2013

Kim SJ, Zhao H, Hardikar S, Singh AK, Goodell MA, and Chen T.  A DNMT3A muation common in AML exhibits dominant-negative effects in murine ES cells. Blood 122, 4086-4089.

Zhao H, and Chen T.  Tet family of 5-methylcytosine dioxygenases in mammalian development. J. Hum. Genet.58, 421-427.

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, and Chen T.  A hypomorphic Lsd1 allele results in heart development defects in mice. PLoS One 8, 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 55, 673-682.

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. 44, 398-405.

2011

Chen T.  Mechanistic and functional links between histone methylation and DNA methylation. Prog. Mol. Biol. Transl. Sci. 101, 335-348.

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. Mol. Cell 42, 451-464. 

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. 25, 263-274.

He X.-J, Chen T, and Zhu J-K.  Regulation and function of DNA methylation in plants and animals. Cell Res. 21, 442-465.

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. 71, 655-660.

2010

Singh P, Han L, Rivas GE, Lee D-H, Nicholson TB, Larson GP, Chen T, and Szabo PE.  Allele-specific H3K79 di- versus tri-methylation distinguishes opposite parental alleles at imprinted regions. Mol. Cell. Biol. 30, 2693-2707.

Lohmann F, Loureiro J, Su H, Fang Q, Lei H, Lewis T, Yang Y, Labow M, Li E, Chen T, and Kadam S.  KMT1E mediated H3K9 methylation is required for the maintenance of embryonic stem cells by repressing trophectoderm differentiation. Stem Cells 28, 201-212.

2009

Ciccone DN, Su H, Hevi S, Gay F, Lei H, Bajko J, Xu G, Li E. and Chen T.  KDM1B is a histone H3K4 demethylase required to establish maternal genomic imprints. Nature 461, 415-418.

Yu Z, Chen, T, Hebert J, Li E. and Richard S.  A mouse PRMT1 null allele defines an essential role for arginine methylation in genome maintenance and cell proliferation. Mol. Cell. Biol. 29, 2982-2996.

Wang J, Hevi S, Kurash JK, Lei H, Gay F, Bajko J, Su H, Sun W, Chang H, Xu G, Gaudet F, Li E, and Chen T.  The lysine demethylase LSD1 (KDM1) is required for maintenance of global DNA methylation. Nat. Genet. 41, 125-129.

Ciccone DN and Chen T.  Histone lysine methylation in genomic imprinting. Epigenetics 4, 216-220.

Nicholson T.B., Chen T and Richard S.  The physiological and pathophysiological role of PRMT1-mediated protein arginine methylation. Pharmacol. Res. 60, 466-474.

Nicholson TB and Chen T.  LSD1 demethylates histone and non-histone proteins. Epigenetics 4, 129-132.

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 and Chen T.  The histone H3K79 methyltransferase Dot1L is essential for mammalian development and heterochromatin structure. PLoS Genet. 4, 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 and Blasco, MA.  A mammalian microRNA cluster controls DNA methylation and telomere recombination via Rbl2-dependent regulation of DNA methyltransferases. Nat. Struct. Mol. Biol. 15, 268-279.

Hu YG, Hirasawa R, Hu JL, Hata K, Jin Y, Chen T, Li E, Rigolet M, Viegas-Pequigno, E, Sasaki H and Xu, GL.  Regulation of DNA methylation activity through DNMT3L promoter methylation by DNMT3 enzymes in embryonic development. Hum. Mol. Genet. 17, 2654-2664.

Schmid RS, Tsujimoto N, Qu Q, Lei H, Li E, Chen T and 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 19, 393-398.

2007

Li JY, Pu MT, Hirasawa R, Li BZ, Huang YN, Zeng R, Jing NH, Chen T, Li E, Sasaki H and Xu GL.  Synergistic function of DNA methyltransferases Dnmt3a and Dnmt3b in the methylation of Oct4 and Nanog. Mol. Cell. Biol. 27, 8748-8759.

Chen T, Hevi S, Gay F, Tsujimoto N, He T, Zhang B, Ueda Y and Li E.  Complete inactivation of DNMT1 leads to mitotic catastrophe in h uman cancer cells. Nat. Genet. 39, 391-396.

2006

Zhu H, Geiman TM, Xi S, Jiang Q, Schmidtmann A, Chen T, Li E and Muegge, K.  Lsh is involved in de novo methylation of DNA. EMBO J. 25, 335-345.

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

Gonzalo S, Fraga MF, Chen T, Li E, Esteller M. and Blasco MA.  DNA methyltransferases controls telomere length and telomere recombination in mammalian cells. Nat. Cell Biol. 8, 416-424.

Ueda Y, Okano M, Williams C, Chen T, Georgopoulos K. and Li E.  Roles for Dnmt3b in mammalian development: a mouse model for the ICF syndrome. Development 133, 1183-1192.

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, pp377-391.

Dodge JE, Okano, M, Dick F, Tsujimoto N, Chen T, Wang S, Ueda Y, Dyson N and Li E.  Inactivation of Dnmt3b in mouse embryonic fibroblasts results in hypomethylation, chromosomal instability, and spontaneous immortalization. J. Biol. Chem. 280, 17986-17991.

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 and Henderson JE.  Ablation of the Sam68 RNA binding protein protects mice from age-related bone loss. PLoS Genet. 1(6), e74, 0676-0688.

2004

Chen T, Tsujimoto N and 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. 24, 9048-9058.

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

Fang J, Chen T, Chadwick B, Li E and Zhang Y.  Ring1b-mediated H2A ubiquitination associates with inactive X chromosomes and is involved in initiation of X inactivation. J. Biol. Chem. 279, 52812-52815.

2003

Chen T, Ueda Y, Dodge JE, Wang Z and Li E.  Establishment and maintenance of genomic methylation patterns in mouse embryonic stem cells by Dnmt3a and Dnmt3b. Mol. Cell. Biol. 23, 5594-5605.

Lehnertz B, Ueda Y, Derijck AAHA, Braunschweig U, Perez-Burgos L, Kubicek S, Chen T, Li E, Jenuwein T and Peters AHFM.  Suv39h-mediated histone H3 lysine 9 methylation directs DNA methylation to major satellite repeats at pericentric heterochromatin. Curr. Biol. 13, 1192-1200.

2002

Chen T, Ueda Y, Xie S and 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. 277, 38746-38754.

Older Publications

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

Chen, T., Cote, J. and 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, J. J., Richard, S., Carvajal, H. V., Ye, X ., Vasioukhin, V., Cochrane, A. W., Chen, T. and 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, D. P. and 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. and 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, M. M., Levy, D., He, B., Stregger, S., Chen, T., Richard, S. and Henderson, J. E. (1999) Parathyroid hormone-related protein interacts with RNA. J. Biol. Chem. 274, 4832-4838.

Chen, T. and 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. and 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. and 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, E. D., Rivas, J. Z., Chen, T., Maddux, N., Huizar, E. and Lieb, C. S. (1997) Differences in fibrinolysis and complement inactivation by venom from different northern blacktailed rattlesnakes (Crotalus molossus molossus). Toxicon  35, 505-513.

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