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Yujiang Shi, Ph.D.

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Research
The research activities and funding listed below are automatically derived from NIH ExPORTER and other sources, which might result in incorrect or missing items. Faculty can login to make corrections and additions.
  1. R01CA194302 (SHI, YUJIANG GENO) Apr 1, 2016 - Mar 31, 2020
    NIH/NCI
    De-Regulation of 5hmC/TET2 Tumor Suppressor under Anti-Estrogen Therapy
    Role: Principal Investigator
  2. R01GM112062 (SHI, YUJIANG GENO) Jul 1, 2015 - Mar 31, 2019
    NIH/NIGMS
    Post Translational Regulation of TET2 Function by Glucose Signaling
    Role: Principal Investigator
  3. R21HD066495 (KAISER, URSULA B) Sep 15, 2010 - Aug 31, 2013
    NIH/NICHD
    The Epigenetic Regulation of Puberty
    Role: Co-Principal Investigator
  4. R01DK077036 (SHI, YUJIANG) Jul 20, 2009 - Jun 30, 2011
    NIH/NIDDK
    Histone Demethylation A Novel Mechanism in Hormone-Mediated Gene Regulation
    Role: Principal Investigator
  5. R01GM078458 (SHI, YUJIANG) Aug 1, 2006 - Apr 30, 2014
    NIH/NIGMS
    Histone Demethylases and Their Regulation
    Role: Principal Investigator

Bibliographic
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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  1. Wen J, Lv R, Ma H, Shen H, He C, Wang J, Jiao F, Liu H, Yang P, Tan L, Lan F, Shi YG, He C, Shi Y, Diao J. Zc3h13 Regulates Nuclear RNA m6A Methylation and Mouse Embryonic Stem Cell Self-Renewal. Mol Cell. 2018 Mar 15; 69(6):1028-1038.e6. PMID: 29547716.
    View in: PubMed
  2. Tan L, Ke Z, Tombline G, Macoretta N, Hayes K, Tian X, Lv R, Ablaeva J, Gilbert M, Bhanu NV, Yuan ZF, Garcia BA, Shi YG, Shi Y, Seluanov A, Gorbunova V. Naked Mole Rat Cells Have a Stable Epigenome that Resists iPSC Reprogramming. Stem Cell Reports. 2017 Nov 14; 9(5):1721-1734. PMID: 29107597.
    View in: PubMed
  3. Ma C, Karwacki-Neisius V, Tang H, Li W, Shi Z, Hu H, Xu W, Wang Z, Kong L, Lv R, Fan Z, Zhou W, Yang P, Wu F, Diao J, Tan L, Shi YG, Lan F, Shi Y. Nono, a Bivalent Domain Factor, Regulates Erk Signaling and Mouse Embryonic Stem Cell Pluripotency. Cell Rep. 2016 10 18; 17(4):997-1007. PMID: 27760330.
    View in: PubMed
  4. Kong L, Tan L, Lv R, Shi Z, Xiong L, Wu F, Rabidou K, Smith M, He C, Zhang L, Qian Y, Ma D, Lan F, Shi Y, Shi YG. A primary role of TET proteins in establishment and maintenance of De Novo bivalency at CpG islands. Nucleic Acids Res. 2016 Oct 14; 44(18):8682-8692. PMID: 27288448.
    View in: PubMed
  5. Shen H, Xu W, Guo R, Rong B, Gu L, Wang Z, He C, Zheng L, Hu X, Hu Z, Shao ZM, Yang P, Wu F, Shi YG, Shi Y, Lan F. Suppression of Enhancer Overactivation by a RACK7-Histone Demethylase Complex. Cell. 2016 Apr 07; 165(2):331-42. PMID: 27058665; PMCID: PMC4826479 [Available on 04/07/17].
  6. Cai JB, Shi GM, Dong ZR, Ke AW, Ma HH, Gao Q, Shen ZZ, Huang XY, Chen H, Yu DD, Liu LX, Zhang PF, Zhang C, Hu MY, Yang LX, Shi YH, Wang XY, Ding ZB, Qiu SJ, Sun HC, Zhou J, Shi YG, Fan J. Ubiquitin-specific protease 7 accelerates p14(ARF) degradation by deubiquitinating thyroid hormone receptor-interacting protein 12 and promotes hepatocellular carcinoma progression. Hepatology. 2015 May; 61(5):1603-14. PMID: 25557975.
    View in: PubMed
  7. Guo R, Zheng L, Park JW, Lv R, Chen H, Jiao F, Xu W, Mu S, Wen H, Qiu J, Wang Z, Yang P, Wu F, Hui J, Fu X, Shi X, Shi YG, Xing Y, Lan F, Shi Y. BS69/ZMYND11 reads and connects histone H3.3 lysine 36 trimethylation-decorated chromatin to regulated pre-mRNA processing. Mol Cell. 2014 Oct 23; 56(2):298-310. PMID: 25263594.
    View in: PubMed
  8. Hu X, Zhang L, Mao SQ, Li Z, Chen J, Zhang RR, Wu HP, Gao J, Guo F, Liu W, Xu GF, Dai HQ, Shi YG, Li X, Hu B, Tang F, Pei D, Xu GL. Tet and TDG mediate DNA demethylation essential for mesenchymal-to-epithelial transition in somatic cell reprogramming. Cell Stem Cell. 2014 Apr 03; 14(4):512-22. PMID: 24529596.
    View in: PubMed
  9. Larson AR, Dresser KA, Zhan Q, Lezcano C, Woda BA, Yosufi B, Thompson JF, Scolyer RA, Mihm MC, Shi YG, Murphy GF, Lian CG. Loss of 5-hydroxymethylcytosine correlates with increasing morphologic dysplasia in melanocytic tumors. Mod Pathol. 2014 Jul; 27(7):936-44. PMID: 24390216; PMCID: PMC4077910.
  10. Hu L, Li Z, Cheng J, Rao Q, Gong W, Liu M, Shi YG, Zhu J, Wang P, Xu Y. Crystal structure of TET2-DNA complex: insight into TET-mediated 5mC oxidation. Cell. 2013 Dec 19; 155(7):1545-55. PMID: 24315485.
    View in: PubMed
  11. Shi YG, Tsukada Y. The discovery of histone demethylases. Cold Spring Harb Perspect Biol. 2013; 5(12). PMID: 24296173.
    View in: PubMed
  12. Shi YG, Tsukada Y. The discovery of histone demethylases. Cold Spring Harb Perspect Biol. 2013 Sep 01; 5(9). PMID: 24003214; PMCID: PMC3753710.
  13. Tan L, Xiong L, Xu W, Wu F, Huang N, Xu Y, Kong L, Zheng L, Schwartz L, Shi Y, Shi YG. Genome-wide comparison of DNA hydroxymethylation in mouse embryonic stem cells and neural progenitor cells by a new comparative hMeDIP-seq method. Nucleic Acids Res. 2013 Apr; 41(7):e84. PMID: 23408859; PMCID: PMC3627583.
  14. Chen F, Yang H, Dong Z, Fang J, Wang P, Zhu T, Gong W, Fang R, Shi YG, Li Z, Xu Y. Structural insight into substrate recognition by histone demethylase LSD2/KDM1b. Cell Res. 2013 Feb; 23(2):306-9. PMID: 23357850; PMCID: PMC3567815.
  15. Chen H, Ma H, Inuzuka H, Diao J, Lan F, Shi YG, Wei W, Shi Y. DNA damage regulates UHRF1 stability via the SCF(ß-TrCP) E3 ligase. Mol Cell Biol. 2013 Mar; 33(6):1139-48. PMID: 23297342; PMCID: PMC3592027.
  16. Fang R, Chen F, Dong Z, Hu D, Barbera AJ, Clark EA, Fang J, Yang Y, Mei P, Rutenberg M, Li Z, Zhang Y, Xu Y, Yang H, Wang P, Simon MD, Zhou Q, Li J, Marynick MP, Li X, Lu H, Kaiser UB, Kingston RE, Xu Y, Shi YG. LSD2/KDM1B and its cofactor NPAC/GLYR1 endow a structural and molecular model for regulation of H3K4 demethylation. Mol Cell. 2013 Feb 07; 49(3):558-70. PMID: 23260659; PMCID: PMC3625064.
  17. Xu Y, Xu C, Kato A, Tempel W, Abreu JG, Bian C, Hu Y, Hu D, Zhao B, Cerovina T, Diao J, Wu F, He HH, Cui Q, Clark E, Ma C, Barbara A, Veenstra GJ, Xu G, Kaiser UB, Liu XS, Sugrue SP, He X, Min J, Kato Y, Shi YG. Tet3 CXXC domain and dioxygenase activity cooperatively regulate key genes for Xenopus eye and neural development. Cell. 2012 Dec 07; 151(6):1200-13. PMID: 23217707; PMCID: PMC3705565.
  18. Lian CG, Xu Y, Ceol C, Wu F, Larson A, Dresser K, Xu W, Tan L, Hu Y, Zhan Q, Lee CW, Hu D, Lian BQ, Kleffel S, Yang Y, Neiswender J, Khorasani AJ, Fang R, Lezcano C, Duncan LM, Scolyer RA, Thompson JF, Kakavand H, Houvras Y, Zon LI, Mihm MC, Kaiser UB, Schatton T, Woda BA, Murphy GF, Shi YG. Loss of 5-hydroxymethylcytosine is an epigenetic hallmark of melanoma. Cell. 2012 Sep 14; 150(6):1135-46. PMID: 22980977; PMCID: PMC3770275.
  19. Tan L, Shi YG. Tet family proteins and 5-hydroxymethylcytosine in development and disease. Development. 2012 Jun; 139(11):1895-902. PMID: 22569552; PMCID: PMC3347683.
  20. Ma H, Chen H, Guo X, Wang Z, Sowa ME, Zheng L, Hu S, Zeng P, Guo R, Diao J, Lan F, Harper JW, Shi YG, Xu Y, Shi Y. M phase phosphorylation of the epigenetic regulator UHRF1 regulates its physical association with the deubiquitylase USP7 and stability. Proc Natl Acad Sci U S A. 2012 Mar 27; 109(13):4828-33. PMID: 22411829; PMCID: PMC3323953.
  21. Gu TP, Guo F, Yang H, Wu HP, Xu GF, Liu W, Xie ZG, Shi L, He X, Jin SG, Iqbal K, Shi YG, Deng Z, Szabó PE, Pfeifer GP, Li J, Xu GL. The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes. Nature. 2011 Sep 04; 477(7366):606-10. PMID: 21892189.
    View in: PubMed
  22. Rajakumara E, Wang Z, Ma H, Hu L, Chen H, Lin Y, Guo R, Wu F, Li H, Lan F, Shi YG, Xu Y, Patel DJ, Shi Y. PHD finger recognition of unmodified histone H3R2 links UHRF1 to regulation of euchromatic gene expression. Mol Cell. 2011 Jul 22; 43(2):275-284. PMID: 21777816; PMCID: PMC4691841.
  23. 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. 2011 May 20; 42(4):451-64. PMID: 21514197.
    View in: PubMed
  24. Zhang H, Zhang X, Clark E, Mulcahey M, Huang S, Shi YG. TET1 is a DNA-binding protein that modulates DNA methylation and gene transcription via hydroxylation of 5-methylcytosine. Cell Res. 2010 Dec; 20(12):1390-3. PMID: 21079648.
    View in: PubMed
  25. Fang R, Barbera AJ, Xu Y, Rutenberg M, Leonor T, Bi Q, Lan F, Mei P, Yuan GC, Lian C, Peng J, Cheng D, Sui G, Kaiser UB, Shi Y, Shi YG. Human LSD2/KDM1b/AOF1 regulates gene transcription by modulating intragenic H3K4me2 methylation. Mol Cell. 2010 Jul 30; 39(2):222-33. PMID: 20670891.
    View in: PubMed
  26. Tahiliani M, Mei P, Fang R, Leonor T, Rutenberg M, Shimizu F, Li J, Rao A, Shi Y. The histone H3K4 demethylase SMCX links REST target genes to X-linked mental retardation. Nature. 2007 May 31; 447(7144):601-5. PMID: 17468742.
    View in: PubMed
  27. Lan F, Zaratiegui M, Villén J, Vaughn MW, Verdel A, Huarte M, Shi Y, Gygi SP, Moazed D, Martienssen RA, Shi Y. S. pombe LSD1 homologs regulate heterochromatin propagation and euchromatic gene transcription. Mol Cell. 2007 Apr 13; 26(1):89-101. PMID: 17434129.
    View in: PubMed
  28. Rosendorff A, Sakakibara S, Lu S, Kieff E, Xuan Y, DiBacco A, Shi Y, Shi Y, Gill G. NXP-2 association with SUMO-2 depends on lysines required for transcriptional repression. PNAS. 2006; 103(14):5308-13.
  29. Lian B, Guo C, Fang R, Wu P, Leonor T, Shimizu F, Adler GK, Williams GH, Shi Y . Histone demethylase LSD1 modulates angiotensin II induced interleukin-6 expression in human aortic smooth muscle cells. Circulation. 2006; 114(18):297-297 Suppl..
  30. Yujiang Shi and Yang Shi. . The CtBP complex. CtBP family proteins edited by Chinnadurai G. 2005.
  31. Shi YJ, Matson C, Lan F, Iwase S, Baba T, Shi Y. Regulation of LSD1 histone demethylase activity by its associated factors. Mol Cell. 2005 Sep 16; 19(6):857-64. PMID: 16140033.
    View in: PubMed
  32. Shi Y, Lan F, Matson C, Mulligan P, Whetstine JR, Cole PA, Casero RA, Shi Y. Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell. 2004 Dec 29; 119(7):941-53. PMID: 15620353.
    View in: PubMed
  33. Alpatov R, Munguba GC, Caton P, Joo JH, Shi Y, Shi Y, Hunt ME, Sugrue SP. Nuclear speckle-associated protein Pnn/DRS binds to the transcriptional corepressor CtBP and relieves CtBP-mediated repression of the E-cadherin gene. Mol Cell Biol. 2004 Dec; 24(23):10223-35. PMID: 15542832; PMCID: PMC529029.
  34. Shi Y, Shi Y. Metabolic enzymes and coenzymes in transcription--a direct link between metabolism and transcription? Trends Genet. 2004 Sep; 20(9):445-52. PMID: 15313554.
    View in: PubMed
  35. Shi Y and Shi Y. . Metabolic enzymes and coenzymes in transcription—a direct link between metabolism and transcription?. Trends in Genetics. 2004; 20(9):445-52.
  36. Sui G, Affar el B, Shi Y, Brignone C, Wall NR, Yin P, Donohoe M, Luke MP, Calvo D, Grossman SR, Shi Y. Yin Yang 1 is a negative regulator of p53. Cell. 2004 Jun 25; 117(7):859-72. PMID: 15210108.
    View in: PubMed
  37. Lin X, Liang YY, Sun B, Liang M, Shi Y, Brunicardi FC, Shi Y, Feng XH. Smad6 recruits transcription corepressor CtBP to repress bone morphogenetic protein-induced transcription. Mol Cell Biol. 2003 Dec; 23(24):9081-93. PMID: 14645520; PMCID: PMC309600.
  38. Zimowska G, Shi J, Munguba G, Jackson MR, Alpatov R, Simmons MN, Shi Y, Sugrue SP. Pinin/DRS/memA interacts with SRp75, SRm300 and SRrp130 in corneal epithelial cells. Invest Ophthalmol Vis Sci. 2003 Nov; 44(11):4715-23. PMID: 14578391.
    View in: PubMed
  39. Shi Y, Sawada J, Sui G, Affar el B, Whetstine JR, Lan F, Ogawa H, Luke MP, Nakatani Y, Shi Y. Coordinated histone modifications mediated by a CtBP co-repressor complex. Nature. 2003 Apr 17; 422(6933):735-8. PMID: 12700765.
    View in: PubMed
  40. Sui G, Soohoo C, Affar el B, Gay F, Shi Y, Forrester WC, Shi Y. A DNA vector-based RNAi technology to suppress gene expression in mammalian cells. Proc Natl Acad Sci U S A. 2002 Apr 16; 99(8):5515-20. PMID: 11960009; PMCID: PMC122801.
  41. Shi Y, Simmons MN, Seki T, Oh SP, Sugrue SP. Change in gene expression subsequent to induction of Pnn/DRS/memA: increase in p21(cip1/waf1). Oncogene. 2001 Jul 05; 20(30):4007-18. PMID: 11494129.
    View in: PubMed
  42. See RH, Calvo D, Shi Y, Kawa H, Luke MP, Yuan Z, Shi Y. Stimulation of p300-mediated transcription by the kinase MEKK1. J Biol Chem. 2001 May 11; 276(19):16310-7. PMID: 11278389.
    View in: PubMed
  43. Shi Y, Tabesh M, Sugrue SP. Role of cell adhesion-associated protein, pinin (DRS/memA), in corneal epithelial migration. Invest Ophthalmol Vis Sci. 2000 May; 41(6):1337-45. PMID: 10798648.
    View in: PubMed
  44. Shi Y, Ouyang P, Sugrue SP. Characterization of the gene encoding pinin/DRS/memA and evidence for its potential tumor suppressor function. Oncogene. 2000 Jan 13; 19(2):289-97. PMID: 10645008.
    View in: PubMed
  45. Yuan W, Tuttle DL, Shi YJ, Ralph GS, Dunn WA. Glucose-induced microautophagy in Pichia pastoris requires the alpha-subunit of phosphofructokinase. J Cell Sci. 1997 Aug; 110 ( Pt 16):1935-45. PMID: 9296392.
    View in: PubMed
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