Harvard Catalyst Profiles

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Yujiang Shi, Ph.D.


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
    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
    Post Translational Regulation of TET2 Function by Glucose Signaling
    Role: Principal Investigator
  3. R21HD066495 (KAISER, URSULA B) Sep 15, 2010 - Aug 31, 2013
    The Epigenetic Regulation of Puberty
    Role: Co-Principal Investigator
  4. R01DK077036 (SHI, YUJIANG) Jul 20, 2009 - Jun 30, 2011
    Histone Demethylation A Novel Mechanism in Hormone-Mediated Gene Regulation
    Role: Principal Investigator
  5. R01GM078458 (SHI, YUJIANG) Aug 1, 2006 - Jul 31, 2011
    Histone Demethylases and Their Regulation
    Role: Principal Investigator

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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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Li W, Karwacki-Neisius V, Ma C, Tan L, Shi Y, Wu F, Shi YG. Nono deficiency compromises TET1 chromatin association and impedes neuronal differentiation of mouse embryonic stem cells. Nucleic Acids Res. 2020 05 21; 48(9):4827-4838. PMID: 32286661.
  2. Wang J, Wang L, Diao J, Shi YG, Shi Y, Ma H, Shen H. Binding to m6A RNA promotes YTHDF2-mediated phase separation. Protein Cell. 2020 04; 11(4):304-307. PMID: 31642031.
  3. Fetahu IS, Ma D, Rabidou K, Argueta C, Smith M, Liu H, Wu F, Shi YG. Epigenetic signatures of methylated DNA cytosine in Alzheimer's disease. Sci Adv. 2019 08; 5(8):eaaw2880. PMID: 31489368.
  4. Lu JC, Zeng HY, Sun QM, Meng QN, Huang XY, Zhang PF, Yang X, Peng R, Gao C, Wei CY, Shen YH, Cai JB, Dong RZ, Shi YH, Sun HC, Shi YG, Zhou J, Fan J, Ke AW, Yang LX, Shi GM. Distinct PD-L1/PD1 Profiles and Clinical Implications in Intrahepatic Cholangiocarcinoma Patients with Different Risk Factors. Theranostics. 2019; 9(16):4678-4687. PMID: 31367249.
  5. Clark EA, Wu F, Chen Y, Kang P, Kaiser UB, Fang R, Shi YG. GR and LSD1/KDM1A-Targeted Gene Activation Requires Selective H3K4me2 Demethylation at Enhancers. Cell Rep. 2019 06 18; 27(12):3522-3532.e3. PMID: 31216473.
  6. Jin Y, Ma D, Gramyk T, Guo C, Fang R, Ji H, Shi YG. Kdm1a promotes SCLC progression by transcriptionally silencing the tumor suppressor Rest. Biochem Biophys Res Commun. 2019 07 12; 515(1):214-221. PMID: 31146914.
  7. Ma H, Wang X, Cai J, Dai Q, Natchiar SK, Lv R, Chen K, Lu Z, Chen H, Shi YG, Lan F, Fan J, Klaholz BP, Pan T, Shi Y, He C. Publisher Correction: N6-Methyladenosine methyltransferase ZCCHC4 mediates ribosomal RNA methylation. Nat Chem Biol. 2019 05; 15(5):549. PMID: 30737498.
  8. Chen H, Yu D, Fang R, Rabidou K, Wu D, Hu D, Jia P, Zhao Z, Wu Z, Peng J, Shi Y, Shi YG. TET2 stabilization by 14-3-3 binding to the phosphorylated Serine 99 is deregulated by mutations in cancer. Cell Res. 2019 03; 29(3):248-250. PMID: 30607016.
    Citations:    Fields:    
  9. Ma H, Wang X, Cai J, Dai Q, Natchiar SK, Lv R, Chen K, Lu Z, Chen H, Shi YG, Lan F, Fan J, Klaholz BP, Pan T, Shi Y, He C. N6-Methyladenosine methyltransferase ZCCHC4 mediates ribosomal RNA methylation. Nat Chem Biol. 2019 01; 15(1):88-94. PMID: 30531910.
    Citations:    Fields:    
  10. Liu L, Shen Y, Zhu X, Lv R, Li S, Zhang Z, Shi YG, Tan L. ERa is a negative regulator of PD-L1 gene transcription in breast cancer. Biochem Biophys Res Commun. 2018 10 20; 505(1):157-161. PMID: 30241942.
    Citations:    Fields:    
  11. Wu D, Hu D, Chen H, Shi G, Fetahu IS, Wu F, Rabidou K, Fang R, Tan L, Xu S, Liu H, Argueta C, Zhang L, Mao F, Yan G, Chen J, Dong Z, Lv R, Xu Y, Wang M, Ye Y, Zhang S, Duquette D, Geng S, Yin C, Lian CG, Murphy GF, Adler GK, Garg R, Lynch L, Yang P, Li Y, Lan F, Fan J, Shi Y, Shi YG. Glucose-regulated phosphorylation of TET2 by AMPK reveals a pathway linking diabetes to cancer. Nature. 2018 07; 559(7715):637-641. PMID: 30022161.
    Citations: 4     Fields:    
  12. 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 03 15; 69(6):1028-1038.e6. PMID: 29547716.
    Citations: 6     Fields:    Translation:HumansAnimalsCells
  13. 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 11 14; 9(5):1721-1734. PMID: 29107597.
    Citations: 3     Fields:    Translation:AnimalsCells
  14. 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.
    Citations: 2     Fields:    Translation:AnimalsCells
  15. 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.
    Citations: 9     Fields:    Translation:HumansAnimalsCells
  16. 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.
    Citations: 31     Fields:    Translation:HumansAnimalsCells
  17. 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.
    Citations: 14     Fields:    Translation:Humans
  18. 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.
    Citations: 46     Fields:    Translation:HumansCells
  19. 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.
    Citations: 79     Fields:    Translation:AnimalsCells
  20. 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.
    Citations: 19     Fields:    Translation:HumansCells
  21. 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.
    Citations: 80     Fields:    Translation:HumansCells
  22. Shi YG, Tsukada Y. The discovery of histone demethylases. Cold Spring Harb Perspect Biol. 2013; 5(12). PMID: 24296173.
  23. Shi YG, Tsukada Y. The discovery of histone demethylases. Cold Spring Harb Perspect Biol. 2013 Sep 01; 5(9). PMID: 24003214.
    Citations: 17     Fields:    
  24. 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.
    Citations: 23     Fields:    Translation:AnimalsCells
  25. 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.
    Citations: 7     Fields:    Translation:HumansCells
  26. 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.
    Citations: 20     Fields:    Translation:HumansCells
  27. 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.
    Citations: 22     Fields:    Translation:HumansCells
  28. 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.
    Citations: 79     Fields:    Translation:AnimalsCells
  29. 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.
    Citations: 218     Fields:    Translation:HumansCells
  30. Tan L, Shi YG. Tet family proteins and 5-hydroxymethylcytosine in development and disease. Development. 2012 Jun; 139(11):1895-902. PMID: 22569552.
    Citations: 107     Fields:    Translation:HumansAnimalsCells
  31. 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.
    Citations: 39     Fields:    Translation:HumansCells
  32. 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.
    Citations: 317     Fields:    Translation:AnimalsCells
  33. 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.
    Citations: 56     Fields:    Translation:HumansCells
  34. 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.
    Citations: 222     Fields:    Translation:AnimalsCells
  35. 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.
    Citations: 63     Fields:    Translation:HumansCells
  36. 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.
    Citations: 74     Fields:    Translation:HumansCells
  37. 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.
    Citations: 172     Fields:    Translation:HumansAnimalsCells
  38. 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.
    Citations: 40     Fields:    Translation:AnimalsCells
  39. 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.
  40. 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..
  41. Yujiang Shi and Yang Shi. . The CtBP complex. CtBP family proteins edited by Chinnadurai G. 2005.
  42. 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.
    Citations: 266     Fields:    Translation:HumansCells
  43. 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.
    Citations: 1055     Fields:    Translation:HumansCells
  44. 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.
    Citations: 26     Fields:    Translation:HumansAnimalsCells
  45. 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.
    Citations: 23     Fields:    Translation:HumansAnimalsCells
  46. 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.
  47. 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.
    Citations: 147     Fields:    Translation:HumansAnimalsCells
  48. 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.
    Citations: 27     Fields:    Translation:HumansAnimalsCells
  49. 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.
    Citations: 22     Fields:    Translation:HumansAnimalsCells
  50. 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.
    Citations: 267     Fields:    Translation:HumansCells
  51. 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.
    Citations: 301     Fields:    Translation:HumansAnimalsCells
  52. 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.
    Citations: 13     Fields:    Translation:HumansCells
  53. 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.
    Citations: 24     Fields:    Translation:HumansAnimalsCells
  54. 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.
    Citations: 16     Fields:    Translation:AnimalsCells
  55. 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.
    Citations: 15     Fields:    Translation:HumansCells
  56. 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.
    Citations: 40     Fields:    Translation:HumansAnimalsCells
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.