Jmjd3 inhibits reprogramming by upregulating expression of INK4a/Arf and targeting PHF20 for ubiquitination

Cell

Volumn 152, Issue 5, 2013, Pages 1037-1050

  Zhao, Wei ^a   Li, Qingtian ^a   Ayers, Stephen ^a   Gu, Yifeng ^a   Shi, Zhong ^b   Zhu, Qingyuan ^a   Chen, Yidong ^c   Wang, Helen Y ^a   Wang, Rong Fu ^a  

^a HOUSTON METHODIST RESEARCH INSTITUTE   (United States)

^b CENTER FOR CELL AND GENE THERAPY   (United States)

^c UNIVERSITY OF TEXAS HEALTH SCIENCE CENTER AT SAN ANTONIO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARF PROTEIN; CYCLIN DEPENDENT KINASE INHIBITOR 2A; HISTONE DEMETHYLASE; NUCLEIC ACID BINDING PROTEIN; PLANT HOMEODOMAIN FINGER PROTEIN 20; PROTEIN P21; UBIQUITIN PROTEIN LIGASE E3; UNCLASSIFIED DRUG;

ANIMAL EXPERIMENT; ARTICLE; CONTROLLED STUDY; GENE; GENE EXPRESSION; GENE SILENCING; JMJD3 GENE; MOUSE; NONHUMAN; NUCLEAR REPROGRAMMING; NUCLEOTIDE SEQUENCE; PLURIPOTENT STEM CELL; PRIORITY JOURNAL; UBIQUITINATION; UPREGULATION; WILD TYPE;

EID: 84874789264     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2013.02.006     Document Type: Article

References (51)

1. M.A. Adams-Cioaba, Z. Li, W. Tempel, Y. Guo, C. Bian, Y. Li, R. Lam, and J. Min Crystal structures of the Tudor domains of human PHF20 reveal novel structural variations on the Royal Family of proteins FEBS Lett. 586 2012 859 865
2. K. Agger, P.A. Cloos, J. Christensen, D. Pasini, S. Rose, J. Rappsilber, I. Issaeva, E. Canaani, A.E. Salcini, and K. Helin UTX and JMJD3 are histone H3K27 demethylases involved in HOX gene regulation and development Nature 449 2007 731 734
3. K. Agger, P.A. Cloos, L. Rudkjaer, K. Williams, G. Andersen, J. Christensen, and K. Helin The H3K27me3 demethylase JMJD3 contributes to the activation of the INK4A-ARF locus in response to oncogene- and stress-induced senescence Genes Dev. 23 2009 1171 1176
4. Y.S. Ang, S.Y. Tsai, D.F. Lee, J. Monk, J. Su, K. Ratnakumar, J. Ding, Y. Ge, H. Darr, and B. Chang Wdr5 mediates self-renewal and reprogramming via the embryonic stem cell core transcriptional network Cell 145 2011 183 197
5. A.I. Badeaux, Y. Yang, K. Cardenas, V. Vemulapalli, K. Chen, D. Kusewitt, E. Richie, W. Li, and M.T. Bedford Loss of the methyl lysine effector protein PHF20 impacts the expression of genes regulated by the lysine acetyltransferase MOF J. Biol. Chem. 287 2012 429 437
6. M. Barradas, E. Anderton, J.C. Acosta, S. Li, A. Banito, M. Rodriguez-Niedenführ, G. Maertens, M. Banck, M.M. Zhou, and M.J. Walsh Histone demethylase JMJD3 contributes to epigenetic control of INK4a/ARF by oncogenic RAS Genes Dev. 23 2009 1177 1182
7. Y. Cai, J. Jin, S.K. Swanson, M.D. Cole, S.H. Choi, L. Florens, M.P. Washburn, J.W. Conaway, and R.C. Conaway Subunit composition and substrate specificity of a MOF-containing histone acetyltransferase distinct from the male-specific lethal (MSL) complex J. Biol. Chem. 285 2010 4268 4272
8. J. Cui, L. Zhu, X. Xia, H.Y. Wang, X. Legras, J. Hong, J. Ji, P. Shen, S. Zheng, Z.J. Chen, and R.F. Wang NLRC5 negatively regulates the NF-kappaB and type I interferon signaling pathways Cell 141 2010 483 496
9. J. Cui, Y. Li, L. Zhu, D. Liu, Z. Songyang, H.Y. Wang, and R.F. Wang NLRP4 negatively regulates type I interferon signaling by targeting the kinase TBK1 for degradation via the ubiquitin ligase DTX4 Nat. Immunol. 13 2012 387 395
10. Y. Dou, T.A. Milne, A.J. Tackett, E.R. Smith, A. Fukuda, J. Wysocka, C.D. Allis, B.T. Chait, J.L. Hess, and R.G. Roeder Physical association and coordinate function of the H3 K4 methyltransferase MLL1 and the H4 K16 acetyltransferase MOF Cell 121 2005 873 885
11. U. Fischer, A.K. Struss, D. Hemmer, C.P. Pallasch, W.I. Steudel, and E. Meese Glioma-expressed antigen 2 (GLEA2): a novel protein that can elicit immune responses in glioblastoma patients and some controls Clin. Exp. Immunol. 126 2001 206 213
12. A. Gaspar-Maia, A. Alajem, E. Meshorer, and M. Ramalho-Santos Open chromatin in pluripotency and reprogramming Nat. Rev. Mol. Cell Biol. 12 2011 36 47
13. J. Hanna, K. Saha, B. Pando, J. van Zon, C.J. Lengner, M.P. Creyghton, A. van Oudenaarden, and R. Jaenisch Direct cell reprogramming is a stochastic process amenable to acceleration Nature 462 2009 595 601
14. M. Hemberger, W. Dean, and W. Reik Epigenetic dynamics of stem cells and cell lineage commitment: digging Waddington's canal Nat. Rev. Mol. Cell Biol. 10 2009 526 537
15. H. Hong, K. Takahashi, T. Ichisaka, T. Aoi, O. Kanagawa, M. Nakagawa, K. Okita, and S. Yamanaka Suppression of induced pluripotent stem cell generation by the p53-p21 pathway Nature 460 2009 1132 1135
16. T. Kawamura, J. Suzuki, Y.V. Wang, S. Menendez, L.B. Morera, A. Raya, G.M. Wahl, and J.C. Izpisúa Belmonte Linking the p53 tumour suppressor pathway to somatic cell reprogramming Nature 460 2009 1140 1144
17. J. Kim, J. Daniel, A. Espejo, A. Lake, M. Krishna, L. Xia, Y. Zhang, and M.T. Bedford Tudor, MBT and chromo domains gauge the degree of lysine methylation EMBO Rep. 7 2006 397 403
18. R.P. Koche, Z.D. Smith, M. Adli, H. Gu, M. Ku, A. Gnirke, B.E. Bernstein, and A. Meissner Reprogramming factor expression initiates widespread targeted chromatin remodeling Cell Stem Cell 8 2011 96 105
19. F. Lan, P.E. Bayliss, J.L. Rinn, J.R. Whetstine, J.K. Wang, S. Chen, S. Iwase, R. Alpatov, I. Issaeva, and E. Canaani A histone H3 lysine 27 demethylase regulates animal posterior development Nature 449 2007 689 694
20. H. Li, M. Collado, A. Villasante, K. Strati, S. Ortega, M. Cañamero, M.A. Blasco, and M. Serrano The Ink4/Arf locus is a barrier for iPS cell reprogramming Nature 460 2009 1136 1139
21. R. Li, J. Liang, S. Ni, T. Zhou, X. Qing, H. Li, W. He, J. Chen, F. Li, and Q. Zhuang A mesenchymal-to-epithelial transition initiates and is required for the nuclear reprogramming of mouse fibroblasts Cell Stem Cell 7 2010 51 63
22. X. Li, L. Li, R. Pandey, J.S. Byun, K. Gardner, Z. Qin, and Y. Dou The histone acetyltransferase MOF is a key regulator of the embryonic stem cell core transcriptional network Cell Stem Cell 11 2012 163 178
23. Y. Li, J. Park, L. Piao, G. Kong, Y. Kim, K.A. Park, T. Zhang, J. Hong, G.M. Hur, and J.H. Seok PKB-mediated PHF20 phosphorylation on Ser291 is required for p53 function in DNA damage Cell. Signal. 25 2013 74 84
24. A.A. Mansour, O. Gafni, L. Weinberger, A. Zviran, M. Ayyash, Y. Rais, V. Krupalnik, M. Zerbib, D. Amann-Zalcenstein, and I. Maza The H3K27 demethylase Utx regulates somatic and germ cell epigenetic reprogramming Nature 488 2012 409 413
25. R. Margueron, and D. Reinberg The Polycomb complex PRC2 and its mark in life Nature 469 2011 343 349
26. R.M. Marión, K. Strati, H. Li, M. Murga, R. Blanco, S. Ortega, O. Fernandez-Capetillo, M. Serrano, and M.A. Blasco A p53-mediated DNA damage response limits reprogramming to ensure iPS cell genomic integrity Nature 460 2009 1149 1153
27. S.A. Miller, S.E. Mohn, and A.S. Weinmann Jmjd3 and UTX play a demethylase-independent role in chromatin remodeling to regulate T-box family member-dependent gene expression Mol. Cell 40 2010 594 605
28. T.T. Onder, N. Kara, A. Cherry, A.U. Sinha, N. Zhu, K.M. Bernt, P. Cahan, B.O. Marcarci, J. Unternaehrer, and P.B. Gupta Chromatin-modifying enzymes as modulators of reprogramming Nature 483 2012 598 602
29. I.H. Park, P.H. Lerou, R. Zhao, H. Huo, and G.Q. Daley Generation of human-induced pluripotent stem cells Nat. Protoc. 3 2008 1180 1186
30. S. Park, D. Kim, H.C. Dan, H. Chen, J.R. Testa, and J.Q. Cheng Identification of Akt interaction protein PHF20/TZP that transcriptionally regulates p53 J. Biol. Chem. 287 2012 11151 11163
31. G. Peng, Z. Guo, Y. Kiniwa, K.S. Voo, W. Peng, T. Fu, D.Y. Wang, Y. Li, H.Y. Wang, and R.-F. Wang Toll-like receptor 8-mediated reversal of CD4+ regulatory T cell function Science 309 2005 1380 1384
32. K. Plath, and W.E. Lowry Progress in understanding reprogramming to the induced pluripotent state Nat. Rev. Genet. 12 2011 253 265
33. D.A. Robinton, and G.Q. Daley The promise of induced pluripotent stem cells in research and therapy Nature 481 2012 295 305
34. M. Stadtfeld, and K. Hochedlinger Induced pluripotency: history, mechanisms, and applications Genes Dev. 24 2010 2239 2263
35. K. Takahashi, and S. Yamanaka Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors Cell 126 2006 663 676
36. K. Takahashi, K. Okita, M. Nakagawa, and S. Yamanaka Induction of pluripotent stem cells from fibroblast cultures Nat. Protoc. 2 2007 3081 3089
37. K. Takahashi, K. Tanabe, M. Ohnuki, M. Narita, T. Ichisaka, K. Tomoda, and S. Yamanaka Induction of pluripotent stem cells from adult human fibroblasts by defined factors Cell 131 2007 861 872
38. R.C. Trievel, and A. Shilatifard WDR5, a complexed protein Nat. Struct. Mol. Biol. 16 2009 678 680
39. J. Utikal, J.M. Polo, M. Stadtfeld, N. Maherali, W. Kulalert, R.M. Walsh, A. Khalil, J.G. Rheinwald, and K. Hochedlinger Immortalization eliminates a roadblock during cellular reprogramming into iPS cells Nature 460 2009 1145 1148
40. Y. Wang, K.J. Han, X.W. Pang, H.A. Vaughan, W. Qu, X.Y. Dong, J.R. Peng, H.T. Zhao, J.A. Rui, and X.S. Leng Large scale identification of human hepatocellular carcinoma-associated antigens by autoantibodies J. Immunol. 169 2002 1102 1109
41. Z. Wang, C. Zang, K. Cui, D.E. Schones, A. Barski, W. Peng, and K. Zhao Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes Cell 138 2009 1019 1031
42. T. Wang, K. Chen, X. Zeng, J. Yang, Y. Wu, X. Shi, B. Qin, L. Zeng, M.A. Esteban, G. Pan, and D. Pei The histone demethylases Jhdm1a/1b enhance somatic cell reprogramming in a vitamin-C-dependent manner Cell Stem Cell 9 2011 575 587
43. J. Wysocka, T. Swigut, T.A. Milne, Y. Dou, X. Zhang, A.L. Burlingame, R.G. Roeder, A.H. Brivanlou, and C.D. Allis WDR5 associates with histone H3 methylated at K4 and is essential for H3 K4 methylation and vertebrate development Cell 121 2005 859 872
44. J. Yu, M.A. Vodyanik, K. Smuga-Otto, J. Antosiewicz-Bourget, J.L. Frane, S. Tian, J. Nie, G.A. Jonsdottir, V. Ruotti, and R. Stewart Induced pluripotent stem cell lines derived from human somatic cells Science 318 2007 1917 1920
45. B. Langmead, C. Trapnell, M. Pop, and S.L. Salzberg Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Genome Biol. 10 2009 R25
46. T. Liu, J.A. Ortiz, L. Taing, C.A. Meyer, B. Lee, Y. Zhang, H. Shin, S.S. Wong, J. Ma, and Y. Lei Cistrome: an integrative platform for transcriptional regulation studies Genome Biol. 12 2011 R83
47. V. Matys, O.V. Kel-Margoulis, E. Fricke, I. Liebich, S. Land, A. Barre-Dirrie, I. Reuter, D. Chekmenev, M. Krull, and K. Hornischer TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes Nucleic Acids Res. 34 Database issue 2006 D108 D110
48. H. Shin, T. Liu, A.K. Manrai, and X.S. Liu CEAS: cis-regulatory element annotation system Bioinformatics 25 2009 2605 2606
49. I.H. Su, A. Basavaraj, A.N. Krutchinsky, O. Hobert, A. Ullrich, B.T. Chait, and A. Tarakhovsky Ezh2 controls B cell development through histone H3 methylation and Igh rearrangement Nat. Immunol. 4 2003 124 131
50. A. Valouev, D.S. Johnson, A. Sundquist, C. Medina, E. Anton, S. Batzoglou, R.M. Myers, and A. Sidow Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data Nat. Methods 5 2008 829 834
51. L. Wang, Z. Feng, X. Wang, X. Wang, and X. Zhang DEGseq: an R package for identifying differentially expressed genes from RNA-seq data Bioinformatics 26 2010 136 138