Distinct and Combinatorial Functions of Jmjd2b/Kdm4b and Jmjd2c/Kdm4c in Mouse Embryonic Stem Cell Identity

Molecular Cell

Volumn 53, Issue 1, 2014, Pages 32-48

  Das, Partha Pratim ^a   Shao, Zhen ^a   Beyaz, Semir ^a   Apostolou, Eftychia ^c,d   Pinello, Luca ^e   Angeles, Alejandro De Los ^a   O'Brien, Kassandra ^a   Atsma, Jennifer Marino ^a   Fujiwara, Yuko ^a   Nguyen, Minh ^a   Ljuboja, Damir ^a   Guo, Guoji ^a   Woo, Andrew ^g   Yuan, Guo Cheng ^e   Onder, Tamer ^a,f   Daley, George ^a,b,c   Hochedlinger, Konrad ^b,c,d   Kim, Jonghwan ^a   Orkin, Stuart H ^a,b  

^a BOSTON CHILDREN S HOSPITAL   (United States)

^b HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^c HARVARD MEDICAL SCHOOL   (United States)

^d MASSACHUSETTS GENERAL HOSPITAL CANCER CENTER   (United States)

^e HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^f KOÇ UNIVERSITY   (Turkey)

^g UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE DEMETHYLASE; JMJD2B PROTEIN; JMJD2C PROTEIN; KDM4B PROTEIN; KDM4C PROTEIN; MYC PROTEIN; POLYCOMB REPRESSIVE COMPLEX 2; RNA; TRANSCRIPTION FACTOR NANOG; UNCLASSIFIED DRUG; HOMEODOMAIN PROTEIN; KDM4B PROTEIN, MOUSE; MYC PROTEIN, MOUSE; NANOG PROTEIN, MOUSE;

ANIMAL CELL; ARTICLE; CELL RENEWAL; CONTROLLED STUDY; EMBRYONIC STEM CELL; ENZYME ANALYSIS; GENE REPRESSION; GENE TARGETING; GENETIC ASSOCIATION; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PLURIPOTENT STEM CELL; PROTEIN FUNCTION; RNA INTERFERENCE; TRANSCRIPTION REGULATION; ANIMAL; CELL LINE; CYTOLOGY; ENZYMOLOGY; GENETIC TRANSCRIPTION; GENETICS; METABOLISM; PHYSIOLOGY;

ANIMALS; CELL LINE; EMBRYONIC STEM CELLS; GENOME-WIDE ASSOCIATION STUDY; HOMEODOMAIN PROTEINS; JUMONJI DOMAIN-CONTAINING HISTONE DEMETHYLASES; MICE; PLURIPOTENT STEM CELLS; POLYCOMB REPRESSIVE COMPLEX 2; PROTO-ONCOGENE PROTEINS C-MYC; TRANSCRIPTION, GENETIC;

EID: 84892369527     PISSN: 10972765     EISSN: 10974164     Source Type: Journal    
DOI: 10.1016/j.molcel.2013.11.011     Document Type: Article

References (33)

1. Agger K., Christensen J., Cloos P.A., Helin K. The emerging functions of histone demethylases. Curr. Opin. Genet. Dev. 2008, 18:159-168.
2. Boyer L.A., Plath K., Zeitlinger J., Brambrink T., Medeiros L.A., Lee T.I., Levine S.S., Wernig M., Tajonar A., Ray M.K., et al. Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature 2006, 441:349-353.
3. Cai L., Rothbart S.B., Lu R., Xu B., Chen W.-Y., Tripathy A., Rockowitz S., Zheng D., Patel D.J., Allis C.D., et al. An H3K36 methylation-engaging Tudor motif of polycomb-like proteins mediates PRC2 complex targeting. Mol. Cell 2013, 49:571-582.
4. Chen X., Xu H., Yuan P., Fang F., Huss M., Vega V.B., Wong E., Orlov Y.L., Zhang W., Jiang J., et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 2008, 133:1106-1117.
5. Chen J., Liu H., Liu J., Qi J., Wei B., Yang J., Liang H., Chen Y., Chen J., Wu Y., et al. H3K9 methylation is a barrier during somatic cell reprogramming into iPSCs. Nat. Genet. 2013, 45:34-42.
6. Cherry A.B.C., Daley G.Q. Reprogramming cellular identity for regenerative medicine. Cell 2012, 148:1110-1122.
7. Cloos P.A.C., Christensen J., Agger K., Maiolica A., Rappsilber J., Antal T., Hansen K.H., Helin K. The putative oncogene GASC1 demethylates tri- and dimethylated lysine 9 on histone H3. Nature 2006, 442:307-311.
8. Fazzio T.G., Huff J.T., Panning B. An RNAi screen of chromatin proteins identifies Tip60-p400 as a regulator of embryonic stem cell identity. Cell 2008, 134:162-174.
9. Hu G., Kim J., Xu Q., Leng Y., Orkin S.H., Elledge S.J. A genome-wide RNAi screen identifies a new transcriptional module required for self-renewal. Genes Dev. 2009, 23:837-848.
10. Kagey M.H., Newman J.J., Bilodeau S., Zhan Y., Orlando D.A., van Berkum N.L., Ebmeier C.C., Goossens J., Rahl P.B., Levine S.S., et al. Mediator and cohesin connect gene expression and chromatin architecture. Nature 2010, 467:430-435.
11. Kim J., Chu J., Shen X., Wang J., Orkin S.H. An extended transcriptional network for pluripotency of embryonic stem cells. Cell 2008, 132:1049-1061.
12. Kim J., Cantor A.B., Orkin S.H., Wang J. Use of in vivo biotinylation to study protein-protein and protein-DNA interactions in mouse embryonic stem cells. Nat. Protoc. 2009, 4:506-517.
13. Kim J., Woo A.J., Chu J., Snow J.W., Fujiwara Y., Kim C.G., Cantor A.B., Orkin S.H. A Myc network accounts for similarities between embryonic stem and cancer cell transcription programs. Cell 2010, 143:313-324.
14. Lee T.I., Jenner R.G., Boyer L.A., Guenther M.G., Levine S.S., Kumar R.M., Chevalier B., Johnstone S.E., Cole M.F., Isono K.-I., et al. Control of developmental regulators by Polycomb in human embryonic stem cells. Cell 2006, 125:301-313.
15. Loh Y.H., Zhang W., Chen X., George J., Ng H.H. Jmjd1a and Jmjd2c histone H3 Lys 9 demethylases regulate self-renewal in embryonic stem cells. Genes Dev. 2007, 21:2545-2557.
16. Margueron R., Reinberg D. The Polycomb complex PRC2 and its mark in life. Nature 2011, 469:343-349.
17. Meshorer E., Misteli T. Chromatin in pluripotent embryonic stem cells and differentiation. Nat. Rev. Mol. Cell Biol. 2006, 7:540-546.
18. Min I.M., Waterfall J.J., Core L.J., Munroe R.J., Schimenti J., Lis J.T. Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells. Genes Dev. 2011, 25:742-754.
19. Mosammaparast N., Shi Y. Reversal of histone methylation: biochemical and molecular mechanisms of histone demethylases. Annu. Rev. Biochem. 2010, 79:155-179.
20. Nechaev S., Adelman K. Pol II waiting in the starting gates: regulating the transition from transcription initiation into productive elongation. Biochim. Biophys. Acta 2011, 1809:34-45.
21. Orkin S.H., Hochedlinger K. Chromatin connections to pluripotency and cellular reprogramming. Cell 2011, 145:835-850.
22. Pedersen M.T., Helin K. Histone demethylases in development and disease. Trends Cell Biol. 2010, 20:662-671.
23. Peterlin B.M., Price D.H. Controlling the elongation phase of transcription with P-TEFb. Mol. Cell 2006, 23:297-305.
24. Rahl P.B., Lin C.Y., Seila A.C., Flynn R.A., McCuine S., Burge C.B., Sharp P.A., Young R.A. c-Myc regulates transcriptional pause release. Cell 2010, 141:432-445.
25. Shao Z., Zhang Y., Yuan G.-C., Orkin S.H., Waxman D.J. MAnorm: a robust model for quantitative comparison of ChIP-seq data sets. Genome Biol. 2012, 13:R16.
26. Shi L., Sun L., Li Q., Liang J., Yu W., Yi X., Yang X., Li Y., Han X., Zhang Y., et al. Histone demethylase JMJD2B coordinates H3K4/H3K9 methylation and promotes hormonally responsive breast carcinogenesis. Proc. Natl. Acad. Sci. USA 2011, 108:7541-7546.
27. Soufi A., Donahue G., Zaret K.S. Facilitators and impediments of the pluripotency reprogramming factors' initial engagement with the genome. Cell 2012, 151:994-1004.
28. Sridharan R., Tchieu J., Mason M.J., Yachechko R., Kuoy E., Horvath S., Zhou Q., Plath K. Role of the murine reprogramming factors in the induction of pluripotency. Cell 2009, 136:364-377.
29. Takahashi K., Yamanaka S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 2006, 126:663-676.
30. Xie L., Pelz C., Wang W., Bashar A., Varlamova O., Shadle S., Impey S. KDM5B regulates embryonic stem cell self-renewal and represses cryptic intragenic transcription. EMBO J. 2011, 30:1473-1484.
31. Young R.A. Control of the embryonic stem cell state. Cell 2011, 144:940-954.
32. Zhang Y., Liu T., Meyer C.A., Eeckhoute J., Johnson D.S., Bernstein B.E., Nusbaum C., Myers R.M., Brown M., Li W., Liu X.S. Model-based analysis of ChIP-seq (MACS). Genome Biol. 2008, 9:R137.
33. Zhou V.W., Goren A., Bernstein B.E. Charting histone modifications and the functional organization of mammalian genomes. Nat. Rev. Genet. 2011, 12:7-18.