Visualization of multivalent histone modification in a single cell reveals highly concerted epigenetic changes on differentiation of embryonic stem cells

Nucleic Acids Research

Volumn 41, Issue 15, 2013, Pages 7231-7239

  Hattori, Naoko ^a   Niwa, Tohru ^a   Kimura, Kana ^a   Helin, Kristian ^b,c   Ushijima, Toshikazu ^a  

^a NATIONAL CANCER CENTER RESEARCH INSTITUTE   (Japan)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

^c UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE H3; MESSENGER RNA; OCTAMER TRANSCRIPTION FACTOR 4; RNA POLYMERASE II;

ANIMAL CELL; ANIMAL TISSUE; ARTICLE; CELL DIFFERENTIATION; CELL HETEROGENEITY; CELL POPULATION; CONTROLLED STUDY; EMBRYO; EMBRYONIC STEM CELL; EPIGENETICS; HISTONE ACETYLATION; HISTONE MODIFICATION; HUMAN; HUMAN TISSUE; MALE; MOUSE; NONHUMAN; OCT 4 GENE; PHENOTYPIC VARIATION; PRIORITY JOURNAL; PROTEIN DETERMINATION; PROTEIN EXPRESSION; PROTEIN PROTEIN INTERACTION; SIGNAL TRANSDUCTION; SINGLE CELL ANALYSIS; WILD TYPE;

ANIMALS; CELL DIFFERENTIATION; CELL NUCLEUS; CHROMATIN; EMBRYONIC STEM CELLS; EPIGENESIS, GENETIC; FIBROBLASTS; HISTONES; HUMANS; MALE; MICE; MICE, INBRED C57BL; POLYCOMB REPRESSIVE COMPLEX 2; SENSITIVITY AND SPECIFICITY;

EID: 84883475114     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt528     Document Type: Article

References (28)

1. Meissner,A. (2010) Epigenetic modifications in pluripotent and differentiated cells. Nat. Biotechnol., 28, 1079-1088
2. Kondo,Y. (2009) Epigenetic cross-talk between DNA methylation and histone modifications in human cancers. Yonsei Med. J., 50, 455-463
3. Bernstein,B.E., Mikkelsen,T.S., Xie,X., Kamal,M., Huebert,D.J., Cuff,J., Fry,B., Meissner,A., Wernig,M., Plath,K. et al. (2006) A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell, 125, 315-326
4. Lien,W.H., Guo,X., Polak,L., Lawton,L.N., Young,R.A., Zheng,D. and Fuchs,E. (2011) Genome-wide maps of histone modifications unwind in vivo chromatin states of the hair follicle lineage. Cell Stem Cell, 9, 219-232
5. Mikkelsen,T.S., Ku,M., Jaffe,D.B., Issac,B., Lieberman,E., Giannoukos,G., Alvarez,P., Brockman,W., Kim,T.K., Koche,R.P. et al. (2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature, 448, 553-560
6. Rada-Iglesias,A., Bajpai,R., Swigut,T., Brugmann,S.A., Flynn,R.A. and Wysocka,J. (2011) A unique chromatin signature uncovers early developmental enhancers in humans. Nature, 470, 279-283
7. Xiao,S., Xie,D., Cao,X., Yu,P., Xing,X., Chen,C.C., Musselman,M., Xie,M., West,F.D., Lewin,H.A. et al. (2012) Comparative epigenomic annotation of regulatory DNA. Cell, 149, 1381-1392
8. Ruthenburg,A.J., Li,H., Milne,T.A., Dewell,S., McGinty,R.K., Yuen,M., Ueberheide,B., Dou,Y., Muir,T.W., Patel,D.J. et al. (2011) Recognition of a mononucleosomal histone modification pattern by BPTF via multivalent interactions. Cell, 145, 692-706
9. Vastenhouw,N.L., Zhang,Y., Woods,I.G., Imam,F., Regev,A., Liu,X.S., Rinn,J. and Schier,A.F. (2010) Chromatin signature of embryonic pluripotency is established during genome activation. Nature, 464, 922-926
10. Roh,T.Y., Cuddapah,S., Cui,K. and Zhao,K. (2006) The genomic landscape of histone modifications in human T cells. Proc. Natl Acad. Sci. USA, 103, 15782-15787
11. Tsai,W.W., Wang,Z., Yiu,T.T., Akdemir,K.C., Xia,W., Winter,S., Tsai,C.Y., Shi,X., Schwarzer,D., Plunkett,W. et al. (2010) TRIM24 links a non-canonical histone signature to breast cancer. Nature, 468, 927-932
12. Geisberg,J.V. and Struhl,K. (2004) Quantitative sequential chromatin immunoprecipitation, a method for analyzing cooccupancy of proteins at genomic regions in vivo. Nucleic Acids Res., 32, e151
13. Voigt,P., LeRoy,G., Drury,W.J3rd, Zee,B.M., Son,J., Beck,D.B., Young,N.L., Garcia,B.A and Reinberg,D. (2012) Asymmetrically modified nucleosomes. Cell, 151, 181-193
14. Soderberg,O., Gullberg,M., Jarvius,M., Ridderstrale,K., Leuchowius,K.J., Jarvius,J., Wester,K., Hydbring,P., Bahram,F., Larsson,L.G. et al. (2006) Direct observation of individual endogenous protein complexes in situ by proximity ligation. Nat. Methods, 3, 995-1000
15. Pasini,D., Bracken,A.P., Hansen,J.B., Capillo,M. and Helin,K. (2007) The polycomb group protein Suz12 is required for embryonic stem cell differentiation. Mol. Cell. Biol., 27, 3769-3779
16. Perez-Burgos,L., Peters,A.H., Opravil,S., Kauer,M., Mechtler,K. and Jenuwein,T. (2004) Generation and characterization of methyl-lysine histone antibodies. Methods Enzymol., 376, 234-254
17. Kimura,H., Hayashi-Takanaka,Y., Goto,Y., Takizawa,N. and Nozaki,N. (2008) The organization of histone H3 modifications as revealed by a panel of specific monoclonal antibodies. Cell Struct. Funct., 33, 61-73
18. Kim,T.H., Barrera,L.O., Qu,C., Van Calcar,S., Trinklein,N.D., Cooper,S.J., Luna,R.M., Glass,C.K., Rosenfeld,M.G., Myers,R.M. et al. (2005) Direct isolation and identification of promoters in the human genome. Genome Res., 15, 830-839
19. Ku,M., Koche,R.P., Rheinbay,E., Mendenhall,E.M., Endoh,M., Mikkelsen,T.S., Presser,A., Nusbaum,C., Xie,X., Chi,A.S. et al. (2008) Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet., 4, e1000242
20. Pasini,D., Bracken,A.P., Jensen,M.R., Lazzerini Denchi,E. and Helin,K. (2004) Suz12 is essential for mouse development and for EZH2 histone methyltransferase activity. EMBO J., 23, 4061-4071
21. Lee,E.R., Murdoch,F.E. and Fritsch,M.K. (2007) High histone acetylation and decreased polycomb repressive complex 2 member levels regulate gene specific transcriptional changes during early embryonic stem cell differentiation induced by retinoic acid. Stem Cells, 25, 2191-2199
22. Feldman,N., Gerson,A., Fang,J., Li,E., Zhang,Y., Shinkai,Y., Cedar,H. and Bergman,Y. (2006) G9a-mediated irreversible epigenetic inactivation of Oct-3/4 during early embryogenesis. Nat. Cell Biol., 8, 188-194
23. Chakravarthy,H., Ormsbee,B.D., Mallanna,S.K. and Rizzino,A. (2011) Rapid activation of the bivalent gene Sox21 requires displacement of multiple layers of gene-silencing machinery. FASEB J., 25, 206-218
24. 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. et al. (2006) Control of developmental regulators by Polycomb in human embryonic stem cells. Cell, 125, 301-313
25. Hanna,J.H., Saha,K. and Jaenisch,R. (2010) Pluripotency and cellular reprogramming: facts, hypotheses, unresolved issues. Cell, 143, 508-525
26. Chi,P., Allis,C.D. and Wang,G.G. (2010) Covalent histone modifications-miswritten, misinterpreted and mis-erased in human cancers. Nat. Rev. Cancer, 10, 457-469
27. Black,J.C., Van Rechem,C. and Whetstine,J.R. (2012) Histone lysine methylation dynamics: establishment, regulation, and biological impact. Mol. Cell, 48, 491-507
28. Takeshima,H., Yamashita,S., Shimazu,T., Niwa,T. and Ushijima,T. (2009) The presence of RNA polymerase II, active or stalled, predicts epigenetic fate of promoter CpG islands. Genome Res., 19, 1974-1982