H3K27me3 forms BLOCs over silent genes and intergenic regions and specifies a histone banding pattern on a mouse autosomal chromosome

Genome Research

Volumn 19, Issue 2, 2009, Pages 221-233

  Pauler, Florian M ^a   Sloane, Mathew A ^a   Huang, Ru ^a   Regha, Kakkad ^a   Koerner, Martha V ^a   Tamir, Ido ^b   Sommer, Andreas ^b   Aszodi, Andras ^b   Jenuwein, Thomas ^b   Barlow, Denise P ^a  

^a ERICH SCHMID INSTITUTE OF MATERIALS SCIENCE   (Austria)

^b RESEARCH INSTITUTE OF MOLECULAR PATHOLOGY   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE H3; LYSINE; SPACER DNA;

ALGORITHM; ANIMAL CELL; ARTICLE; AUTOSOME; BASE PAIRING; BROAD LOCAL ENRICHMENT; CHROMATIN; CHROMOSOME 17; EMBRYO; FIBROBLAST; LONG INTERSPERSED REPEAT; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN MODIFICATION; RETROPOSON; SHORT INTERSPERSED REPEAT; SILENT GENE; TRANSPOSON;

ALGORITHMS; ANIMALS; CHROMATIN IMMUNOPRECIPITATION; CHROMOSOME BANDING; CHROMOSOMES, MAMMALIAN; DNA, INTERGENIC; GENE SILENCING; HISTONES; LYSINE; METHYLATION; MICE; MODELS, BIOLOGICAL; PROTEIN METHYLTRANSFERASES; PROTEIN MULTIMERIZATION; PROTEIN PROCESSING, POST-TRANSLATIONAL; SUBSTRATE SPECIFICITY;

MAMMALIA;

EID: 59949085939     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.080861.108     Document Type: Article

References (39)

1. Azuara, V., Perry, P., Sauer, S., Spivakov, M., Jorgensen, H.F., John, R.M., Gouti, M., Casanova, M., Warnes, G., Merkenschlager, M. et al. 2006. Chromatin signatures of pluripotent cell lines. Nat. Cell Biol. 8: 532-538.
2. Barski, A., Cuddapah, S., Cui, K., Roh, T.Y., Schones, D.E., Wang, Z., Wei, G., Chepelev, I., and Zhao, K. 2007. High-resolution profiling of histone methylations in the human genome. Cell 129: 823-837.
3. Beisel, C., Buness, A., Roustan-Espinosa, I.M., Koch, B., Schmitt, S., Haas, S.A., Hild, M., Katsuyama, T., and Paro, R. 2007. Comparing active and repressed expression states of genes controlled by the Polycomb/Trithorax group proteins. Proc. Natl. Acad. Sci. 104: 16615-16620.
4. 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. 2006a. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125: 315-326.
5. Bernstein, E., Duncan, E.M., Masui, O., Gil, J., Heard, E., and Allis, C.D. 2006b. Mouse polycomb proteins bind differentially to methylated histone H3 and RNA and are enriched in facultative heterochromatin. Mol. Cell. Biol. 26: 2560-2569.
6. Bernstein, B.E., Meissner, A., and Lander, E.S. 2007. The mammalian epigenome. Cell 128: 669-681.
7. 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. 2006. Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature 441: 349-353.
8. Boyle, A.L., Ballard, S.G., and Ward, D.C. 1990. Differential distribution of long and short interspersed element sequences in the mouse genome: Chromosome karyotyping by fluorescence in situ hybridization. Proc. Natl. Acad. Sci. 87: 7757-7761.
9. Bracken, A.P., Dietrich, N., Pasini, D., Hansen, K.H., and Helin, K. 2006. Genome-wide mapping of Polycomb target genes unravels their roles in cell fate transitions. Genes &Dev. 20: 1123-1136.
10. Buck, M.J., Nobel, A.B., and Lieb, J.D. 2005. ChIPOTle: A user-friendly tool for the analysis ofChIP-chip data. Genome Biol. 6: R97. doi: 10.1186/gb-2005-6-11-r97.
11. Chadwick, B.P. 2007. Variation in Xi chromatin organization and correlation of the H3K27me3 chromatin territories to transcribed sequences by microarray analysis. Chromosoma 116: 147-157.
12. Chadwick, B.P. and Willard, H.F. 2004. Multiple spatially distinct types of facultative heterochromatin on the human inactive X chromosome. Proc. Natl. Acad. Sci. 101: 17450-17455.
13. Chamberlain, S.J., Yee, D., and Magnuson, T. 2008. Polycomb repressive complex 2 is dispensable for maintenance of embryonic stem cell pluripotency. Stem Cells 26: 1496-1505.
14. Craig, J.M. and Bickmore, W.A. 1993. Chromosome bands-Flavours to savour. Bioessays 15: 349-354.
15. Day, N., Hemmaplardh, A., Thurman, R.E., Stamatoyannopoulos, J.A., and Noble, W.S. 2007. Unsupervised segmentation of continuous genomic data. Bioinformatics 23: 1424-1426.
16. Garrick, D., De Gobbi, M., Samara, V., Rugless, M., Holland, M., Ayyub, H., Lower, K., Sloane-Stanley, J., Gray, N., Koch, C., et al. 2008. The role of the polycomb complex in silencing α-globin gene expression in nonerythroid cells. Blood 112: 3889-3899.
17. Heintzman, N.D., Stuart, R.K., Hon, G., Fu, Y., Ching, C.W., Hawkins, R.D., Barrera, L.O., Van Calcar, S., Qu, C., Ching, K.A., et al. 2007. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat. Genet. 39: 311-318.
18. Karachentsev, D., Sarma, K., Reinberg, D., and Steward, R. 2005. PR-Set7-dependent methylation of histone H4 Lys 20 functions in repression of gene expression and is essential for mitosis. Genes &Dev. 19: 431-435.
19. Kazazian Jr., H.H. 2004. Mobile elements: Drivers of genome evolution. Science 303: 1626-1632.
20. 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.
21. Martens, J.H., O'Sullivan, R.J., Braunschweig, U., Opravil, S., Radolf, M., Steinlein, P., and Jenuwein, T. 2005. The profile of repeat-associated histone lysine methylation states in the mouse epigenome. EMBO J. 24: 800-812.
22. 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: 552-560.
23. Pan, G., Tian, S., Nie, J., Yang, C., Ruotti, V., Wei, H., Jonsdottir, G.A., Stewart, R., and Thomson, J.A. 2007. Whole-genome analysis of histone H3 lysine 4 and lysine 27 methylation in human embryonic stem cells. Cell Stem Cell 1: 299-312.
24. Papp, B. and Muller, J. 2006. Histone trimethylation and the maintenance of transcriptional ON and OFF states by trxG and PcG proteins. Genes & Dev. 20: 2041-2054.
25. 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.
26. 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.
27. Peters, A.H., Kubicek, S., Mechtler, K., O'Sullivan, R.J., Derijck, A.A., Perez-Burgos, L., Kohlmaier, A., Opravil, S., Tachibana, M., Shinkai, Y. et al. 2003. Partitioning and plasticity of repressive histone methylation states in mammalian chromatin. Mol. Cell 12: 1577-1589.
28. Regha, K., Sloane, M.A., Huang, R., Pauler, F.M., Warczok, K.E., Melikant, B.,Radolf, M., Martens, J.H., Schotta, G., Jenuwein, T., et al. 2007. Active and repressive chromatin are interspersed without spreading in an imprinted gene cluster in the mammalian genome. Mol. Cell 27: 353-366.
29. Ringrose, L. 2007. Polycomb comes of age: Genome-wide profiling of target sites. Curr. Opin. Cell Biol. 19: 290-297.
30. 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. 103: 15782-15787.
31. Schones, D.E. and Zhao, K. 2008. Genome-wide approaches to studying chromatin modifications. Nat. Rev. Genet. 9: 179-191.
32. Schotta, G., Lachner, M., Sarma, K., Ebert, A., Sengupta, R., Reuter, G., Reinberg, D., and Jenuwein, T. 2004. A silencing pathway to induce H3-K9 and H4-K20 trimethylation at constitutive heterochromatin. Genes &Dev. 18: 1251-1262.
33. Schwartz, Y.B., Kahn, T.G., Nix, D.A., Li, X.Y., Bourgon, R., Biggin, M., and Pirrotta, V. 2006. Genome-wide analysis of Polycomb targets in Drosophila melanogaster. Nat. Genet. 38: 700-705.
34. Smith, E.R., Lee, M.G., Winter, B., Droz, N.M., Eissenberg, J.C., Shiekhattar, R., and Shilatifard, A. 2008. Drosophila UTX is a histone H3 Lys27 demethylase that colocalizes with the elongating form of RNA polymerase II. Mol. Cell. Biol. 28: 1041-1046.
35. Squazzo, S.L., O'Geen, H., Komashko, V.M., Krig, S.R., Jin, V.X., Jang, S.W., Margueron, R., Reinberg, D., Green, R., and Farnham, P.J. 2006. Suz12 binds to silenced regions of the genome in a cell-type-specific manner. Genome Res. 16: 890-900.
36. Thurman, R.E., Day, N., Noble, W.S., and Stamatoyannopoulos, J.A. 2007. Identification of higher-order functional domains in the human ENCODE regions. Genome Res. 17: 917-927.
37. Weil, C. and Martienssen, R. 2008. Epigenetic interactions between transposons and genes: Lessons from plants. Curr. Opin. Genet. Dev. 18: 188-192.
38. Wutz, A. 2007. Xist function: Bridging chromatin and stem cells. Trends Genet. 23: 457-464.
39. Zhao, X.D., Han, X., Chew, J.L., Liu, J., Chiu, K.P., Choo, A., Orlov, Y.L., Sung, W.K., Shahab, A., Kuznetsove, V.A., et al. 2007. Whole-genome mapping of histone H3 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells. Cell Stem Cell 1: 286-298.