High-Resolution Profiling of Histone Methylations in the Human Genome

Cell

Volumn 129, Issue 4, 2007, Pages 823-837

  Barski, Artem ^a   Cuddapah, Suresh ^a   Cui, Kairong ^a   Roh, Tae Young ^a   Schones, Dustin E ^a   Wang, Zhibin ^a   Wei, Gang ^a   Chepelev, Iouri ^b   Zhao, Keji ^a  

^a NATIONAL HEART LUNG AND BLOOD INSTITUTE   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

DNA; PROTEINS; SYSBIO

Indexed keywords

ARGININE; CTCF PROTEIN; HISTONE; LYSINE; RNA POLYMERASE II; UNCLASSIFIED DRUG; ZINC FINGER PROTEIN;

ARTICLE; CELLULAR DISTRIBUTION; CHROMATIN STRUCTURE; CHROMOSOME BANDING PATTERN; CHROMOSOME HIGH RESOLUTION BANDING ANALYSIS; CONTROLLED STUDY; ENHANCER REGION; GENE ACTIVATION; GENE REPRESSION; GENE SEQUENCE; GENE TECHNOLOGY; GENETIC LINKAGE; GENOME ANALYSIS; HUMAN; HUMAN CELL; HUMAN GENOME; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN METHYLATION; PROTEIN MODIFICATION; SEQUENCE ANALYSIS; T LYMPHOCYTE;

CHROMATIN; CHROMOSOME BREAKAGE; ENHANCER ELEMENTS (GENETICS); EPIGENESIS, GENETIC; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENOME, HUMAN; HISTONE-LYSINE N-METHYLTRANSFERASE; HISTONES; HUMANS; LYMPHOMA; METHYLATION; PROMOTER REGIONS (GENETICS); REGULATORY ELEMENTS, TRANSCRIPTIONAL; RNA POLYMERASE II; TRANS-ACTIVATION (GENETICS);

EID: 34249026300     PISSN: 00928674     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cell.2007.05.009     Document Type: Article

References (54)

1. Abeysinghe S.S., Stenson P.D., Krawczak M., and Cooper D.N. Gross Rearrangement Breakpoint Database (GRaBD). Hum. Mutat. 23 (2004) 219-221
2. Allis C.D., Glover C.V., Bowen J.K., and Gorovsky M.A. Histone variants specific to the transcriptionally active, amitotically dividing macronucleus of the unicellular eucaryote, Tetrahymena thermophila. Cell 20 (1980) 609-617
3. An W., Kim J., and Roeder R.G. Ordered cooperative functions of PRMT1, p300 and CARM1 in transcriptional activation by p53. Cell 117 (2004) 735-748
4. Bannister A.J., Schneider R., Myers F.A., Thorne A.W., Crane-Robinson C., and Kouzarides T. Spatial distribution of di- and tri-methyl lysine 36 of histone H3 at active genes. J. Biol. Chem. 280 (2005) 17732-17736
5. Bannister A.J., Zegerman P., Partridge J.F., Miska E.A., Thomas J.O., Allshire R.C., and Kouzarides T. Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature 410 (2001) 120-124
6. Bernstein B.E., Humphrey E.L., Erlich R.L., Schneider R., Bouman P., Liu J.S., Kouzarides T., and Schreiber S.L. Methylation of histone H3 Lys 4 in coding regions of active genes. Proc. Natl. Acad. Sci. USA 99 (2002) 8695-8700
7. Bernstein B.E., Kamal M., Lindblad-Toh K., Bekiranov S., Bailey D.K., Huebert D.J., McMahon S., Karlsson E.K., Kulbokas III E.J., Gingeras T.R., et al. Genomic maps and comparative analysis of histone modifications in human and mouse. Cell 120 (2005) 169-181
8. 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. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125 (2006) 315-326
9. Bernstein B.E., Meissner A., and Lander E.S. The mammalian epigenome. Cell 128 (2007) 669-681
10. 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 441 (2006) 349-353
11. Bruce K., Myers F.A., Mantouvalou E., Lefevre P., Greaves I., Bonifer C., Tremethick D.J., Thorne A.W., and Crane-Robinson C. The replacement histone H2A.Z in a hyperacetylated form is a feature of active genes in the chicken. Nucleic Acids Res. 33 (2005) 5633-5639
12. Cheng J., Kapranov P., Drenkow J., Dike S., Brubaker S., Patel S., Long J., Stern D., Tammana H., Helt G., et al. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 308 (2005) 1149-1154
13. Craig J.M., and Bickmore W.A. Chromosome bands - flavours to savour. Bioessays 15 (1993) 349-354
14. Crawford G.E., Holt I.E., Whittle J., Webb B.D., Tai D., Davis S., Margulies E.H., Chen Y., Bernat J.A., Ginsburg D., et al. Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Res. 16 (2006) 123-131
15. Gaszner M., and Felsenfeld G. Insulators: exploiting transcriptional and epigenetic mechanisms. Nat. Rev. Genet. 7 (2006) 703-713
16. Guillemette B., and Gaudreau L. Reuniting the contrasting functions of H2A.Z. Biochem Cell Biol 84 (2006) 528-535
17. Hatton R.D., Harrington L.E., Luther R.J., Wakefield T., Janowski K.M., Oliver J.R., Lallone R.L., Murphy K.M., and Weaver C.T. A distal conserved sequence element controls Ifng gene expression by T cells and NK cells. Immunity 25 (2006) 717-729
18. 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. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat. Genet. 39 (2007) 311-318
19. Huang S., Litt M., and Felsenfeld G. Methylation of histone H4 by arginine methyltransferase PRMT1 is essential in vivo for many subsequent histone modifications. Genes Dev. 19 (2005) 1885-1893
20. Kent W.J., Sugnet C.W., Furey T.S., Roskin K.M., Pringle T.H., Zahler A.M., and Haussler D. The Human Genome Browser at UCSC. Genome Res. 12 (2002) 996-1006
21. Kim T.H., Barrera L.O., Zheng M., Qu C., Singer M.A., Richmond T.A., Wu Y., Green R.D., and Ren B. A high-resolution map of active promoters in the human genome. Nature 436 (2005) 876-880
22. Kim T.H., Abdullaev Z.K., Smith A.D., Ching K.A., Loukinov D.I., Green R.D., Zhang M.Q., Lobanenkov V.V., and Ren B. Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell 128 (2007) 1231-1245
23. Kouzarides T. Chromatin modifications and their function. Cell 128 (2007) 693-705
24. Lee Y.H., Koh S.S., Zhang X., Cheng X., and Stallcup M.R. Synergy among nuclear receptor coactivators: selective requirement for protein methyltransferase and acetyltransferase activities. Mol. Cell. Biol. 22 (2002) 3621-3632
25. Lee C.K., Shibata Y., Rao B., Strahl B.D., and Lieb J.D. Evidence for nucleosome depletion at active regulatory regions genome-wide. Nat. Genet. 36 (2004) 900-905
26. 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. Control of developmental regulators by Polycomb in human embryonic stem cells. Cell 125 (2006) 301-313
27. Liu C.L., Kaplan T., Kim M., Buratowski S., Schreiber S.L., Friedman N., and Rando O.J. Single-nucleosome mapping of histone modifications in S. cerevisiae. PLoS Biol. 3 (2005) e328
28. Loots G.G., Locksley R.M., Blankespoor C.M., Wang Z.E., Miller W., Rubin E.M., and Frazer K.A. Identification of a coordinate regulator of interleukins 4, 13 and 5 by cross-species sequence comparisons. Science 288 (2000) 136-140
29. Meneghini M.D., Wu M., and Madhani H.D. Conserved histone variant H2A.Z protects euchromatin from the ectopic spread of silent heterochromatin. Cell 112 (2003) 725-736
30. Miller W., Makova K.D., Nekrutenko A., and Hardison R.C. Comparative genomics. Annu. Rev. Genomics Hum. Genet. 5 (2004) 15-56
31. Mito Y., Henikoff J.G., and Henikoff S. Histone replacement marks the boundaries of cis-regulatory domains. Science 315 (2007) 1408-1411
32. Okada Y., Feng Q., Lin Y., Jiang Q., Li Y., Coffield V.M., Su L., Xu G., and Zhang Y. hDOT1L links histone methylation to leukemogenesis. Cell 121 (2005) 167-178
33. Pennacchio L.A., and Rubin E.M. Genomic strategies to identify mammalian regulatory sequences. Nat. Rev. Genet. 2 (2001) 100-109
34. 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. Partitioning and plasticity of repressive histone methylation states in mammalian chromatin. Mol. Cell 12 (2003) 1577-1589
35. Pokholok D.K., Harbison C.T., Levine S., Cole M., Hannett N.M., Lee T.I., Bell G.W., Walker K., Rolfe P.A., Herbolsheimer E., et al. Genome-wide map of nucleosome acetylation and methylation in yeast. Cell 122 (2005) 517-527
36. Raisner R.M., Hartley P.D., Meneghini M.D., Bao M.Z., Liu C.L., Schreiber S.L., Rando O.J., and Madhani H.D. Histone variant H2A.Z marks the 5′ ends of both active and inactive genes in euchromatin. Cell 123 (2005) 233-248
37. Rangasamy D., Berven L., Ridgway P., and Tremethick D.J. Pericentric heterochromatin becomes enriched with H2A.Z during early mammalian development. EMBO J. 22 (2003) 1599-1607
38. Roh T.Y., Cuddapah S., and Zhao K. Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping. Genes Dev. 19 (2005) 542-552
39. Roh T.Y., Ngau W.C., Cui K., Landsman D., and Zhao K. High-resolution genome-wide mapping of histone modifications. Nat. Biotechnol. 22 (2004) 1013-1016
40. Roh T.Y., Cuddapah S., Cui K., and Zhao K. The genomic landscape of histone modifications in human T cells. Proc. Natl. Acad. Sci. USA 103 (2006) 15782-15787
41. Roh T.Y., Wei G., Farrell C.M., and Zhao K. Genome-wide prediction of conserved and nonconserved enhancers by histone acetylation patterns. Genome Res. 17 (2007) 74-81
42. Schotta G., Lachner M., Sarma K., Ebert A., Sengupta R., Reuter G., Reinberg D., and Jenuwein T. A silencing pathway to induce H3-K9 and H4-K20 trimethylation at constitutive heterochromatin. Genes Dev. 18 (2004) 1251-1262
43. Schubeler D., MacAlpine D.M., Scalzo D., Wirbelauer C., Kooperberg C., van Leeuwen F., Gottschling D.E., O'Neill L.P., Turner B.M., Delrow J., et al. The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote. Genes Dev. 18 (2004) 1263-1271
44. Sekinger E.A., Moqtaderi Z., and Struhl K. Intrinsic histone-DNA interactions and low nucleosome density are important for preferential accessibility of promoter regions in yeast. Mol. Cell 18 (2005) 735-748
45. Shnyreva M., Weaver W.M., Blanchette M., Taylor S.L., Tompa M., Fitzpatrick D.R., and Wilson C.B. Evolutionarily conserved sequence elements that positively regulate IFN-gamma expression in T cells. Proc. Natl. Acad. Sci. USA 101 (2004) 12622-12627
46. Sims J.K., Houston S.I., Magazinnik T., and Rice J.C. A trans-tail histone code defined by monomethylated H4 Lys-20 and H3 Lys-9 demarcates distinct regions of silent chromatin. J. Biol. Chem. 281 (2006) 12760-12766
47. 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. Suz12 binds to silenced regions of the genome in a cell-type-specific manner. Genome Res. 16 (2006) 890-900
48. Strahl B.D., Grant P.A., Briggs S.D., Sun Z.W., Bone J.R., Caldwell J.A., Mollah S., Cook R.G., Shabanowitz J., Hunt D.F., and Allis C.D. Set2 is a nucleosomal histone H3-selective methyltransferase that mediates transcriptional repression. Mol. Cell. Biol. 22 (2002) 1298-1306
49. Su A.I., Wiltshire T., Batalov S., Lapp H., Ching K.A., Block D., Zhang J., Soden R., Hayakawa M., Kreiman G., et al. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc. Natl. Acad. Sci. USA 101 (2004) 6062-6067
50. Talasz H., Lindner H.H., Sarg B., and Helliger W. Histone H4-lysine 20 monomethylation is increased in promoter and coding -regions of active genes and correlates with hyperacetylation. J. Biol. Chem. 280 (2005) 38814-38822
51. Vakoc C.R., Sachdeva M.M., Wang H., and Blobel G.A. Profile of histone lysine methylation across transcribed mammalian chromatin. Mol. Cell. Biol. 26 (2006) 9185-9195
52. Yuan G.C., Liu Y.J., Dion M.F., Slack M.D., Wu L.F., Altschuler S.J., and Rando O.J. Genome-scale identification of nucleosome positions in S. cerevisiae. Science 309 (2005) 626-630
53. Zhang Y., and Rowley J.D. Chromatin structural elements and chromosomal translocations in leukemia. DNA Repair (Amst.) 5 (2006) 1282-1297
54. Zhang J., Zhang L., and Coombes K.R. Gene sequence signatures revealed by mining the UniGene affiliation network. Bioinformatics 22 (2006) 385-391