CpG islands under selective pressure are enriched with H3K4me3, H3K27ac and H3K36me3 histone modifications

BMC Evolutionary Biology

Volumn 13, Issue 1, 2013, Pages

  Akhtar, Most Mauluda ^a   Scala, Giovanni ^a,b   Cocozza, Sergio ^a   Miele, Gennaro ^a,b   Monticelli, Antonella ^a,c  

^a UNIVERSITY OF NAPLES FEDERICO II   (Italy)

^b INFN SEZIONE DI NAPOLI   (Italy)

^c CNR   (Italy)

Author keywords

CpG islands; Epigenetic; H3K27ac; H3K36me3; H3K4me3; Selective pressure

Indexed keywords

ADAPTATION; CELL ORGANELLE; EUKARYOTE; GENE EXPRESSION; GENOMICS; PRESSURE EFFECT; PRIMATE; PROTEIN;

EUKARYOTA; HOMO SAPIENS;

HISTONE; LYSINE;

ACETYLATION; ARTICLE; BIOLOGY; CELL LINE; CHEMISTRY; CHROMATIN; CPG ISLAND; GENETIC EPIGENESIS; GENETIC SELECTION; HUMAN; METABOLISM; METHYLATION; MOLECULAR EVOLUTION; PROMOTER REGION;

ACETYLATION; CELL LINE; CHROMATIN; COMPUTATIONAL BIOLOGY; CPG ISLANDS; EPIGENESIS, GENETIC; EVOLUTION, MOLECULAR; HISTONES; HUMANS; LYSINE; METHYLATION; PROMOTER REGIONS, GENETIC; SELECTION, GENETIC;

EID: 84880031190     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-13-145     Document Type: Article

References (47)

1. A fraction of the mouse genome that is derived from islands of nonmethylated, CpG-rich DNA. Bird A, Taggart M, Frommer M, Miller OJ, Macleod D, Cell 1985 40 1 91 99 10.1016/0092-8674(85)90312-5 2981636 (Pubitemid 15169310)
2. CpG islands-"a rough guide" Illingworth RS, Bird AP, FEBS Lett 2009 583 11 1713 1720 10.1016/j.febslet.2009.04.012 19376112
3. CpG islands as gene markers in the human genome. Larsen F, Gundersen G, Lopez R, Prydz H, Genomics 1992 13 4 1095 1107 10.1016/0888-7543(92)90024-M 1505946
4. Orphan CpG islands identify numerous conserved promoters in the mammalian genome. Illingworth RS, Gruenewald-Schneider U, Webb S, Kerr ARW, James KD, Turner DJ, Smith C, Harrison DJ, Andrews R, Bird AP, PLoS Genet 2010 6 9 1001134 10.1371/journal.pgen.1001134 20885785
5. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Jones PA, Nat Rev Genet 2012 13 7 484 492 10.1038/nrg3230 22641018
6. Intergenic, gene terminal, and intragenic CpG islands in the human genome. Medvedeva YA, Fridman MV, Oparina NJ, Malko DB, Ermakova EO, Kulakovskiy IV, Heinzel A, Makeev VJ, BMC Genomics 2010 11 48 10.1186/1471-2164-11-48 20085634
7. CpG island chromatin: a platform for gene regulation. Blackledge NP, Klose R, Epigenetics: official journal of the DNA Methylation Society 2011 6 2 147 10.4161/epi.6.2.13640
8. The role of chromatin during transcription. Li B, Carey M, Workman JL, Cell 2007 128 4 707 719 10.1016/j.cell.2007.01.015 17320508 (Pubitemid 46273570)
9. Chromatin modifications and their function. Kouzarides T, Cell 2007 128 4 693 705 10.1016/j.cell.2007.02.005 17320507 (Pubitemid 46273577)
10. Regulation of MLL1 H3K4 methyltransferase activity by its core components. Dou Y, Milne TA, Ruthenburg AJ, Lee S, Lee JW, Verdine GL, Allis CD, Roeder RG, Nat Struct Mol Biol 2006 13 8 713 719 10.1038/nsmb1128 16878130 (Pubitemid 44175164)
11. Mammalian ASH1L is a histone methyltransferase that occupies the transcribed region of active genes. Gregory GD, Vakoc CR, Rozovskaia T, Zheng X, Patel S, Nakamura T, Canaani E, Blobel GA, Mol Cell Biol 2007 27 24 8466 10.1128/MCB.00993-07 17923682
12. A chromatin landmark and transcription initiation at most promoters in human cells. Guenther MG, Levine SS, Boyer LA, Jaenisch R, Young RA, Cell 2007 130 1 77 88 10.1016/j.cell.2007.05.042 17632057 (Pubitemid 47031323)
13. H3K4me3 inversely correlates with DNA methylation at a large class of non-CpG-island containing start sites. Balasubramanian D, Akhtar-Zaidi B, Song L, Bartels CF, Veigl M, Beard L, Myeroff L, Guda K, Lutterbaugh J, Willis J, et al. Genome Med 2012 4 5 47 10.1186/gm346 22640407
14. DNA methylation dictates histone H3K4 methylation. Okitsu CY, Hsieh CL, Mol Cell Biol 2007 27 7 2746 10.1128/MCB.02291-06 17242185 (Pubitemid 46581362)
15. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, Fry B, Meissner A, Wernig M, Plath K, Cell 2006 125 2 315 326 10.1016/j.cell.2006. 02.041 16630819
16. Genome-wide profiling of histone h3 lysine 4 and lysine 27 trimethylation reveals an epigenetic signature in prostate carcinogenesis. Ke XS, Qu Y, Rostad K, Li WC, Lin B, Halvorsen OJ, Haukaas SA, Jonassen I, Petersen K, Goldfinger N, PLoS One 2009 4 3 4687 10.1371/journal.pone.0004687 19262738
17. Integrative epigenomic and genomic analysis of malignant pheochromocytoma. Sandgren J, Andersson R, Rada-Iglesias A, Enroth S, Akerstrom G, Dumanski JP, Komorowski J, Westin G, Wadelius C, Exp Mol Med 2010 42 7 484 10.3858/emm.2010.42.7.050 20534969
18. Genome-wide histone methylation profile for heart failure. Kaneda R, Takada S, Yamashita Y, Choi YL, Nonaka-Sarukawa M, Soda M, Misawa Y, Isomura T, Shimada K, Mano H, Genes Cells 2009 14 1 69 77 10.1111/j.1365-2443.2008.01252.x 19077033
19. Combinatorial patterns of histone acetylations and methylations in the human genome. Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, Cuddapah S, Cui K, Roh TY, Peng W, Zhang MQ, et al. Nat Genet 2008 40 7 897 903 10.1038/ng.154 18552846 (Pubitemid 351913645)
20. High-resolution profiling of histone methylations in the human genome. Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K, Cell 2007 129 4 823 837 10.1016/j.cell.2007.05.009 17512414 (Pubitemid 46802390)
21. Understanding the language of Lys36 methylation at histone H3. Wagner EJ, Carpenter PB, Nat Rev Mol Cell Biol 2012 13 2 115 126 10.1038/nrm3274 22266761
22. Gene regulation for higher cells: a theory. Britten RJ, Davidson EH, Science 1969 165 891 349 357 5789433
23. Gene expression differences among primates are associated with changes in a histone epigenetic modification. Cain CE, Blekhman R, Marioni JC, Gilad Y, Genetics 2011 187 4 1225 1234 10.1534/genetics.110.126177 21321133
24. Human-Specific Histone Methylation Signatures at Transcription Start Sites in Prefrontal Neurons. Shulha HP, Crisci JL, Reshetov D, Tushir JS, Cheung I, Bharadwaj R, Chou HJ, Houston IB, Peter CJ, Mitchell AC, PLoS Biol 2012 10 11 1001427 10.1371/journal.pbio.1001427 23185133
25. An integrated encyclopedia of DNA elements in the human genome. The-ENCODE-Project-Consortium, Nature 2012 489 7414 57 74 10.1038/nature11247 22955616
26. CpG Islands Undermethylation in Human Genomic Regions under Selective Pressure. Cocozza S, Akhtar MM, Miele G, Monticelli A, PLoS One 2011 6 8 23156 10.1371/journal.pone.0023156 21829712
27. Unlocking the secrets of the genome. Celniker SE, Dillon LA, Gerstein MB, Gunsalus KC, Henikoff S, Karpen GH, Kellis M, Lai EC, Lieb JD, MacAlpine DM, et al. Nature 2009 459 7249 927 930 10.1038/459927a 19536255
28. Mapping and analysis of chromatin state dynamics in nine human cell types. Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M, et al. Nature 2011 473 7345 43 49 10.1038/nature09906 21441907
29. Molecular signatures of natural selection. Nielsen R, Annu Rev Genet 2005 39 197 218 10.1146/annurev.genet.39.073003.112420 16285858 (Pubitemid 43011113)
30. A map of recent positive selection in the human genome. Voight BF, Kudaravalli S, Wen X, Pritchard JK, PLoS Biol 2006 4 3 72 10.1371/journal.pbio. 0040072 16494531
31. A draft sequence of the Neandertal genome. Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH, et al. Science 2010 328 5979 710 722 10.1126/science.1188021 20448178
32. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, et al. Genome Res 2005 15 8 1034 1050 10.1101/gr.3715005 16024819 (Pubitemid 41126859)
33. Primate CpG islands are maintained by heterogeneous evolutionary regimes involving minimal selection. Cohen NM, Kenigsberg E, Tanay A, Cell 2011 145 5 773 10.1016/j.cell.2011.04.024 21620139
34. GREAT improves functional interpretation of cis-regulatory regions. McLean CY, Bristor D, Hiller M, Clarke SL, Schaar BT, Lowe CB, Wenger AM, Bejerano G, Nat Biotechnol 2010 28 5 495 501 10.1038/nbt.1630 20436461
35. Evolutionary conservation of histone modifications in mammals. Woo YH, Li WH, Mol Biol Evol 2012 29 7 1757 1767 10.1093/molbev/mss022 22319170
36. CpG islands influence chromatin structure via the CpG-binding protein Cfp1. Thomson JP, Skene PJ, Selfridge J, Clouaire T, Guy J, Webb S, Kerr ARW, Deaton A, Andrews R, James KD, Nature 2010 464 7291 1082 1086 10.1038/nature08924 20393567
37. DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines. Bell JT, Pai AA, Pickrell JK, Gaffney DJ, Pique-Regi R, Degner JF, Gilad Y, Pritchard JK, Genome Biol 2011 12 1 10 10.1186/gb-2011-12-1-r10 21251332
38. Differential chromatin marking of introns and expressed exons by H3K36me3. Kolasinska-Zwierz P, Down T, Latorre I, Liu T, Liu XS, Ahringer J, Nat Genet 2009 41 3 376 381 10.1038/ng.322 19182803
39. Functional relevance of CpG island length for regulation of gene expression. Elango N, Soojin VY, Genetics 2011 187 4 1077 1083 10.1534/genetics.110.126094 21288871
40. Methylation of lysine 4 on histone H3: intricacy of writing and reading a single epigenetic mark. Ruthenburg AJ, Allis CD, Wysocka J, Mol Cell 2007 25 1 15 30 10.1016/j.molcel.2006.12.014 17218268 (Pubitemid 46049068)
41. Epigenetic features are significantly associated with alternative splicing. Zhou Y, Lu Y, Tian W, BMC Genomics 2012 13 1 123 10.1186/1471-2164-13- 123 22455468
42. Epigenetics in alternative pre-mRNA splicing. Luco RF, Allo M, Schor IE, Kornblihtt AR, Misteli T, Cell 2012 144 1 16 26
43. The evolutionary landscape of alternative splicing in vertebrate species. Barbosa-Morais NL, Irimia M, Pan Q, Xiong HY, Gueroussov S, Lee LJ, Slobodeniuc V, Kutter C, Watt S, Colak R, et al. Science 2012 338 6114 1587 1593 10.1126/science.1230612 23258890
44. Personal and population genomics of human regulatory variation. Vernot B, Stergachis AB, Maurano MT, Vierstra J, Neph S, Thurman RE, Stamatoyannopoulos JA, Akey JM, Genome Res 2012 22 9 1689 1697 10.1101/gr.134890.111 22955981
45. CpG islands and the regulation of transcription. Deaton AM, Bird A, Genes Dev 2011 25 10 1010 10.1101/gad.2037511 21576262
46. Detecting recent positive selection in the human genome from haplotype structure. Sabeti PC, Reich DE, Higgins JM, Levine HZ, Richter DJ, Schaffner SF, Gabriel SB, Platko JV, Patterson NJ, McDonald GJ, et al. Nature 2002 419 6909 832 837 10.1038/nature01140 12397357 (Pubitemid 35238568)
47. Detection of nonneutral substitution rates on mammalian phylogenies. Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A, Genome Res 2010 20 1 110 121 10.1101/gr.097857.109 19858363