Primate CpG islands are maintained by heterogeneous evolutionary regimes involving minimal selection

Cell

Volumn 145, Issue 5, 2011, Pages 773-786

  Cohen, Netta Mendelson ^a   Kenigsberg, Ephraim ^a   Tanay, Amos ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ANIMAL CELL; ARTICLE; CONTROLLED STUDY; CPG ISLAND; DEAMINATION; DNA METHYLATION; DNA POLYMORPHISM; FEMALE; GENE CONVERSION; GENETIC ASSOCIATION; GENETIC SELECTION; HUMAN; HUMAN CELL; MALE; MOLECULAR EVOLUTION; MOUSE; NONHUMAN; POPULATION GENETICS; PRIMATE; PRIORITY JOURNAL;

MAMMALIA; PRIMATES;

EID: 79957577720     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2011.04.024     Document Type: Article

References (45)

1. P.F. Arndt Reconstruction of ancestral nucleotide sequences and estimation of substitution frequencies in a star phylogeny Gene 390 2007 75 83 (Pubitemid 46241752)
2. G. Baele, Y. Van de Peer, and S. Vansteelandt Modelling the ancestral sequence distribution and model frequencies in context-dependent models for primate noncoding sequences BMC Evol. Biol. 10 2010 244
3. T. Bartke, M. Vermeulen, B. Xhemalce, S.C. Robson, M. Mann, and T. Kouzarides Nucleosome-interacting proteins regulated by DNA and histone methylation Cell 143 2010 470 484
4. S. Baylin, and T.H. Bestor Altered methylation patterns in cancer cell genomes: cause or consequence? Cancer Cell 1 2002 299 305 (Pubitemid 41039130)
5. S.B. Baylin, and J.G. Herman DNA hypermethylation in tumorigenesis: epigenetics joins genetics Trends Genet. 16 2000 168 174 (Pubitemid 30169152)
6. A. Bird, M. Taggart, M. Frommer, O.J. Miller, and D. Macleod A fraction of the mouse genome that is derived from islands of nonmethylated, CpG-rich DNA Cell 40 1985 91 99 (Pubitemid 15169310)
7. A.P. Bird DNA methylation and the frequency of CpG in animal DNA Nucleic Acids Res. 8 1980 1499 1504
8. T.C. Brown, and J. Jiricny A specific mismatch repair event protects mammalian cells from loss of 5-methylcytosine Cell 50 1987 945 950
9. N.M. Cohen, V. Dighe, G. Landan, S. Reynisdottir, A. Palsson, S. Mitalipov, and A. Tanay DNA methylation programming and reprogramming in primate embryonic stem cells Genome Res. 19 2009 2193 2201
10. I. Cohn, T. El-Hay, N. Friedman, and R. Kupferman Mean Field Variational Approximation for Continuous-Time Bayesian Networks J. Mach. Learn. Res. 11 2010 2745 2783
11. S.V. Dindot, R. Person, M. Strivens, R. Garcia, and A.L. Beaudet Epigenetic profiling at mouse imprinted gene clusters reveals novel epigenetic and genetic features at differentially methylated regions Genome Res. 19 2009 1374 1383
12. A. Doi, I.H. Park, B. Wen, P. Murakami, M.J. Aryee, R. Irizarry, B. Herb, C. Ladd-Acosta, J. Rho, and S. Loewer Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts Nat. Genet. 41 2009 1350 1353
13. T.R. Dreszer, G.D. Wall, D. Haussler, and K.S. Pollard Biased clustered substitutions in the human genome: the footprints of male-driven biased gene conversion Genome Res. 17 2007 1420 1430 (Pubitemid 47529426)
14. L. Duret, and N. Galtier Biased Gene Conversion and the Evolution of Mammalian Genomic Landscapes Annu Rev Genom Hum G 10 2009 285 311
15. J.R. Edwards, A.H. O'Donnell, R.A. Rollins, H.E. Peckham, C. Lee, M.H. Milekic, B. Chanrion, Y. Fu, T. Su, and H. Hibshoosh Chromatin and sequence features that define the fine and gross structure of genomic methylation patterns Genome Res. 20 2010 972 980
16. A. Eyre-Walker Recombination and Mamm. Genome evolution Proc Biol Sci 252 1993 237 243
17. E.N. Gal-Yam, G. Egger, L. Iniguez, H. Holster, S. Einarsson, X. Zhang, J.C. Lin, G. Liang, P.A. Jones, and A. Tanay Frequent switching of Polycomb repressive marks and DNA hypermethylation in the PC3 prostate cancer cell line Proc. Natl. Acad. Sci. USA 105 2008 12979 12984
18. N. Galtier, G. Piganeau, D. Mouchiroud, and L. Duret GC-content evolution in Mamm. Genomes: The biased gene conversion hypothesis Genetics 159 2001 907 911 (Pubitemid 33035129)
19. M. Gardiner-Garden, and M. Frommer CpG islands in vertebrate genomes J. Mol. Biol. 196 1987 261 282 (Pubitemid 17122132)
20. D.G. Hwang, and P. Green Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution Proc. Natl. Acad. Sci. USA 101 2004 13994 14001 (Pubitemid 39305018)
21. R.S. Illingworth, U. Gruenewald-Schneider, S. Webb, A.R. Kerr, K.D. James, D.J. Turner, C. Smith, D.J. Harrison, R. Andrews, and A.P. Bird Orphan CpG islands identify numerous conserved promoters in the Mamm. Genome PLoS Genet. 6 2010 e1001134
22. R.A. Irizarry, C. Ladd-Acosta, B. Wen, Z. Wu, C. Montano, P. Onyango, H. Cui, K. Gabo, M. Rongione, and M. Webster The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores Nat. Genet. 41 2009 178 186
23. H. Ji, L.I. Ehrlich, J. Seita, P. Murakami, A. Doi, P. Lindau, H. Lee, M.J. Aryee, R.A. Irizarry, and K. Kim Comprehensive methylome map of lineage commitment from haematopoietic progenitors Nature 467 2010 338 342
24. H.F. Jorgensen, and A. Bird MeCP2 and other methyl-CpG binding proteins Ment. Retard. Dev. Disabil. Res. Rev. 8 2002 87 93 (Pubitemid 34606519)
25. E. Kenigsberg, A. Bar, E. Segal, and A. Tanay Widespread compensatory evolution conserves DNA-encoded nucleosome organization in yeast PLoS Comput. Biol. 6 2010 e1001039
26. I. Keshet, Y. Schlesinger, S. Farkash, E. Rand, M. Hecht, E. Segal, E. Pikarski, R.A. Young, A. Niveleau, and H. Cedar Evidence for an instructive mechanism of de novo methylation in cancer cells Nat. Genet. 38 2006 149 153 (Pubitemid 43177227)
27. K. Kim, A. Doi, B. Wen, K. Ng, R. Zhao, P. Cahan, J. Kim, M.J. Aryee, H. Ji, and L.I. Ehrlich Epigenetic memory in induced pluripotent stem cells Nature 467 2010 285 290
28. T.H. Kim, Z.K. Abdullaev, A.D. Smith, K.A. Ching, D.I. Loukinov, R.D. Green, M.Q. Zhang, V.V. Lobanenkov, and B. Ren Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome Cell 128 2007 1231 1245 (Pubitemid 46427876)
29. F.R. Kschischang, B.J. Frey, and H.-A. Loeliger Factor Graphs and the Sum-Product Algorithm IEEE Trans. Inf. Theory 47 2001 21
30. R. Lister, M. Pelizzola, R.H. Dowen, R.D. Hawkins, G. Hon, J. Tonti-Filippini, J.R. Nery, L. Lee, Z. Ye, and Q.M. Ngo Human DNA methylomes at base resolution show widespread epigenomic differences Nature 462 2009 315 322
31. A. Meissner, T.S. Mikkelsen, H. Gu, M. Wernig, J. Hanna, A. Sivachenko, X. Zhang, B.E. Bernstein, C. Nusbaum, and D.B. Jaffe Genome-scale DNA methylation maps of pluripotent and differentiated cells Nature 454 2008 766 770
32. V.K. Rakyan, T.A. Down, N.P. Thorne, P. Flicek, E. Kulesha, S. Graf, E.M. Tomazou, L. Backdahl, N. Johnson, and M. Herberth An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs) Genome Res. 18 2008 1518 1529
33. W. Reik Stability and flexibility of epigenetic gene regulation in mammalian development Nature 447 2007 425 432 (Pubitemid 46816749)
34. R. Schulz, C. Proudhon, T.H. Bestor, K. Woodfine, C.S. Lin, S.P. Lin, M. Prissette, R.J. Oakey, and D. Bourc'his The parental nonequivalence of imprinting control regions during mammalian development and evolution PLoS Genet. 6 2010 e1001214
35. R. Straussman, D. Nejman, D. Roberts, I. Steinfeld, B. Blum, N. Benvenisty, I. Simon, Z. Yakhini, and H. Cedar Developmental programming of CpG island methylation profiles in the human genome Nat. Struct. Mol. Biol. 16 2009 564 571
36. D. Takai, and P.A. Jones Comprehensive analysis of CpG islands in human chromosomes 21 and 22 Proc. Natl. Acad. Sci. USA 99 2002 3740 3745 (Pubitemid 34252176)
37. A. Tanay, A.H. O'Donnell, M. Damelin, and T.H. Bestor Hyperconserved CpG domains underlie Polycomb-binding sites Proc. Natl. Acad. Sci. USA 104 2007 5521 5526 (Pubitemid 47175713)
38. M. Weber, J.J. Davies, D. Wittig, E.J. Oakeley, M. Haase, W.L. Lam, and D. Schubeler Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells Nat. Genet. 37 2005 853 862 (Pubitemid 41077111)
39. M. Weber, I. Hellmann, M.B. Stadler, L. Ramos, S. Paabo, M. Rebhan, and D. Schubeler Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome Nat. Genet. 39 2007 457 466 (Pubitemid 46514772)
40. Cohen, N.M., Dighe, V., Landan, G., Reynisdottir, S., Palsson, A., Mitalipov, S., and Tanay, A. (2009). DNA methylation programming and reprogramming in primate embryonic stem cells. Genome Res. 19, 2193-2201.
41. Irizarry, R.A., Ladd-Acosta, C., Wen, B., Wu, Z., Montano, C., Onyango, P., Cui, H., Gabo, K., Rongione, M., Webster, M., et al. (2009). The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat. Genet. 41, 178-186.
42. Kenigsberg, E., Bar, A., Segal, E., and Tanay, A. (2010). Widespread compensatory evolution conserves DNA-encoded nucleosome organization in yeast. PLoS Comput. Biol. 6, e1001039.
43. Lister, R., Pelizzola, M., Dowen, R.H., Hawkins, R.D., Hon, G., Tonti-Filippini, J., Nery, J.R., Lee, L., Ye, Z., Ngo, Q.M., et al. (2009). Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462, 315-322.
44. Rakyan, V.K., Down, T.A., Thorne, N.P., Flicek, P., Kulesha, E., Graf, S., Tomazou, E.M., Backdahl, L., Johnson, N., Herberth, M., et al. (2008). An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). Genome Res. 18, 1518-1529.
45. Yedidia, J.S., Freeman, W.T., and Weiss, Y. (2005). Constructing free-energy approximations and generalized belief propagation algorithms. Information Theory, IEEE. 51, 2282-2312. (Pubitemid 41136394)