Large-scale structure of genomic methylation patterns

Genome Research

Volumn 16, Issue 2, 2006, Pages 157-163

  Rollins, Robert A ^a   Haghighi, Fatemeh ^a   Edwards, John R ^a,b   Das, Rajdeep ^c   Zhang, Michael Q ^c   Ju, Jingyue ^a,b   Bestor, Timothy H ^a  

^a Columbia University ^*  (United States)

^b Cold Spring Harbor Laboratory ^*  (United States)

^c Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSINE; DINUCLEOTIDE; DNA;

ANALYTIC METHOD; ARTICLE; BRAIN; CONTROLLED STUDY; CPG ISLAND; DNA METHYLATION; EXON; GENE NUMBER; GENE SEQUENCE; GENETIC VARIABILITY; GENOME ANALYSIS; GENOME SIZE; GENOMICS; HUMAN; HUMAN CELL; HUMAN GENOME; HUMAN TISSUE; MALE; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; REGULATORY SEQUENCE; TANDEM REPEAT;

ANIMALS; BRAIN; CPG ISLANDS; DNA METHYLATION; GENOME, HUMAN; HUMANS; ORGAN SPECIFICITY; PROMOTER REGIONS (GENETICS);

EUKARYOTA; MAMMALIA;

EID: 32044455298     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.4362006     Document Type: Article

References (36)

1. Aerts, S., Thijs, G., Dabrowski, M., Moreau, Y., and De Moor, B. 2004. Comprehensive analysis of the base composition around the transcription start site in Metazoa. BMC Genomics 5: 34.
2. Antequera, F., Macleod, D., and Bird, A.P. 1989. Specific protection of methylated CpGs in mammalian nuclei. Cell 58: 509-517.
3. Bestor, T.H. 2003. Cytosine methylation mediates sexual conflict. Trends Genet. 19: 185-190.
4. Biniszkiewicz, D., Gribnau, J., Ramsahoye, B., Gaudet, F., Eggan, K., Humpherys, D., Mastrangelom, M.A., Jun, Z., Walter, J., and Jaenisch, R. 2002. Dnmt1 overexpression causes genomic hypermethylation, loss of imprinting, and embryonic lethality. Mol. Cell. Biol. 22: 2124-2135.
5. Bourc'his, D. and Bestor, T.H. 2004. Meiotic catastrophe and retrotransposons in male germ cells lacking Dnmt3L. Nature 431: 96-99.
6. Eichler, E.E., Clark, R., and She, X. 2004. An assessment of the sequence gaps: Unfinished business in a finished human genome. Nat. Rev. Genet. 5: 345-354.
7. Gardiner-Garden, M. and Frommer, M. 1987. CpG islands in vertebrate genomes. J. Mol. Biol. 196: 261-282.
8. Gaudet, F., Hodgson, J.G., Eden, A., Jackson-Grusby, L., Dausman, J., Gray, J.W., Leonhardt, H., and Jaenisch, R. 2002. Induction of tumors in mice by genomic hypomethylation. Science 300: 489-492.
9. Goelz, S.E., Vogelstein, B., Hamilton, S.R., and Feinberg, A.P. 1985. Hypomethylation of DNA from benign and malignant human colon neoplasms. Science 228: 187-190.
10. Goll, M.G. and Bestor, T.H. 2005. Eukaryotic cytosine methyltransferases. Annu. Rev. Biochem. 74: 481-514.
11. Greger, V., Passarge, E., Hopping, W., Messmer, E., and Horsthemke, B. 1989. Epigenetic changes may contribute to the formation and spontaneous regression of retinoblastoma. Hum. Genet. 83: 155-158.
12. Gregory, T.R. 2005. The C-value enigma in plants and animals: A review of parallels and an appeal for partnership. Ann. Bot. (Lond). 95: 133-146.
13. Ioshikhes, I.P. and Zhang, M.Q. 2000. Large-scale human promoter mapping using CpG islands. Nat. Genet. 26: 61-63.
14. Jojic, V., Jojic, N., Meek, C., Geiger, D., Siepel, A., Haussler, D., and Heckerman, D. 2004. Efficient approximations for learning phylogenetic HMM models from data. Bioinformatics 20: I161-I168.
15. Kent, W.J. 2002. BLAT-the BLAST-like alignment tool. Genome Res. 12: 656-664.
16. Keshet, I., Lieman-Hurwitz, J., and Cedar, H. 1986. DNA methylation affects the formation of active chromatin. Cell 44: 535-543.
17. Kidwell, M.G. 2002. Transposable elements and the evolution of genome size in eukaryotes. Genetica 115: 49-63.
18. Kondrashov, A.S. 2002. Direct estimates of human per nucleotide mutation rates at 20 loci causing Mendelian diseases. Human Mutat. 21: 12-27.
19. Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., et al. 2002. Initial sequencing and analysis of the human genome. Nature 409: 860-921.
20. Lee, D.U., Agarwal, S., and Rao, A. 2002. Th2 lineage commitment and efficient IL-4 production involves extended demethylation of the IL-4 gene. Immunity 16: 649-660.
21. Li, E., Bestor, T.H., and Jaenisch, R. 1992. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 69: 915-926.
22. Majewski, J. and Ott, J. 2002. Distribution and characterization of regulatory elements in the human genome. Genome Res. 12: 1827-1836.
23. Miller, O.J., Schnedl, W., Allen, J., and Erlanger, B.F. 1974. 5-Methylcytosine localised in mammalian constitutive heterochromatin.Nature 251: 636-637.
24. Oda, M., Furukawa, K., Ogata, K., Sarai, A., and Nakamura, H. 1998. Thermodynamics of specific and non-specific DNA binding by the c-Myb DNA-binding domain. J. Mol. Biol. 276: 571-590.
25. Palmer, L.E., Rabinowicz, P.D., O'Shaughnessy, A.L., Balija, V.S., Nascimento, L.U., Dike, S., de la Bastide, M., Martienssen, R.A., and McCombie, W.R. 2003. Maize genome sequencing by methylation filtration. Science 302: 135-138.
26. Schubeler, D., Lorincz, M.C., Cimbora, D.M., Telling, A., Feng, Y.Q., Bouhassira, E.E., and Groudine, M. 2000. Genomic targeting of methylated DNA: Influence of methylation on transcription, replication, chromatin structure, and histone acetylation. Mol. Cell. Biol. 20: 9103-9112.
27. Selker, E.U., Tountas, N.A., Cross, S.H., Margolin, B.S., Murphy, J.G., Bird, A.P., and Freitag, M. 2003. The methylated component of the Neurospora crassa genome. Nature 422: 893-897.
28. Stein, R., Razin, A., and Cedar, H. 1982. In vitro methylation of the hamster adenine phosphoribosyltransferase gene inhibits its expression in mouse L cells. Proc. Natl. Acad. Sci. 79: 3418-3422.
29. Thomas Jr., C.A. 1971. The genetic organization of chromosomes. Annu. Rev. Genet. 5: 237-256.
30. Tompa, R., McCallum, C.M., Delrow, J., Henikoff, J.G., van Steensel, B., and Henikoff, S. 2002. Genome-wide profiling of DNA methylation reveals transposon targets of CHROMOMETHYLASE3. Curr. Biol. 12: 65-68.
31. Trinklein, N.D., Aldred, S.J., Saldanha, A.J., and Myers, R.M. 2003. Identification and functional analysis of human transcriptional promoters. Genome Res. 13: 308-312.
32. Tykocinski, M.L. and Max, E.E. 1984. CG dinucleotide clusters in MHC genes and in 5′ demethylated genes. Nucleic Acids Res. 12: 4385-4396.
33. Weber, M., Davies, J.J., Wittig, D., Oakeley, E.J., Haase, M., Lam, W.L., and Schubeler, D. 2005. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat. Genet. 37: 853-862.
34. Wigler, M., Levy, D., and Perucho, M. 1981. The somatic replication of DNA methylation. Cell 24: 33-40.
35. Xu, G.L., Bestor, T.H., Bourc'his, D., Hsieh, C.L., Tommerup, N., Bugge, M., Hulten, M., Qu, X., Russo, J.J., and Viegas-Pequignot, E. 1999. Chromosome instability and immunodeficiency syndrome caused by mutations in a DNA methyltransferase gene. Nature 402: 187-189.
36. Yoder, J.A., Walsh, C.P., and Bestor, T.H. 1997. Cytosine methylation and the ecology of intragenomic parasites. Trends Genet. 13: 335-340.