Developmental programming of CpG island methylation profiles in the human genome (original) (raw)

• Kafri, T. et al. Developmental pattern of gene-specific DNA methylation in the mouse embryo and germline. Genes Dev. 6, 705–714 (1992).
  Article CAS Google Scholar
• Monk, M., Boubelik, M. & Lehnert, S. Temporal and regional changes in DNA methylation in the embryonic, extraembryonic and germ cell lineages during mouse embryo development. Development 99, 371–382 (1987).
  CAS PubMed Google Scholar
• Brandeis, M. et al. Sp1 elements protect a CpG island from de novo methylation. Nature 371, 435–438 (1994).
  Article CAS Google Scholar
• Frank, D. et al. Demethylation of CpG islands in embryonic cells. Nature 351, 239–241 (1991).
  Article CAS Google Scholar
• Macleod, D., Charlton, J., Mullins, J. & Bird, A.P. Sp1 sites in the mouse Aprt gene promoter are required to prevent methylation of the CpG island. Genes Dev. 8, 2282–2292 (1994).
  Article CAS Google Scholar
• Yamada, Y. et al. A comprehensive analysis of allelic methylation status of CpG islands on human chromosome 11q: comparison with chromosome 21q. DNA Seq. 17, 300–306 (2006).
  Article CAS Google Scholar
• Yamada, Y. et al. A comprehensive analysis of allelic methylation status of CpG islands on human chromosome 21q. Genome Res. 14, 247–266 (2004).
  Article CAS Google Scholar
• Shen, L. et al. Genome-wide profiling of DNA methylation reveals a class of normally methylated CpG island promoters. PLoS Genet. 3, 2023–2036 (2007).
  Article CAS Google Scholar
• Weber, M. et al. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat. Genet. 39, 457–466 (2007).
  Article CAS Google Scholar
• Illingworth, R. et al. A novel CpG island set identifies tissue-specific methylation at developmental gene loci. PLoS Biol. 6, e22 (2008).
  Article Google Scholar
• Rakyan, V.K. et al. An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). Genome Res. 18, 1518–1529 (2008).
  Article CAS Google Scholar
• Rauch, T.A., Wu, X., Zhong, X., Riggs, A.D. & Pfeifer, G.P. A human B cell methylome at 100-base pair resolution. Proc. Natl. Acad. Sci. USA 106, 671–678 (2009).
  Article CAS Google Scholar
• Siegfried, Z. et al. DNA methylation represses transcription in vivo. Nat. Genet. 22, 203–206 (1999).
  Article CAS Google Scholar
• Lorincz, M.C. & Schubeler, D. RNA polymerase II: just stopping by. Cell 130, 16–18 (2007).
  Article CAS Google Scholar
• Meissner, A. et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454, 766–770 (2008).
  Article CAS Google Scholar
• Gal-Yam, E.N. et al. Frequent switching of Polycomb repressive marks and DNA hypermethylation in the PC3 prostate cancer cell line. Proc. Natl. Acad. Sci. USA 105, 12979–12984 (2008).
  Article Google Scholar
• Keshet, I. et al. Evidence for an instructive mechanism of de novo methylation in cancer cells. Nat. Genet. 38, 149–153 (2006).
  Article CAS Google Scholar
• Weber, M. et al. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat. Genet. 37, 853–862 (2005).
  Article CAS Google Scholar
• Guenther, M.G., Levine, S.S., Boyer, L.A., Jaenisch, R. & Young, R.A. A chromatin landmark and transcription initiation at most promoters in human cells. Cell 130, 77–88 (2007).
  Article CAS Google Scholar
• Zhao, X.D. et al. 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 (2007).
  Article CAS Google Scholar
• Ooi, S.K. et al. DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature 448, 714–717 (2007).
  Article CAS Google Scholar
• Eden, E., Lipson, D., Yogev, S. & Yakhini, Z. Discovering motifs in ranked lists of DNA sequences. PLOS Comput. Biol. 3, e39 (2007).
  Article Google Scholar
• Bock, C., Walter, J., Paulsen, M. & Lengauer, T. CpG island mapping by epigenome prediction. PLOS Comput. Biol. 3, e110 (2007).
  Article Google Scholar
• Bock, C. et al. CpG island methylation in human lymphocytes is highly correlated with DNA sequence, repeats, and predicted DNA structure. PLoS Genet. 2, e26 (2006).
  Article Google Scholar
• Gidekel, S. & Bergman, Y. A unique developmental pattern of Oct-3/4 DNA methylation is controlled by a _cis_-demodification element. J. Biol. Chem. 277, 34521–34530 (2002).
  Article CAS Google Scholar
• Eckhardt, F. et al. DNA methylation profiling of human chromosomes 6, 20 and 22. Nat. Genet. 38, 1378–1385 (2006).
  Article CAS Google Scholar
• Koslowski, M. et al. Frequent nonrandom activation of germ-line genes in human cancer. Cancer Res. 64, 5988–5993 (2004).
  Article CAS Google Scholar
• Simpson, A.J., Caballero, O.L., Jungbluth, A., Chen, Y.T. & Old, L.J. Cancer/testis antigens, gametogenesis and cancer. Nat. Rev. Cancer 5, 615–625 (2005).
  Article CAS Google Scholar
• Hajkova, P. et al. Epigenetic reprogramming in mouse primordial germ cells. Mech. Dev. 117, 15–23 (2002).
  Article CAS Google Scholar
• Oakes, C.C., La Salle, S., Smiraglia, D.J., Robaire, B. & Trasler, J.M. Developmental acquisition of genome-wide DNA methylation occurs prior to meiosis in male germ cells. Dev. Biol. 307, 368–379 (2007).
  Article CAS Google Scholar
• Hellman, A. & Chess, A. Gene body-specific methylation on the active X chromosome. Science 315, 1141–1143 (2007).
  Article CAS Google Scholar
• Lock, L.F., Melton, D.W., Caskey, C.T. & Martin, G.R. Methylation of the mouse Hprt gene differs on the active and inactive X chromosomes. Mol. Cell. Biol. 6, 914–924 (1986).
  Article CAS Google Scholar
• Antequera, F., Boyes, J. & Bird, A. High levels of de novo methylations and altered chromatin structure at CpG islands in cell lines. Cell 62, 503–514 (1990).
  Article CAS Google Scholar
• Feldman, N. et al. G9a-mediated irreversible epigenetic inactivation of Oct-3/4 during early embryogenesis. Nat. Cell Biol. 8, 188–194 (2006).
  Article CAS Google Scholar
• Epsztejn-Litman, S. et al. De novo DNA methylation promoted by G9a prevents reprogramming of embryonically silenced genes. Nat. Struct. Mol. Biol. 15, 1176–1183 (2008).
  Article CAS Google Scholar
• Imamura, M. et al. Transcriptional repression and DNA hypermethylation of a small set of ES cell marker genes in male germline stem cells. BMC Dev. Biol. 6, 34 (2006).
  Article Google Scholar
• Ma, D.K., Chiang, C.H., Ponnusamy, K., Ming, G.L. & Song, H. G9a and Jhdm2a regulate embryonic stem cell fusion-induced reprogramming of adult neural stem cells. Stem Cells 26, 2131–2141 (2008).
  Article CAS Google Scholar
• Mikkelsen, T.S. et al. Dissecting direct reprogramming through integrative genomic analysis. Nature 454, 49–55 (2008).
  Article CAS Google Scholar
• Wutz, A. et al. Imprinted expression of the Igf2r gene depends on an intronic CpG island. Nature 389, 745–749 (1997).
  Article CAS Google Scholar
• Yu, W. et al. Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA. Nature 451, 202–206 (2008).
  Article CAS Google Scholar
• Watanabe, T. et al. Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes. Nature 453, 539–543 (2008).
  Article CAS Google Scholar
• He, Y., Vogelstein, B., Velculescu, V.E., Papadopoulos, N. & Kinzler, K.W. The antisense transcriptomes of human cells. Science 322, 1855–1857 (2008).
  Article CAS Google Scholar
• Jones, P.A. The DNA methylation paradox. Trends Genet. 15, 34–37 (1999).
  Article CAS Google Scholar
• Lehnertz, B. et al. Suv39h-mediated histone H3 lysine 9 methylation directs DNA methylation to major satellite repeats at pericentric heterochromatin. Curr. Biol. 13, 1192–1200 (2003).
  Article CAS Google Scholar
• Vire, E. et al. The Polycomb group protein EZH2 directly controls DNA methylation. Nature 439, 871–874 (2006).
  Article CAS Google Scholar
• Schlesinger, Y. et al. Polycomb-mediated methylation on Lys27 of histone H3 methylation pre-marks genes for de novo methylation in cancer. Nat. Genet. 39, 232–236 (2007).
  Article CAS Google Scholar
• Mohn, F. et al. Lineage-specific Polycomb targets and de novo DNA methylation define restriction and potential of neuronal progenitors. Mol. Cell 30, 755–766 (2008).
  Article CAS Google Scholar
• Ohm, J.E. et al. A stem cell-like chromatin pattern may predispose tumor suppressor genes to DNA hypermethylation and heritable silencing. Nat. Genet. 39, 237–242 (2007).
  Article CAS Google Scholar
• Widschwendter, M. et al. Epigenetic stem cell signature in cancer. Nat. Genet. 39, 157–158 (2007).
  Article CAS Google Scholar
• Reynaud, C. et al. Monitoring of urinary excretion of modified nucleosides in cancer patients using a set of six monoclonal antibodies. Cancer Lett. 61, 255–262 (1992).
  Article CAS Google Scholar
• Gardiner-Garden, M. & Frommer, M. CpG island in vertebrate genomes. J. Mol. Biol. 196, 261–282 (1987).
  Article CAS Google Scholar
• Matys, V. et al. TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res. 34, D108–D110 (2006).
  Article CAS Google Scholar
• Witten, I.H. & Frank, E. Data Mining: Practical Machine Learning Tools and Techniques (Morgan Kaufmann, San Francisco, 2005).
  Google Scholar
• Farthing, C.R. et al. Global mapping of DNA methylation in mouse promoters reveals epigenetic reprogramming of pluripotency genes. PLoS Genet. 4, e1000116 (2008).
  Article Google Scholar
• Cowan, C.A., Atienza, J., Melton, D.A. & Eggan, K. Nuclear reprogramming of somatic cells after fusion with human embryonic stem cells. Science 309, 1369–1373 (2005).
  Article CAS Google Scholar