A unique regulatory phase of DNA methylation in the early mammalian embryo (original) (raw)

• Bird, A. DNA methylation patterns and epigenetic memory. Genes Dev. 16, 6–21 (2002)
  Article CAS Google Scholar
• Jaenisch, R. & Bird, A. Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nature Genet. 33 (Suppl.). 245–254 (2003)
  Article CAS Google Scholar
• Suzuki, M. M. & Bird, A. DNA methylation landscapes: provocative insights from epigenomics. Nature Rev. Genet. 9, 465–476 (2008)
  Article CAS Google Scholar
• Meissner, A. et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454, 766–770 (2008)
  Article ADS 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. Nature Genet. 37, 853–862 (2005)
  Article CAS Google Scholar
• Weber, M. et al. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nature Genet. 39, 457–466 (2007)
  Article CAS Google Scholar
• Ji, H. et al. Comprehensive methylome map of lineage commitment from haematopoietic progenitors. Nature 467, 338–342 (2010)
  Article ADS CAS Google Scholar
• Wossidlo, M. et al. 5-Hydroxymethylcytosine in the mammalian zygote is linked with epigenetic reprogramming. Nature Commun. 2, 241 (2011)
  Article Google Scholar
• Gu, T. P. et al. The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes. Nature 477, 606–610 (2011)
  Article ADS CAS Google Scholar
• Inoue, A. & Zhang, Y. Replication-dependent loss of 5-hydroxymethylcytosine in mouse preimplantation embryos. Science 334, 194 (2011)
  Article ADS CAS Google Scholar
• Reik, W., Dean, W. & Walter, J. Epigenetic reprogramming in mammalian development. Science 293, 1089–1093 (2001)
  Article CAS Google Scholar
• Kafri, T. et al. Developmental pattern of gene-specific DNA methylation in the mouse embryo and germ line. Genes Dev. 6, 705–714 (1992)
  Article CAS Google Scholar
• Borgel, J. et al. Targets and dynamics of promoter DNA methylation during early mouse development. Nature Genet. 42, 1093–1100 (2010)
  Article CAS Google Scholar
• Meissner, A. Epigenetic modifications in pluripotent and differentiated cells. Nature Biotechnol. 28, 1079–1088 (2010)
  Article CAS Google Scholar
• Razin, A. & Shemer, R. DNA methylation in early development. Hum. Mol. Genet. 4, 1751–1755 (1995)
  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
• Rougier, N. et al. Chromosome methylation patterns during mammalian preimplantation development. Genes Dev. 12, 2108–2113 (1998)
  Article CAS Google Scholar
• Mayer, W., Niveleau, A., Walter, J., Fundele, R. & Haaf, T. Demethylation of the zygotic paternal genome. Nature 403, 501–502 (2000)
  Article ADS CAS Google Scholar
• Lane, N. et al. Resistance of IAPs to methylation reprogramming may provide a mechanism for epigenetic inheritance in the mouse. Genesis 35, 88–93 (2003)
  Article CAS Google Scholar
• Oswald, J. et al. Active demethylation of the paternal genome in the mouse zygote. Curr. Biol. 10, 475–478 (2000)
  Article CAS Google Scholar
• Santos, F., Hendrich, B., Reik, W. & Dean, W. Dynamic reprogramming of DNA methylation in the early mouse embryo. Dev. Biol. 241, 172–182 (2002)
  Article CAS Google Scholar
• Kim, S. H. et al. Differential DNA methylation reprogramming of various repetitive sequences in mouse preimplantation embryos. Biochem. Biophys. Res. Commun. 324, 58–63 (2004)
  Article CAS Google Scholar
• Bock, C. et al. Quantitative comparison of genome-wide DNA methylation mapping technologies. Nature Biotechnol. 28, 1106–1114 (2010)
  Article CAS Google Scholar
• Harris, R. A. et al. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nature Biotechnol. 28, 1097–1105 (2010)
  Article CAS Google Scholar
• Smallwood, S. A. et al. Dynamic CpG island methylation landscape in oocytes and preimplantation embryos. Nature Genet. 43, 811–814 (2011)
  Article CAS Google Scholar
• Davis, T. & Vaisvila, R. High sensitivity 5-hydroxymethylcytosine detection in Balb/C brain tissue. J. Vis. Exp. 48, (2011)
• Ficz, G. et al. Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation. Nature 473, 398–402 (2011)
  Article ADS CAS Google Scholar
• Szulwach, K. E. et al. Integrating 5-hydroxymethylcytosine into the epigenomic landscape of human embryonic stem cells. PLoS Genet. 7, e1002154 (2011)
  Article CAS Google Scholar
• Williams, K. et al. TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity. Nature 473, 343–348 (2011)
  Article ADS CAS Google Scholar
• Wu, H. et al. Genome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cells. Genes Dev. 25, 679–684 (2011)
  Article CAS Google Scholar
• Xu, Y. et al. Genome-wide regulation of 5hmC, 5mC, and gene expression by Tet1 hydroxylase in mouse embryonic stem cells. Mol. Cell 42, 451–464 (2011)
  Article CAS Google Scholar
• Branco, M. R., Ficz, G. & Reik, W. Uncovering the role of 5-hydroxymethylcytosine in the epigenome. Nature Rev. Genet. 13, 7–13 (2011)
  Article Google Scholar
• Santos, F., Hendrich, B., Reik, W. & Dean, W. Dynamic reprogramming of DNA methylation in the early mouse embryo. Dev. Biol. 241, 172–182 (2002)
  Article CAS Google Scholar
• Hajkova, P. et al. Genome-wide reprogramming in the mouse germ line entails the base excision repair pathway. Science 329, 78–82 (2010)
  Article ADS CAS Google Scholar
• Wossidlo, M. et al. Dynamic link of DNA demethylation, DNA strand breaks and repair in mouse zygotes. EMBO J. 29, 1877–1888 (2010)
  Article CAS Google Scholar
• Popp, C. et al. Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency. Nature 463, 1101–1105 (2010)
  Article ADS CAS Google Scholar
• Mouse Genome Sequencing Consortium Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520–562 (2002)
  Article Google Scholar
• Ichiyanagi, K. et al. Locus- and domain-dependent control of DNA methylation at mouse B1 retrotransposons during male germ cell development. Genome Res. 21, 2058–2066 (2011)
  Article CAS Google Scholar
• Goodier, J. L., Ostertag, E. M., Du, K. & Kazazian, H. H., Jr A novel active L1 retrotransposon subfamily in the mouse. Genome Res. 11, 1677–1685 (2001)
  Article CAS Google Scholar
• Edwards, C. A. & Ferguson-Smith, A. Mechanisms regulating imprinted genes in clusters. Curr. Opin. Cell Biol. 19, 281–289 (2007)
  Article CAS Google Scholar
• Bestor, T. H. The DNA methyltransferases of mammals. Hum. Mol. Genet. 9, 2395–2402 (2000)
  Article CAS Google Scholar
• Hirasawa, R. et al. Maternal and zygotic Dnmt1 are necessary and sufficient for the maintenance of DNA methylation imprints during preimplantation development. Genes Dev. 22, 1607–1616 (2008)
  Article CAS Google Scholar
• Lucifero, D. et al. Coordinate regulation of DNA methyltransferase expression during oogenesis. BMC Dev. Biol. 7, 36 (2007)
  Article Google Scholar
• Ramsahoye, B. H. et al. Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a. Proc. Natl Acad. Sci. USA 97, 5237–5242 (2000)
  Article ADS CAS Google Scholar
• Ziller, M. J. et al. Genomic distribution and inter-sample variation of non-CpG methylation across human cell types. PLoS Genet. 7, e1002389 (2011)
  Article CAS Google Scholar
• Haines, T., Rodenhiser, D. & Ainsworth, P. Allele-specific non-CpG methylation of the Nf1 gene during early mouse development. Dev. Biol. 240, 585–598 (2001)
  Article CAS Google Scholar
• Tomizawa, S. et al. Dynamic stage-specific changes in imprinted differentially methylated regions during early mammalian development and prevalence of non-CpG methylation in oocytes. Development 138, 811–820 (2011)
  Article CAS Google Scholar
• Beraldi, R., Pittoggi, C., Sciamanna, I., Mattei, E. & Spadafora, C. Expression of LINE-1 retroposons is essential for murine preimplantation development. Mol. Reprod. Dev. 73, 279–287 (2006)
  Article CAS Google Scholar
• Kigami, D., Minami, N., Takayama, H. & Imai, H. MuERV-L is one of the earliest transcribed genes in mouse one-cell embryos. Biol. Reprod. 68, 651–654 (2003)
  Article CAS Google Scholar
• Okada, Y., Yamagata, K., Hong, K., Wakayama, T. & Zhang, Y. A role for the elongator complex in zygotic paternal genome demethylation. Nature 463, 554–558 (2010)
  Article ADS CAS Google Scholar
• Nagy, A. Manipulating the Mouse Embryo: a Laboratory Manual 3rd edn (Cold Spring Harbor Laboratory Press, 2003)
  Google Scholar
• Smith, Z. D., Gu, H., Bock, C., Gnirke, A. & Meissner, A. High-throughput bisulfite sequencing in mammalian genomes. Methods 48, 226–232 (2009)
  Article CAS Google Scholar
• Gu, H. et al. Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling. Nature Protocols 6, 468–481 (2011)
  Article CAS Google Scholar
• Gu, H. et al. Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nature Methods 7, 133–136 (2010)
  Article CAS Google Scholar
• Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. B 57, 289–300 (1995)
  MathSciNet MATH Google Scholar
• Blake, J. A., Bult, C. J., Kadin, J. A., Richardson, J. E. & Eppig, J. T. The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics. Nucleic Acids Res. 39, D842–D848 (2011)
  Article CAS Google Scholar