DNMT1 maintains progenitor function in self-renewing somatic tissue (original) (raw)

• Morrison, S. J. & Spradling, A. C. Stem cells and niches: mechanisms that promote stem cell maintenance throughout life. Cell 132, 598–611 (2008)
  Article CAS PubMed PubMed Central Google Scholar
• Orford, K. W. & Scadden, D. T. Deconstructing stem cell self-renewal: genetic insights into cell-cycle regulation. Nature Rev. Genet. 9, 115–128 (2008)
  Article CAS PubMed Google Scholar
• Reik, W. Stability and flexibility of epigenetic gene regulation in mammalian development. Nature 447, 425–432 (2007)
  Article ADS CAS PubMed Google Scholar
• Bird, A. DNA methylation patterns and epigenetic memory. Genes Dev. 16, 6–21 (2002)
  Article CAS PubMed Google Scholar
• Fuks, F. DNA methylation and histone modifications: teaming up to silence genes. Curr. Opin. Genet. Dev. 15, 490–495 (2005)
  Article CAS PubMed Google Scholar
• Bestor, T., Laudano, A., Mattaliano, R. & Ingram, V. Cloning and sequencing of a cDNA encoding DNA methyltransferase of mouse cells. The carboxyl-terminal domain of the mammalian enzymes is related to bacterial restriction methyltransferases. J. Mol. Biol. 203, 971–983 (1988)
  Article CAS PubMed Google Scholar
• Li, E., Bestor, T. H. & Jaenisch, R. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 69, 915–926 (1992)
  Article CAS PubMed Google Scholar
• Fouse, S. D. et al. Promoter CpG methylation contributes to ES cell gene regulation in parallel with Oct4/Nanog, PcG complex, and histone H3 K4/K27 trimethylation. Cell Stem Cell 2, 160–169 (2008)
  Article CAS PubMed PubMed Central Google Scholar
• Bostick, M. et al. UHRF1 plays a role in maintaining DNA methylation in mammalian cells. Science 317, 1760–1764 (2007)
  Article ADS CAS PubMed Google Scholar
• Sharif, J. et al. The SRA protein Np95 mediates epigenetic inheritance by recruiting Dnmt1 to methylated DNA. Nature 450, 908–912 (2007)
  Article ADS CAS PubMed Google Scholar
• Rai, K. et al. DNA demethylation in zebrafish involves the coupling of a deaminase, a glycosylase, and Gadd45. Cell 135, 1201–1212 (2008)
  Article CAS PubMed PubMed Central Google Scholar
• Barreto, G. et al. Gadd45a promotes epigenetic gene activation by repair-mediated DNA demethylation. Nature 445, 671–675 (2007)
  Article CAS PubMed Google Scholar
• Ma, D. K. et al. Neuronal activity-induced Gadd45b promotes epigenetic DNA demethylation and adult neurogenesis. Science 323, 1074–1077 (2009)
  Article ADS CAS PubMed PubMed Central Google Scholar
• (SEER Incidence) Surveillance Epidemiology, and End Results (SEER) Program SEER*Stat Database. Incidence - SEER 9 Regs, Nov 2002 Sub (1973–2000), National Cancer Institute, DCCPS, Surveillance Research Program, Cancer Statistics Branch, released April 2003, based on the November 2002 submission 〈http://www.seer.cancer.gov〉.
• Jaenisch, R. & Bird, A. Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nature Genet. 33, 245–254 (2003)
  Article CAS PubMed Google Scholar
• Lei, H. et al. De novo DNA cytosine methyltransferase activities in mouse embryonic stem cells. Development 122, 3195–3205 (1996)
  PubMed CAS Google Scholar
• Khavari, P. A. Modelling cancer in human skin tissue. Nature Rev. Cancer 6, 270–280 (2006)
  Article CAS Google Scholar
• Robbins, P. B. et al. In vivo restoration of laminin 5 β3 expression and function in junctional epidermolysis bullosa. Proc. Natl Acad. Sci. USA 98, 5193–5198 (2001)
  Article ADS CAS PubMed Google Scholar
• Maurelli, R. et al. Inactivation of p16INK4a (inhibitor of cyclin-dependent kinase 4A) immortalizes primary human keratinocytes by maintaining cells in the stem cell compartment. FASEB J. 20, 1516–1518 (2006)
  Article CAS PubMed Google Scholar
• Carlson, M. E., Hsu, M. & Conboy, I. M. Imbalance between pSmad3 and Notch induces CDK inhibitors in old muscle stem cells. Nature 454, 528–532 (2008)
  Article ADS CAS PubMed Google Scholar
• He, J., Kallin, E. M., Tsukada, Y. & Zhang, Y. The H3K36 demethylase Jhdm1b/Kdm2b regulates cell proliferation and senescence through p15Ink4b . Nature Struct. Mol. Biol. 15, 1169–1175 (2008)
  Article CAS Google Scholar
• Lazarov, M. et al. CDK4 coexpression with Ras generates malignant human epidermal tumorigenesis. Nature Med. 8, 1105–1114 (2002)
  Article CAS PubMed Google Scholar
• Damelin, M. & Bestor, T. H. Biological functions of DNA methyltransferase 1 require its methyltransferase activity. Mol. Cell. Biol. 27, 3891–3899 (2007)
  Article CAS PubMed PubMed Central 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 PubMed Google Scholar
• Weber, M. & Schubeler, D. Genomic patterns of DNA methylation: targets and function of an epigenetic mark. Curr. Opin. Cell Biol. 19, 273–280 (2007)
  Article CAS PubMed Google Scholar
• Irizarry, R. A. et al. The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nature Genet. 41, 178–186 (2009)
  Article CAS PubMed Google Scholar
• Andersen, B. et al. Functions of the POU domain genes Skn-1a/i and Tst-1/Oct-6/SCIP in epidermal differentiation. Genes Dev. 11, 1873–1884 (1997)
  Article CAS PubMed Google Scholar
• Eckert, R. L., Crish, J. F., Banks, E. B. & Welter, J. F. The epidermis: genes on – genes off. J. Invest. Dermatol. 109, 501–509 (1997)
  Article CAS PubMed Google Scholar
• Motohashi, H., Katsuoka, F., Engel, J. D. & Yamamoto, M. Small Maf proteins serve as transcriptional cofactors for keratinocyte differentiation in the Keap1–Nrf2 regulatory pathway. Proc. Natl Acad. Sci. USA 101, 6379–6384 (2004)
  Article ADS CAS PubMed Google Scholar
• Nakamura, Y. et al. The combination of ubiquitous transcription factors AP-1 and Sp1 directs keratinocyte-specific and differentiation-specific gene expression in vitro . Exp. Dermatol. 16, 143–150 (2007)
  Article CAS PubMed Google Scholar
• Sen, G. L., Webster, D. E., Barragan, D. I., Chang, H. Y. & Khavari, P. A. Control of differentiation in a self-renewing mammalian tissue by the histone demethylase JMJD3. Genes Dev. 22, 1865–1870 (2008)
  Article CAS PubMed PubMed Central Google Scholar
• Tusher, V. G., Tibshirani, R. & Chu, G. Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl Acad. Sci. USA 98, 5116–5121 (2001)
  Article ADS CAS PubMed MATH Google Scholar
• Huang, D. W., Sherman, B. T. & Lempicki, R. A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protocols 4, 44–57 (2009)
  Article CAS Google Scholar
• Truong, A. B., Kretz, M., Ridky, T. W., Kimmel, R. & Khavari, P. A. p63 regulates proliferation and differentiation of developmentally mature keratinocytes. Genes Dev. 20, 3185–3197 (2006)
  Article CAS PubMed PubMed Central 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 PubMed 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 PubMed Google Scholar
• Giardine, B. et al. Galaxy: a platform for interactive large-scale genome analysis. Genome Res. 15, 1451–1455 (2005)
  Article CAS PubMed PubMed Central Google Scholar
• Gardiner-Garden, M. & Frommer, M. CpG islands in vertebrate genomes. J. Mol. Biol. 196, 261–282 (1987)
  Article CAS PubMed Google Scholar
• Kuhn, R. M. et al. The UCSC Genome Browser Database: update 2009. Nucleic Acids Res. 37, D755–D761 (2009)
  Article CAS PubMed Google Scholar