Large conserved domains of low DNA methylation maintained by Dnmt3a (original) (raw)
Bird, A., Taggart, M., Frommer, M., Miller, O.J. & Macleod, D. A fraction of the mouse genome that is derived from islands of nonmethylated, CpG-rich DNA. Cell40, 91–99 (1985). ArticleCASPubMed Google Scholar
Irizarry, R.A. et al. The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat. Genet.41, 178–186 (2009). ArticleCASPubMedPubMed Central Google Scholar
Yan, X.J. et al. Exome sequencing identifies somatic mutations of DNA methyltransferase gene DNMT3A in acute monocytic leukemia. Nat. Genet.43, 309–315 (2011). ArticleCASPubMed Google Scholar
Delhommeau, F. et al. Mutation in TET2 in myeloid cancers. N. Engl. J. Med.360, 2289–2301 (2009). ArticlePubMed Google Scholar
Abdel-Wahab, O. et al. Genetic characterization of TET1, TET2, and TET3 alterations in myeloid malignancies. Blood114, 144–147 (2009). ArticleCASPubMedPubMed Central Google Scholar
Stadler, M.B. et al. DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature480, 490–495 (2011). ArticleCASPubMed 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). ArticleCASPubMedPubMed Central Google Scholar
Hodges, E. et al. Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment. Mol. Cell44, 17–28 (2011). ArticleCASPubMedPubMed Central Google Scholar
Gardiner-Garden, M. & Frommer, M. CpG islands in vertebrate genomes. J. Mol. Biol.196, 261–282 (1987). ArticleCASPubMed Google Scholar
Lowe, C.B., Bejerano, G. & Haussler, D. Thousands of human mobile element fragments undergo strong purifying selection near developmental genes. Proc. Natl. Acad. Sci. USA104, 8005–8010 (2007). ArticleCASPubMedPubMed Central Google Scholar
Hendrix, D.A., Hong, J.W., Zeitlinger, J., Rokhsar, D.S. & Levine, M.S. Promoter elements associated with RNA Pol II stalling in the Drosophila embryo. Proc. Natl. Acad. Sci. USA105, 7762–7767 (2008). ArticleCASPubMedPubMed Central Google Scholar
Bellen, H.J. et al. The Drosophila gene disruption project: progress using transposons with distinctive site specificities. Genetics188, 731–743 (2011). ArticleCASPubMedPubMed Central Google Scholar
Kikuta, H. et al. Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates. Genome Res.17, 545–555 (2007). ArticleCASPubMedPubMed Central Google Scholar
Whyte, W.A. et al. Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell153, 307–319 (2013). ArticleCASPubMedPubMed Central Google Scholar
Wilson, N.K. et al. Combinatorial transcriptional control in blood stem/progenitor cells: genome-wide analysis of ten major transcriptional regulators. Cell Stem Cell7, 532–544 (2010). ArticleCASPubMed Google Scholar
Bernstein, B.E. et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell125, 315–326 (2006). ArticleCASPubMed Google Scholar
Stadler, M.B. et al. DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature480, 490–495 (2011). ArticleCASPubMed Google Scholar
Coolen, M.W. et al. Consolidation of the cancer genome into domains of repressive chromatin by long-range epigenetic silencing (LRES) reduces transcriptional plasticity. Nat. Cell Biol.12, 235–246 (2010). ArticleCASPubMedPubMed Central Google Scholar
Bert, S.A. et al. Regional activation of the cancer genome by long-range epigenetic remodeling. Cancer Cell23, 9–22 (2013). ArticleCASPubMed Google Scholar
Patel, J.P. et al. Prognostic relevance of integrated genetic profiling in acute myeloid leukemia. N. Engl. J. Med.366, 1079–1089 (2012). ArticleCASPubMedPubMed Central Google Scholar
Challen, G.A. et al. Dnmt3a is essential for hematopoietic stem cell differentiation. Nat. Genet.44, 23–31 (2012). ArticleCAS Google Scholar
Pastor, W.A., Aravind, L. & Rao, A. TETonic shift: biological roles of TET proteins in DNA demethylation and transcription. Nat. Rev. Mol. Cell Biol.14, 341–356 (2013). ArticleCASPubMedPubMed Central Google Scholar
Booth, M.J. et al. Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution. Science336, 934–937 (2012). ArticleCASPubMed Google Scholar
Roller, A. et al. Landmark analysis of DNMT3A mutations in hematological malignancies. Leukemia27, 1573–1578 (2013). ArticleCASPubMed Google Scholar
Long, H.K. et al. Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates. eLife2, e00348 (2013). ArticlePubMedPubMed Central Google Scholar
Goodell, M.A., Brose, K., Paradis, G., Conner, A.S. & Mulligan, R.C. Isolation and functional properties of murine hematopoietic stem cells that are replicating in vivo. J. Exp. Med.183, 1797–1806 (1996). ArticleCASPubMed Google Scholar
Mayle, A., Luo, M., Jeong, M. & Goodell, M.A. Flow cytometry analysis of murine hematopoietic stem cells. Cytometry A83, 27–37 (2013). ArticlePubMed Google Scholar
Gu, H. et al. Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling. Nat. Protoc.6, 468–481 (2011). ArticleCASPubMed Google Scholar
Huang, Y., Pastor, W.A., Zepeda-Martinez, J.A. & Rao, A. The anti-CMS technique for genome-wide mapping of 5-hydroxymethylcytosine. Nat. Protoc.7, 1897–1908 (2012). ArticleCASPubMedPubMed Central Google Scholar
Krueger, F. & Andrews, S.R. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics27, 1571–1572 (2011). ArticleCASPubMedPubMed Central Google Scholar
Dahl, J.A. & Collas, P. A rapid micro chromatin immunoprecipitation assay (microChIP). Nat. Protoc.3, 1032–1045 (2008). ArticleCASPubMed Google Scholar
Robinson, M.D., McCarthy, D.J. & Smyth, G.K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics26, 139–140 (2010). CASPubMed Google Scholar
Kuhn, A., Luthi-Carter, R. & Delorenzi, M. Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'. BMC Bioinformatics9, 26 (2008). ArticlePubMedPubMed Central Google Scholar
Eisen, M.B., Spellman, P.T., Brown, P.O. & Botstein, D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA95, 14863–14868 (1998). ArticleCASPubMedPubMed Central Google Scholar