Robertson, K.D. DNA methylation and human disease. Nat. Rev. Genet. 6, 597–610 (2005).
Bird, A. DNA methylation patterns and epigenetic memory. Genes Dev. 16, 6–21 (2002).
Feinberg, A.P. & Vogelstein, B. Hypomethylation distinguishes genes of some human cancers from their normal counterparts. Nature 301, 89–92 (1983).
Gama-Sosa, M.A. et al. Tissue-specific differences in DNA methylation in various mammals. Biochim. Biophys. Acta 740, 212–219 (1983).
Tahiliani, M. et al. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324, 930–935 (2009).
Kriaucionis, S. & Heintz, N. The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 324, 929–930 (2009).
Ito, S. et al. Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification. Nature 466, 1129–1133 (2010).
Lister, R. et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462, 315–322 (2009).
Meissner, A. et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454, 766–770 (2008).
Jacinto, F.V., Ballestar, E. & Esteller, M. Methyl-DNA immunoprecipitation (MeDIP): hunting down the DNA methylome. Biotechniques 44, 35–43 (2008).
Down, T.A. et al. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat. Biotechnol. 26, 779–785 (2008).
Serre, D., Lee, B.H. & Ting, A.H. MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome. Nucleic Acids Res. 38, 391–399 (2010).
Maunakea, A.K. et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature 466, 253–257 (2010).
Ball, M.P. et al. Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat. Biotechnol. 27, 361–368 (2009).
Cokus, S.J. et al. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452, 215–219 (2008).
Lister, R. et al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133, 523–536 (2008).
The American Association for Cancer Research Human Epigenome Task Force European Union, Network of Excellence, Scientific Advisory Board Moving AHEAD with an international human epigenome project. Nature 454, 711–715 (2008).
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
Xi, Y. & Li, W. BSMAP: whole genome bisulfite sequence MAPping program. BMC Bioinformatics 10, 232 (2009).
Coarfa, C. & Milosavljevic, A. Pash 2.0: scaleable sequence anchoring for next-generation sequencing technologies. Pac. Symp. Biocomput. 2008, 102–113 (2008).
Smith, A.D. et al. Updates to the RMAP short-read mapping software. Bioinformatics 25, 2841–2842 (2009).
Lin, H., Zhang, Z., Zhang, M.Q., Ma, B. & Li, M. ZOOM! Zillions of oligos mapped. Bioinformatics 24, 2431–2437 (2008).
Wang, T. et al. Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53. Proc. Natl. Acad. Sci. USA 104, 18613–18618 (2007).
Kunarso, G. et al. Transposable elements have rewired the core regulatory network of human embryonic stem cells. Nat. Genet. 42, 631–634 (2010).
Pant, P.V.K. et al. Analysis of allelic differential expression in human white blood cells. Genome Res. 16, 331–339 (2006).
Pollard, K.S. et al. A genome-wide approach to identifying novel-imprinted genes. Hum. Genet. 122, 625–634 (2008).
Schalkwyk, L.C. et al. Allelic skewing of DNA methylation is widespread across the genome. Am. J. Hum. Genet. 86, 196–212 (2010).
Pick, M. et al. Clone- and gene-specific aberrations of parental imprinting in human induced pluripotent stem cells. Stem Cells 27, 2686–2690 (2009).
Arnaud, P. et al. Conserved methylation imprints in the human and mouse GRB10 genes with divergent allelic expression suggests differential reading of the same mark. Hum. Mol. Genet. 12, 1005–1019 (2003).
Li, N. et al. Whole genome DNA methylation analysis based on high throughput sequencing technology. Methods published online, doi: 10.1016/j.ymeth.2010.04.009 (27 April 2010).
Deng, J. et al. Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming. Nat. Biotechnol. 27, 353–360 (2009).
Bourque, G. Transposable elements in gene regulation and in the evolution of vertebrate genomes. Curr. Opin. Genet. Dev. 19, 607–612 (2009).
Duhl, D.M., Vrieling, H., Miller, K.A., Wolff, G.L. & Barsh, G.S. Neomorphic agouti mutations in obese yellow mice. Nat. Genet. 8, 59–65 (1994).
Waterland, R.A. & Jirtle, R.L. Transposable elements: targets for early nutritional effects on epigenetic gene regulation. Mol. Cell. Biol. 23, 5293–5300 (2003).
Hellman, A. & Chess, A. Gene body-specific methylation on the active X chromosome. Science 315, 1141–1143 (2007).
Ludwig, T.E. et al. Feeder-independent culture of human embryonic stem cells. Nat. Methods 3, 637–646 (2006).
Gu, H. et al. Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nat. Methods 7, 133–136 (2010).
Smith, Z.D., Gu, H., Bock, C., Gnirke, A. & Meissner, A. High-throughput bisulfite sequencing in mammalian genomes. Methods 48, 226–232 (2009).
O'Geen, H., Frietze, S. & Farnham, P.J. Using ChIP-seq technology to identify targets of zinc finger transcription factors. Methods Mol. Biol. 649, 437–455 (2010).
Robertson, G. et al. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat. Methods 4, 651–657 (2007).
Blahnik, K.R. et al. Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data. Nucleic Acids Res. 38, e13 (2010).
Waterland, R.A., Lin, J., Smith, C.A. & Jirtle, R.L. Post-weaning diet affects genomic imprinting at the insulin-like growth factor 2 (Igf2) locus. Hum. Mol. Genet. 15, 705–716 (2006).
Shen, L., Guo, Y., Chen, X., Ahmed, S. & Issa, J.J. Optimizing annealing temperature overcomes bias in bisulfite PCR methylation analysis. Biotechniques 42, 48, 50, 52 passim (2007).
Grunau, C., Clark, S.J. & Rosenthal, A. Bisulfite genomic sequencing: systematic investigation of critical experimental parameters. Nucleic Acids Res 29, E65 (2001).