Epigenetic regulation plays a critical role in gene expression, cellular differentiation, and disease. There is a complex interplay between the different layers of epigenetic information, including DNA methylation, nucleosome positions, histone modifications, histone variants, and other important epigenetic regulators. The different modifications do not act independently of each other and their relationship plays an important role in governing the regulation of the epigenome. Of these, DNA methylation is the best-studied epigenetic modification in mammals. However, the direct relationship between DNA methylation and chromatin modifications has been difficult to unravel with existing technologies, with epigenome-wide integration studies still based on “overlaying” independent chromatin modification and DNA methylation maps. Bisulphite sequencing enables the methylation state of every cytosine residue to be analyzed across a given molecule in a strand-specific context. Here, we describe a direct approach to interrogating the DNA methylation status of specific chromatin-marked DNA, using high-throughput sequencing of bisulphite-treated chromatin immunoprecipitated DNA (BisChIP-seq). This combined approach enables the exquisite relationship between chromatin-modified DNA or transcription factor-associated DNA and the methylation state of each targeted allele to be directly interrogated. BisChIP-Seq can now be widely applied genome-wide to further understand the molecular relationship between DNA methylation and other important epigenetic regulators.
Bisulphite-sequencing Chromatin immunoprecipitation BisChIP-seq DNA methylation
This is a preview of subscription content, log in to check access.
Springer Nature is developing a new tool to find and evaluate Protocols. Learn more
We thank Dr. Warwick Locke for careful reading of the manuscript. S.J.C. is a National Health and Medical Research Council (NH&MRC) Senior Principal Research Fellow. This work was further supported by an NH&MRC Project Grant (1029584).
Gal-Yam EN, Egger G, Iniguez L et al (2008) Frequent switching of Polycomb repressive marks and DNA hypermethylation in the PC3 prostate cancer cell line. Proc Natl Acad Sci U S A 105:12979–12984CrossRefPubMedPubMedCentralGoogle Scholar
Kondo Y, Shen L, Cheng AS et al (2008) Gene silencing in cancer by histone H3 lysine 27 trimethylation independent of promoter DNA methylation. Nat Genet 40:741–750CrossRefPubMedGoogle Scholar
Coolen MW, Stirzaker C, Song JZ et al (2010) Consolidation of the cancer genome into domains of repressive chromatin by long-range epigenetic silencing (LRES) reduces transcriptional plasticity. Nat Cell Biol 12:235–246PubMedPubMedCentralGoogle Scholar
Brinkman AB, Gu H, Bartels SJ et al (2012) Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk. Genome Res 22:1128–1138CrossRefPubMedPubMedCentralGoogle Scholar
Statham AL, Robinson MD, Song JZ et al (2012) Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA. Genome Res 22:1120–1127CrossRefPubMedPubMedCentralGoogle Scholar