Combined chromatin immunoprecipitation and bisulfite methylation sequencing analysis

Epigenetic mechanisms control gene transcription primarily through regulating chromatin structures and DNA methylation. Transcription factors can also affect gene transcription through binding of the key transcriptional machinery to the gene promoter. These factors normally jointly influence the transcriptional processes, leading to silencing or activation of gene expression. A novel technique has been recently explored in our laboratory, which is a combination of conventional chromatin immunoprecipitation (ChIP) with bisulfite methylation sequencing assays, so-called ChIP and bisulfite methylation sequencing (ChIP-BMS). This technique provides precise information of DNA methylation status at the selected DNA fragments precipitated by the antibodies to histone molecules or transcription factors of interest. This method also helps to investigate the interactions between histone modification and DNA methylation, and how this crosstalking can affect gene expression. More importantly, it is easy to determine potential methylation-sensitive transcription factors that influence transcription mainly depending on methylation status of the binding sites. In this chapter, we discuss the detailed procedures of this novel technique and its broad application in epigenetic and genetic fields.