from Sebastian Lunke and Assam El-Osta writing in Epigenetics: A Reference Manual:
With the advances in traditional genetics failing to provide causal genes for many complex diseases, the focus of research is shifting towards determining the importance of gene-environment interactions, more specifically epigenetic regulation. Paramount to answering this question is the knowledge of which transcription factors bind to what sequence, as well as a detailed understanding of how the transcriptional state of a genetic sequence is epigenetically distinguished. The chromatin immuno-precipitation (ChIP) strategy has proven to be a powerful tool to investigate these mechanisms, but has been limited for a long time to single locus analysis. The recent emergence of next-generation sequencing (NGS) technology however has revolutionized the field of epigenomics and for the first time enabled unbiased genome-wide analysis of ChIPed DNA. Here we provide a detailed discussion and protocol on how to best perform ChIP for NGS analysis.
Further reading: Epigenetics: A Reference Manual