Chromatin Immunoprecipitation Sequencing in Cancer Cells

Analysis of DNA co-immunoprecipitated with proteins of interest has been foundational to our understanding of chromatin and its regulation. Despite the emergence of crosslink-free techniques such as CUT&RUN and CUT&TAG, Chromatin Immunoprecipitation followed by sequencing (ChIP) remains a method of choice for profiling of protein binding at individual DNA sites and, when combined with sequencing (ChIP-seq), across the genome. ChIP-seq can provide insights into transcription factor binding sites, histone modification patterns and chromatin structure, and has broad applications in the study of cancer and other diseases. Here, we outline the protocols for ChIP-seq, including immunoprecipitation, library preparation for high-throughput sequencing, and bioinformatics analysis of sequencing data that we routinely perform in our lab groups. We also include troubleshooting tips for each step. We hope this guide will be helpful to laboratories that wish to adopt this method for their cancer biology studies.