This comprehensive guide delves into the protocols and strategies for investigating gene regulation both experimentally and computationally. It focuses on the use of Chromatin Immunoprecipitation (ChIP) coupled with next-generation sequencing, providing a robust framework for profiling DNA-binding proteins, examining DNA footprinting, and analyzing histone modifications. As part of the highly successful Methods in Molecular Biology series, this book offers introductions on the topics covered, detailed lists of the necessary materials and reagents, step-by-step laboratory protocols that are easy to follow, and expert tips for troubleshooting and avoiding known pitfalls. Authoritative and practical, Chromatin Immunoprecipitation: Methods and Protocols is the perfect resource for the new wave of genome biologists looking to master ChIP techniques.