The state-of-the-art methods collected here are designed to analyze the relationship between chromatin structure and function, and to elucidate the molecular mechanisms that control such vital cellular functions as transcription, replication, recombination, and DNA repair. These proven methods cover a wide range of topics, from powerful cell-free systems for the reconstitution of chromatin heterogeneity in vitro, to both classical and cutting-edge techniques for in vivo analysis of protein-DNA interactions. Each method includes detailed step-by-step instructions to ensure successful replication along with helpful notes about how to avoid pitfalls. All authors are leading scientists, well known for their methodological expertise in the chromatin research.