Analysis of Chromatin Organization by Deep Sequencing Technologies

Micrococcal nuclease (MNase) is an endonuclease that cleaves native DNA at high frequency, but is blocked in chromatin by sites of intimate DNA–protein interaction, including nucleosomal regions. Protection from MNase cleavage has often been used to map transcription factor binding sites and nucleosomal positions on a single-gene basis; however, by combining MNase digestion with high-�throughput, paired-end DNA sequencing, it is now possible to simultaneously map DNA-protein interaction regions across the entire genome. Biochemical and bioinformatic protocols are detailed for global mono-nucleosome positioning at ∼160 bp spacing coverage, but are applicable to mapping more broadly or for site-specific binding of transcription factors at ∼50 bp resolution.