title: Analysis of chromatin organization by deep sequencing technologies.
abstract: 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.
authors.affiliation: Laboratory of Cellular and Developmental Biology, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
authors.forename: James L
authors.initials: JL
authors.lastname: Platt
authors.forename: Nick A
authors.initials: NA
authors.lastname: Kent
authors.forename: Adrian J
authors.initials: AJ
authors.lastname: Harwood
authors.forename: Alan R
authors.initials: AR
authors.lastname: Kimmel
mesh_terms: D002843:Chromatin / Q000235:genetics; D002874:Chromosome Mapping / Q000379:methods*; D053837:DNA Cleavage; D016054:DNA, Protozoan / Q000235:genetics / Q000302:isolation & purification; D004023:Dictyostelium / Q000235:genetics; D015723:Gene Library; D018503:Genome, Protozoan; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D008836:Micrococcal Nuclease / Q000737:chemistry; D009707:Nucleosomes / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods
chemical_list: D002843:Chromatin; D016054:DNA, Protozoan; D009707:Nucleosomes; D008836:Micrococcal Nuclease