title: DNase I digestion of isolated nulcei for genome-wide mapping of DNase hypersensitivity sites in chromatin.
abstract: DNase I hypersensitivity (DHS) analysis is a powerful method to analyze chromatin structure and identify genomic regulatory elements. Integration of a high-throughput detection method into DHS analysis makes genome-wide mapping of DHS sites possible at a reasonable cost. Here we describe methods for DHS analysis carried out with mouse liver nuclei, involving DNase I digestion followed by isolation of DNase I-released DNA fragments suitable for high-throughput, next generation DNA sequencing (DNase-seq). A real-time PCR-based assay used to optimize DNase I digestion conditions is also described.
authors: Department of Biology, Boston University, Boston, MA, USA.
authors: Guoyu
authors: G
authors: Ling
authors: David J
authors: DJ
authors: Waxman
mesh_terms: D000818:Animals; D002467:Cell Nucleus / Q000737:chemistry* / Q000235:genetics; D002843:Chromatin / Q000737:chemistry* / Q000235:genetics / Q000302:isolation & purification; D053837:DNA Cleavage; D003850:Deoxyribonuclease I / Q000737:chemistry*; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D008099:Liver / Q000737:chemistry; D051379:Mice; D009690:Nucleic Acid Conformation; D060888:Real-Time Polymerase Chain Reaction; D017422:Sequence Analysis, DNA
chemical_list: D002843:Chromatin; D003850:Deoxyribonuclease I