DNase I digestion of isolated nulcei for genome-wide mapping of DNase hypersensitivity sites in chromatin.

Guoyu Ling, David J Waxman

Methods in molecular biology (Clifton, N.J.) 2013

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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.

Citation

Guoyu Ling, David J Waxman. DNase I digestion of isolated nulcei for genome-wide mapping of DNase hypersensitivity sites in chromatin. Methods in molecular biology (Clifton, N.J.). 2013;977:21-33