DNase I Digestion of Isolated Nulcei for Genome-Wide Mapping of DNase Hypersensitivity Sites in Chromatin

  • Guoyu Ling
  • David J. Waxman
Part of the Methods in Molecular Biology book series (MIMB, volume 977)


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.

Key words

DNase I hypersensitivity assay Next generation DNA sequencing DNase-seq Chromatin structure 



Supported in part by NIH grant DK33765 (to DJW).


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Copyright information

© Springer Science+Business Media, LLC 2013

Authors and Affiliations

  • Guoyu Ling
    • 1
  • David J. Waxman
    • 1
  1. 1.Department of BiologyBoston UniversityBostonUSA

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