Unit

UNIT 21.27 Genome-Scale Mapping of DNase I Hypersensitivity

  1. Sam John1,3,
  2. Peter J. Sabo1,3,
  3. Theresa K. Canfield1,
  4. Kristen Lee1,
  5. Shinny Vong1,
  6. Molly Weaver1,
  7. Hao Wang1,
  8. Jeff Vierstra1,
  9. Alex P. Reynolds1,
  10. Robert E. Thurman1,
  11. John A. Stamatoyannopoulos1,2

Published Online: 1 JUL 2013

DOI: 10.1002/0471142727.mb2127s103

Current Protocols in Molecular Biology

Current Protocols in Molecular Biology

How to Cite

John, S., Sabo, P. J., Canfield, T. K., Lee, K., Vong, S., Weaver, M., Wang, H., Vierstra, J., Reynolds, A. P., Thurman, R. E. and Stamatoyannopoulos, J. A. 2013. Genome-Scale Mapping of DNase I Hypersensitivity. Current Protocols in Molecular Biology. 103:21.27:21.27.1–21.27.20.

Author Information

  1. 1

    Department of Genome Sciences, University of Washington, Seattle, Washington

  2. 2

    Department of Medicine, University of Washington, Seattle, Washington

  3. 3

    Authors contributed equally to this work.

Publication History

  1. Published Online: 1 JUL 2013
  2. Published Print: JUL 2013

Abstract

DNase I-seq is a global and high-resolution method that uses the nonspecific endonuclease DNase I to map chromatin accessibility. These accessible regions, designated as DNase I hypersensitive sites (DHSs), define the regulatory features, (e.g., promoters, enhancers, insulators, and locus control regions) of complex genomes. In this unit, methods are described for nuclei isolation, digestion of nuclei with limiting concentrations of DNase I, and the biochemical fractionation of DNase I hypersensitive sites in preparation for high-throughput sequencing. DNase I-seq is an unbiased and robust method that is not predicated on an a priori understanding of regulatory patterns or chromatin features. Curr. Protoc. Mol. Biol. 103:21.27.1–21.27.20. © 2013 by John Wiley & Sons, Inc.

Keywords:

  • chromatin;
  • nucleosome;
  • DNase I-seq;
  • transcription;
  • regulatory DNA