UNIT 21.17 Methylation-Sensitive Single-Molecule Analysis of Chromatin Structure

  1. Tina B. Miranda1,
  2. Theresa K. Kelly1,
  3. Karim Bouazoune2,
  4. Peter A. Jones1

Published Online: 1 JAN 2010

DOI: 10.1002/0471142727.mb2117s89

Current Protocols in Molecular Biology

Current Protocols in Molecular Biology

How to Cite

Miranda, T. B., Kelly, T. K., Bouazoune, K. and Jones, P. A. 2010. Methylation-Sensitive Single-Molecule Analysis of Chromatin Structure. Current Protocols in Molecular Biology. 89:21.17:21.17.1–21.17.16.

Author Information

  1. 1

    Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California

  2. 2

    Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts

Publication History

  1. Published Online: 1 JAN 2010
  2. Published Print: JAN 2010


Methylation-sensitive single-molecule analysis of chromatin structure is a high-resolution method for studying nucleosome positioning. As described in this unit, this method allows for the analysis of the chromatin structure of unmethylated CpG islands or in vitro–remodeled nucleosomes by treatment with the CpG-specific DNA methyltransferase SssI (M.SssI), followed by bisulfite sequencing of individual progeny DNA molecules. Unlike nuclease-based approaches, this method allows each molecule to be viewed as an individual entity instead of an average population. Curr. Protoc. Mol. Biol. 89:21.17.1-21.17.16. © 2010 by John Wiley & Sons, Inc.


  • chromatin remodeling;
  • nucleosome positioning;
  • methylation footprint