Unit

UNIT 21.19 ChIP-Seq: A Method for Global Identification of Regulatory Elements in the Genome

  1. Debasish Raha,
  2. Miyoung Hong,
  3. Michael Snyder

Published Online: 1 JUL 2010

DOI: 10.1002/0471142727.mb2119s91

Current Protocols in Molecular Biology

Current Protocols in Molecular Biology

How to Cite

Raha, D., Hong, M. and Snyder, M. 2010. ChIP-Seq: A Method for Global Identification of Regulatory Elements in the Genome. Current Protocols in Molecular Biology. 91:21.19:21.19.1–21.19.14.

Author Information

  1. Stanford University, Stanford, California

Publication History

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

Abstract

This unit describes ChIP-Seq methodology, which involves chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (Seq), and enables the genome-wide identification of binding sites of transcription factors (TFs) and other DNA-binding proteins. The process is initiated by cross-linking DNA and DNA-bound proteins. Subsequently, chromatin is isolated from nuclei and subjected to sonication. An antibody against a specific TF or DNA-binding protein is then used to immunoprecipitate specific DNA-TF complexes. ChIP DNA is purified, sequencing adapters are ligated, and 30- to 35-nucleotide (nt) sequence reads are generated. The sequence of the DNA fragments is mapped back to the reference genome for determination of the binding sites. Curr. Protoc. Mol. Biol. 91:21.19.1-21.19.14. © 2010 by John Wiley & Sons, Inc.

Keywords:

  • mammalian cells;
  • ChIP;
  • ChIP-Seq;
  • binding site;
  • genome-wide