ChIP-seq: Using high-throughput sequencing to discover protein–DNA interactions

• Published in: Methods (San Diego, Calif.) Vol. 48; no. 3; pp. 240 - 248
• Main Authors: Schmidt, Dominic, Wilson, Michael D., Spyrou, Christiana, Brown, Gordon D., Hadfield, James, Odom, Duncan T.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01-07-2009
• Subjects: Cells, Cultured; ChIP-seq; ChIPseq; Chromatin - chemistry; Chromatin immunoprecipitation; Chromatin Immunoprecipitation - methods; Cross-Linking Reagents - chemistry; Formaldehyde - chemistry; High-throughput sequencing; Humans; Polymerase Chain Reaction - methods; Protein Interaction Mapping - methods; Sequence Analysis, DNA - methods; Chromatin immunoprecipitation; ChIP-seq; High-throughput sequencing; ChIPseq
• ISSN: 1046-2023; 1095-9130
• DOI: 10.1016/j.ymeth.2009.03.001

Chromatin immunoprecipitation (ChIP) allows specific protein–DNA interactions to be isolated. Combining ChIP with high-throughput sequencing reveals the DNA sequence involved in these interactions. Here, we describe how to perform ChIP-seq starting with whole tissues or cell lines, and ending with millions of short sequencing tags that can be aligned to the reference genome of the species under investigation. We also outline additional procedures to recover ChIP-chip libraries for ChIP-seq and discuss contemporary issues in data analysis.