ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions.
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.
Schmidt
Dominic
D
Department of Oncology, Hutchison/MRC Research Centre, Hills Road, Cambridge CB20XZ, UK.
Wilson
Michael D
MD
Spyrou
Christiana
C
Brown
Gordon D
GD
Hadfield
James
J
Odom
Duncan T
DT
D002478:Cells, Cultured; D002843:Chromatin / Q000737:chemistry; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D003432:Cross-Linking Reagents / Q000737:chemistry; D005557:Formaldehyde / Q000737:chemistry; D006801:Humans; D016133:Polymerase Chain Reaction / Q000379:methods; D025941:Protein Interaction Mapping / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*
D002843:Chromatin; D003432:Cross-Linking Reagents; D005557:Formaldehyde