title: Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing.
abstract: We developed a method, ChIP-sequencing (ChIP-seq), combining chromatin immunoprecipitation (ChIP) and massively parallel sequencing to identify mammalian DNA sequences bound by transcription factors in vivo. We used ChIP-seq to map STAT1 targets in interferon-gamma (IFN-gamma)-stimulated and unstimulated human HeLa S3 cells, and compared the method's performance to ChIP-PCR and to ChIP-chip for four chromosomes. By ChIP-seq, using 15.1 and 12.9 million uniquely mapped sequence reads, and an estimated false discovery rate of less than 0.001, we identified 41,582 and 11,004 putative STAT1-binding regions in stimulated and unstimulated cells, respectively. Of the 34 loci known to contain STAT1 interferon-responsive binding sites, ChIP-seq found 24 (71%). ChIP-seq targets were enriched in sequences similar to known STAT1 binding motifs. Comparisons with two ChIP-PCR data sets suggested that ChIP-seq sensitivity was between 70% and 92% and specificity was at least 95%.
authors.affiliation: British Columbia Cancer Agency Genome Sciences Centre, 675 West 10th Avenue, Vancouver, British Columbia V5Z 4S6, Canada.
authors.forename: Gordon
authors.initials: G
authors.lastname: Robertson
authors.forename: Martin
authors.initials: M
authors.lastname: Hirst
authors.forename: Matthew
authors.initials: M
authors.lastname: Bainbridge
authors.forename: Misha
authors.initials: M
authors.lastname: Bilenky
authors.forename: Yongjun
authors.initials: Y
authors.lastname: Zhao
authors.forename: Thomas
authors.initials: T
authors.lastname: Zeng
authors.forename: Ghia
authors.initials: G
authors.lastname: Euskirchen
authors.forename: Bridget
authors.initials: B
authors.lastname: Bernier
authors.forename: Richard
authors.initials: R
authors.lastname: Varhol
authors.forename: Allen
authors.initials: A
authors.lastname: Delaney
authors.forename: Nina
authors.initials: N
authors.lastname: Thiessen
authors.forename: Obi L
authors.initials: OL
authors.lastname: Griffith
authors.forename: Ann
authors.initials: A
authors.lastname: He
authors.forename: Marco
authors.initials: M
authors.lastname: Marra
authors.forename: Michael
authors.initials: M
authors.lastname: Snyder
authors.forename: Steven
authors.initials: S
authors.lastname: Jones
mesh_terms: D047369:Chromatin Immunoprecipitation; D004247:DNA / Q000235:genetics*; D016678:Genome; D016133:Polymerase Chain Reaction; D011485:Protein Binding; D050794:STAT1 Transcription Factor / Q000235:genetics* / Q000378:metabolism
chemical_list: D050794:STAT1 Transcription Factor; D004247:DNA