Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing.
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%.
Robertson
Gordon
G
British Columbia Cancer Agency Genome Sciences Centre, 675 West 10th Avenue, Vancouver, British Columbia V5Z 4S6, Canada.
Hirst
Martin
M
Bainbridge
Matthew
M
Bilenky
Misha
M
Zhao
Yongjun
Y
Zeng
Thomas
T
Euskirchen
Ghia
G
Bernier
Bridget
B
Varhol
Richard
R
Delaney
Allen
A
Thiessen
Nina
N
Griffith
Obi L
OL
He
Ann
A
Marra
Marco
M
Snyder
Michael
M
Jones
Steven
S
D047369:Chromatin Immunoprecipitation; D004247:DNA / Q000235:genetics*; D016678:Genome; D016133:Polymerase Chain Reaction; D011485:Protein Binding; D050794:STAT1 Transcription Factor / Q000235:genetics* / Q000378:metabolism
D050794:STAT1 Transcription Factor; D004247:DNA