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Article
Nature Methods - 4, 651 - 657 (2007)
Published online: 11 June 2007; | doi:10.1038/nmeth1068

Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing

Gordon Robertson1, Martin Hirst1, Matthew Bainbridge1, Misha Bilenky1, Yongjun Zhao1, Thomas Zeng1, Ghia Euskirchen2, Bridget Bernier1, Richard Varhol1, Allen Delaney1, Nina Thiessen1, Obi L Griffith1, Ann He1, Marco Marra1, Michael Snyder2 & Steven Jones1

1  British Columbia Cancer Agency Genome Sciences Centre, 675 West 10th Avenue, Vancouver, British Columbia V5Z 4S6, Canada.

2  Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA.

Correspondence should be addressed to Steven Jones sjones@bcgsc.ca

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-bold gamma (IFN-bold 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%.

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Nature Methods
ISSN: 1548-7091
EISSN: 1548-7105
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