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

Gordon Robertson, Martin Hirst, Matthew Bainbridge, Misha Bilenky, Yongjun Zhao, Thomas Zeng, Ghia Euskirchen, Bridget Bernier, Richard Varhol, Allen Delaney, Nina Thiessen, Obi L. Griffith, Ann He, Marco Marra, Michael Snyder, Steven Jones

Research output: Contribution to journalArticlepeer-review

961 Scopus citations

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-γ (IFN-γ)-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%.

Original languageEnglish
Pages (from-to)651-657
Number of pages7
JournalNature Methods
Volume4
Issue number8
DOIs
StatePublished - Aug 1 2007
Externally publishedYes

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