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- Title
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing.
- Authors
Robertson, Gordon; Hirst, Martin; Bainbridge, Matthew; Bilenky, Misha; Yongjun Zhao; Zeng, Thomas; Euskirchen, Ghia; Bernier, Bridget; Varhol, Richard; Delaney, Allen; Thiessen, Nina; Griffith, Obi L; He, Ann; Marra, Marco; Snyder, Michael; Jones, Steven
- 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%.
- Subjects
ANTIVIRAL agents; INTERFERONS; NUCLEOTIDE sequence; HUMAN genome; GENETICS
- Publication
Nature Methods, 2007, Vol 4, Issue 8, p651
- ISSN
1548-7091
- Publication type
Article
- DOI
10.1038/nmeth1068