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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-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%.

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Figure 1: FDR-thresholded XSET profiles and peaks.
Figure 2: Stimulated and unstimulated peak sets had distinct global properties.
Figure 3: Relationship of peak height to absolute distance from the peak maximum to an overlapped known STAT1 binding site.
Figure 4: Peak enrichment in sequences similar to STAT1 binding sites.

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We gratefully acknowledge the expert technical assistance of the Genome Sciences Centre Functional Genomics team. This study received funding support from Genome British Columbia (Platform and MORGEN project), Genome Canada and the BC Cancer Foundation. M.M. and S.J. are Scholars of the Michael Smith Foundation for Health Research. M.M. is a Terry Fox Young Investigator.

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Correspondence to Steven Jones.

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Supplementary Texts and Figures

Supplementary Figures 1–14, Supplementary Tables 1–5, Supplementary Results, Supplementary Methods, Supplementary Data 2 (PDF 3100 kb)

Supplementary Data 1

Data files for significant peaks. (ZIP 8165 kb)

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Robertson, G., Hirst, M., Bainbridge, M. et al. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods 4, 651–657 (2007).

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