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 ChIPseq 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%.