Robertson Gordon, Hirst Martin, Bainbridge Matthew, Bilenky Misha, Zhao Yongjun, Zeng Thomas, Euskirchen Ghia, Bernier Bridget, Varhol Richard, Delaney Allen, Thiessen Nina, Griffith Obi L, He Ann, Marra Marco, Snyder Michael, Jones Steven
British Columbia Cancer Agency Genome Sciences Centre, 675 West 10th Avenue, Vancouver, British Columbia V5Z 4S6, Canada.
Nat Methods. 2007 Aug;4(8):651-7. doi: 10.1038/nmeth1068. Epub 2007 Jun 11.
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-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%.
我们开发了一种名为染色质免疫沉淀测序（ChIP-seq）的方法，该方法结合了染色质免疫沉淀（ChIP）和大规模平行测序技术，用于在体内鉴定与转录因子结合的哺乳动物DNA序列。我们使用ChIP-seq技术绘制了干扰素-γ（IFN-γ）刺激和未刺激的人HeLa S3细胞中STAT1的靶点，并将该方法的性能与ChIP-PCR以及针对四条染色体的ChIP芯片进行了比较。通过ChIP-seq技术，利用1510万和1290万条唯一比对的序列读数，估计错误发现率小于0.001，我们分别在刺激和未刺激的细胞中鉴定出41582个和11004个假定的STAT1结合区域。在已知包含STAT1干扰素应答结合位点的34个基因座中，ChIP-seq技术找到了24个（71%）。ChIP-seq技术的靶点在与已知STAT1结合基序相似的序列中富集。与两个ChIP-PCR数据集的比较表明，ChIP-seq技术的灵敏度在70%至92%之间，特异性至少为95%。
