Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing
复制标题
DOI：
10.1038/nmeth1068
复制
发表时间：
2007-08-01
期刊：
影响因子：
48
通讯作者：
Jones, Steven
中科院分区：
文献类型：
--
作者：
Robertson, Gordon;Hirst, Martin;Jones, Steven
我们开发了一种方法，即芯片测序（芯片SEQ），结合了染色质免疫沉淀（CHIP）和大规模平行的测序，以鉴定由体内转录因子结合的哺乳动物DNA序列。我们使用Chipseq绘制干扰素γ（IFN-GAMMA）中的STAT1靶标刺激和未刺激的人类HELA S3细胞，并将该方法的性能与Chip-PCR和四个染色体的芯片进行了比较。通过Chip-Seq，使用15.1和1,290万个唯一映射的序列读取，估计的错误发现率小于0.001，我们在受刺激和未刺激的细胞中分别鉴定了41,582和11,004个假定的STAT1-结合区域。在已知包含STAT1干扰素反应性结合位点的34个基因座中，Chip-Seq发现了24（71％）。将芯片靶标以类似于已知的STAT1结合基序的序列富集。与两个芯片PCR数据集的比较表明，芯片SEQ灵敏度在70％至92％之间，特异性至少为95％。
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%.