Johnson David S, Mortazavi Ali, Myers Richard M, Wold Barbara
Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305-5120, USA.
Science. 2007 Jun 8;316(5830):1497-502. doi: 10.1126/science.1141319. Epub 2007 May 31.
In vivo protein-DNA interactions connect each transcription factor with its direct targets to form a gene network scaffold. To map these protein-DNA interactions comprehensively across entire mammalian genomes, we developed a large-scale chromatin immunoprecipitation assay (ChIPSeq) based on direct ultrahigh-throughput DNA sequencing. This sequence census method was then used to map in vivo binding of the neuron-restrictive silencer factor (NRSF; also known as REST, for repressor element-1 silencing transcription factor) to 1946 locations in the human genome. The data display sharp resolution of binding position [+/-50 base pairs (bp)], which facilitated our finding motifs and allowed us to identify noncanonical NRSF-binding motifs. These ChIPSeq data also have high sensitivity and specificity [ROC (receiver operator characteristic) area >/= 0.96] and statistical confidence (P <10(-4)), properties that were important for inferring new candidate interactions. These include key transcription factors in the gene network that regulates pancreatic islet cell development.
体内蛋白质与DNA的相互作用将每个转录因子与其直接靶标相连，形成一个基因网络支架。为了在整个哺乳动物基因组中全面绘制这些蛋白质与DNA的相互作用图谱，我们基于直接超高通量DNA测序开发了一种大规模染色质免疫沉淀测定法（ChIPSeq）。然后，这种序列普查方法被用于绘制神经元限制性沉默因子（NRSF；也称为REST，即阻遏元件1沉默转录因子）在人类基因组中1946个位置的体内结合图谱。数据显示出结合位置的高分辨率[±50碱基对（bp）]，这有助于我们找到基序，并使我们能够识别非规范的NRSF结合基序。这些ChIPSeq数据还具有高灵敏度和特异性[ROC（受试者工作特征）面积≥0.96]以及统计可信度（P<10⁻⁴），这些特性对于推断新的候选相互作用很重要。这些相互作用包括调节胰岛细胞发育的基因网络中的关键转录因子。
