Genome-Wide Mapping of in Vivo Protein-DNA Interactions

作者：David S. Johnson, A Mortazavi, R Myers, B Wold · 发表于：Science · 年份：2007 · DOI：10.1126/science.1141319 · 被引用次数：3063 · 研究领域：Genomics and Chromatin Dynamics、Genetics and Neurodevelopmental Disorders、Epigenetics and DNA Methylation

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.