Genome-Wide Mapping of in Vivo Protein-DNA Interactions

Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305-5120, USA.
Science (Impact Factor: 33.61). 07/2007; 316(5830):1497-502. DOI: 10.1126/science.1141319
Source: PubMed


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.

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    • "All TFs recognize short DNA sequences (6– 12 bp) and their motifs show varying levels of degeneracy (D'haeseleer 2006). ChIP-seq experiments allow the identification of regions in the genome that are bound by TFs (Johnson et al. 2007). Analyses of a wide variety of different TFs have shown that only a small subset of possible binding sites is occupied by the TF (Carr and Biggin 1999; Iyer et al. 2001; Yang et al. 2006). "
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