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Science 316 (5830): 1497-1502

Copyright © 2007 by the American Association for the Advancement of Science

Genome-Wide Mapping of in Vivo Protein-DNA Interactions

David S. Johnson,1* Ali Mortazavi,2* Richard M. Myers,1{dagger} Barbara Wold2,3{dagger}

Abstract: 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.

1 Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305–5120, USA.
2 Biology Division, California Institute of Technology, Pasadena, CA 91125, USA.
3 California Institute of Technology Beckman Institute, Pasadena, CA 91125, USA.

* These authors contributed equally to this work.

{dagger} To whom correspondence should be addressed. E-mail: woldb{at}its.caltech.edu (B.W.); myers{at}shgc.stanford.edu (R.M.M.)

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