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Published June 8, 2007 | Supplemental Material
Journal Article Open

Genome-Wide Mapping of in Vivo Protein-DNA Interactions


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.

Additional Information

© 2007 American Association for the Advancement of Science. Received 14 February 2007; accepted 26 April 2007; Published online 31 May 2007. We thank G. Schroth and his group at Solexa/Illumina, Inc., for access to the sequencing platform, without which this work would not have been possible. We thank B. Anton, L. Nguyen, C. Medina, and L. Tsavaler for outstanding experimental work and K. F. McCue for invaluable counsel on statistical analyses. We are grateful to D. Anderson of Caltech for the gift of monoclonal antibody against NRSF. This work was supported by NIH grant U01 HG003162 to R.M.M. with a supplement to B.W. and by a grant from the Caltech Beckman Institute. A.M. was supported by NIH/National Research Service Award 5T32GM07616; B.W. by a Bren Chair endowment at Caltech, and R.M.M. by the Stanford W. Ascherman Chair endowment at Stanford University.

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