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Originally published in Science Express on 31 May 2007
Science 8 June 2007:
Vol. 316. no. 5830, pp. 1497 - 1502
DOI: 10.1126/science.1141319
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Reports

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}

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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   Abstract »    PDF »
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   Abstract »    Full Text »    PDF »
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   Abstract »    Full Text »    PDF »
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   Abstract »    Full Text »    PDF »
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   Abstract »    Full Text »    PDF »
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   Abstract »    Full Text »    PDF »
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   Abstract »    Full Text »    PDF »
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   Abstract »    Full Text »    PDF »
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   Abstract »    Full Text »    PDF »
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J. M. Rosenbluth, D. J. Mays, M. F. Pino, L. J. Tang, and J. A. Pietenpol (2008)
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   Abstract »    Full Text »    PDF »
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S. A. Vokes, H. Ji, W. H. Wong, and A. P. McMahon (2008)
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   Abstract »    Full Text »    PDF »
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   Abstract »    Full Text »    PDF »
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R. Jothi, S. Cuddapah, A. Barski, K. Cui, and K. Zhao (2008)
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   Abstract »    Full Text »    PDF »
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E. D. Wederell, M. Bilenky, R. Cullum, N. Thiessen, M. Dagpinar, A. Delaney, R. Varhol, Y. Zhao, T. Zeng, B. Bernier, et al. (2008)
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   Abstract »    Full Text »    PDF »
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J. M. Oliver-Krasinski and D. A. Stoffers (2008)
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   Abstract »    Full Text »    PDF »
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A. P. Fejes, G. Robertson, M. Bilenky, R. Varhol, M. Bainbridge, and S. J. M. Jones (2008)
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   Abstract »    Full Text »    PDF »
Four-color DNA sequencing with 3'-O-modified nucleotide reversible terminators and chemically cleavable fluorescent dideoxynucleotides.
J. Guo, N. Xu, Z. Li, S. Zhang, J. Wu, D. H. Kim, M. Sano Marma, Q. Meng, H. Cao, X. Li, et al. (2008)
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   Abstract »    Full Text »    PDF »
The new paradigm of flow cell sequencing.
R. A. Holt and S. J.M. Jones (2008)
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   Abstract »    Full Text »    PDF »
Identification of active transcriptional regulatory modules by the functional assay of DNA from nucleosome-free regions.
M. Yaragatti, C. Basilico, and L. Dailey (2008)
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   Abstract »    Full Text »    PDF »
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M. B. Noyes, X. Meng, A. Wakabayashi, S. Sinha, M. H. Brodsky, and S. A. Wolfe (2008)
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   Abstract »    Full Text »    PDF »
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J. Butler, I. MacCallum, M. Kleber, I. A. Shlyakhter, M. K. Belmonte, E. S. Lander, C. Nusbaum, and D. B. Jaffe (2008)
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   Abstract »    Full Text »    PDF »
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D. R. Zerbino and E. Birney (2008)
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   Abstract »    Full Text »    PDF »
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K. Century, T. L. Reuber, and O. J. Ratcliffe (2008)
Plant Physiology 147, 20-29
   Full Text »    PDF »
High-throughput biochemical analysis of in vivo location data reveals novel distinct classes of POU5F1(Oct4)/DNA complexes.
D. Tantin, M. Gemberling, C. Callister, and W. Fairbrother (2008)
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   Abstract »    Full Text »    PDF »
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C. B. M. Oudejans (2008)
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   Full Text »    PDF »
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets.
D. S. Johnson, W. Li, D. B. Gordon, A. Bhattacharjee, B. Curry, J. Ghosh, L. Brizuela, J. S. Carroll, M. Brown, P. Flicek, et al. (2008)
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   Abstract »    Full Text »    PDF »
Transcription of laminin {gamma}1 chain gene in rat mesangial cells: constitutive and inducible RNA polymerase II recruitment and chromatin states.
J. D. Nelson, S. Flanagin, Y. Kawata, O. Denisenko, and K. Bomsztyk (2008)
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   Abstract »    Full Text »    PDF »
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A. C. Roman, D. A. Benitez, J. M. Carvajal-Gonzalez, and P. M. Fernandez-Salguero (2008)
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   Abstract »    Full Text »    PDF »
Model-based deconvolution of genome-wide DNA binding.
D. J. Reiss, M. T. Facciotti, and N. S. Baliga (2008)
Bioinformatics 24, 396-403
   Abstract »    Full Text »    PDF »
ORegAnno: an open-access community-driven resource for regulatory annotation.
O. L. Griffith, S. B. Montgomery, B. Bernier, B. Chu, K. Kasaian, S. Aerts, S. Mahony, M. C. Sleumer, M. Bilenky, M. Haeussler, et al. (2008)
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   Abstract »    Full Text »    PDF »
3'-O-modified nucleotides as reversible terminators for pyrosequencing.
J. Wu, S. Zhang, Q. Meng, H. Cao, Z. Li, X. Li, S. Shi, D. H. Kim, L. Bi, N. J. Turro, et al. (2007)
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   Abstract »    Full Text »    PDF »
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Development 134, 3227-3238
   Abstract »    Full Text »    PDF »
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P. D. Patel, D. A. Bochar, D. L. Turner, F. Meng, H. M. Mueller, and C. G. Pontrello (2007)
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   Abstract »    Full Text »    PDF »


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