Genome-wide mapping of in vivo protein-DNA interactions

Science

Volumn 316, Issue 5830, 2007, Pages 1497-1502

  Johnson, David S ^a   Mortazavi, Ali ^b   Myers, Richard M ^a   Wold, Barbara ^b,c  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b California Institute of Technology HHMI   (United States)

^c CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NEURON RESTRICTIVE SILENCER FACTOR; REPRESSOR ELEMENT 1 SILENCING TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG;

DNA; GENE EXPRESSION; GENOME; IMMUNOASSAY; MAMMAL; MAPPING; PROTEIN; PROTEOMICS;

ARTICLE; BASE PAIRING; CHROMATIN IMMUNOPRECIPITATION; DNA SEQUENCE; GENE LOCATION; GENE MAPPING; GENOME ANALYSIS; HUMAN; HUMAN GENOME; IN VIVO STUDY; MAMMAL; PANCREAS ISLET; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN MOTIF; REGULATORY MECHANISM; SENSITIVITY AND SPECIFICITY;

ALGORITHMS; AMINO ACID MOTIFS; BINDING SITES; CHROMATIN IMMUNOPRECIPITATION; DNA; DNA-BINDING PROTEINS; GENE REGULATORY NETWORKS; GENOME, HUMAN; HUMANS; INSULIN-SECRETING CELLS; MICRORNAS; NEURONS; PROMOTER REGIONS (GENETICS); PROTEIN BINDING; REPRESSOR PROTEINS; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, DNA; SYNAPTIC TRANSMISSION; T-LYMPHOCYTES; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC; ZINC FINGERS;

MAMMALIA;

EID: 34250159524     PISSN: 00368075     EISSN: 10959203     Source Type: Journal    
DOI: 10.1126/science.1141319     Document Type: Article

References (27)

1. T. H. Kim, B. Ren, Annu. Rev. Genom. Hum. Genet. 7, 81 (2006).
2. ENCODE Project Consortium, Science 306, 636 (2004).
3. S. Impey et al., Cell 119, 1041 (2004).
4. C. L. Wei et al., Cell 124, 207 (2006).
5. Materials and methods are available as supporting material on Science Online.
6. N. Ballas, G. Mandel, Curr. Opin. Neurobiol. 15, 500 (2005).
7. A. Mortazavi, E. C. Thompson, S. T. Garcia, R. M. Myers, B. Wold, Genome Res. 16, 1208 (2006).
8. C. J. Schoenherr, A. J. Paquette, D. J. Anderson, Proc. Natl. Acad. Sci. U.S.A. 93, 9881 (1996).
9. A. W. Bruce et al., Proc. Natl. Acad. Sci. U.S.A. 101, 10458 (2004).
10. C. Zhang et al., Nucleic Acids Res. 34, 2238 (2006).
11. J. Wu, X, Xie, Genome Biol. 7, R85 (2006).
12. Z. F. Chen, A. J. Paquette, D. J. Anderson, Nat. Genet. 20, 136 (1998).
13. Solexa sequencing technology, www.illumina.com/pages.ilmn?ID=203.
14. ChlPSeq peak finder, available at http://woldlab.caltech.edu.
15. V. V. Lunyak et al., Science 298, 1747 (2002).
16. S. Cawley et al., Cell 116, 499 (2004).
17. N. C. Jones, P. A. Pevzner, Bioinformatics 22, e236 (2006).
18. T. L. Bailey, C. Elkan, Mach. Learn. 21, 51 (1995).
19. E. Peisach, C. O. Pabo, J. Mol. Biol. 330, 1 (2003).
20. N. Ballas, C. Grunseich, D. D. Lu, J. C. Speh, G. Mandel, Cell 121, 645 (2005).
21. M. Yeo et al., Science 307, 596 (2005).
22. S. Huntley et al., Genome Res. 16, 669 (2006).
23. E. H. Davidson, The Regulatory Genome: Gene Regulatory Networks in Development and Evolution (Academic Press/Elsevier, San Diego, CA, 2006).
24. J. Gaudet, S. E. Mango, Science 295, 821 (2002).
25. F. Atouf, P. Czernichow, R. Scharfmann, J. Biol. Chem. 272, 1929 (1997).
26. Web-based sequence logo generating application; Weblogo.berkeley.edu.
27. We thank G. Schroth and his group at Solexa/lllumina, 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.