A genomic code for nucleosome positioning

Nature

Volumn 442, Issue 7104, 2006, Pages 772-778

  Segal, Eran ^a   Fondufe Mittendorf, Yvonne ^b   Chen, Lingyi ^b   Thåström, Annchristine ^b   Field, Yair ^a   Moore, Irene K ^b   Wang, Ji Ping Z ^b   Widom, Jonathan ^b  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

^b NORTHWESTERN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMEDICAL ENGINEERING; COMPUTATIONAL METHODS; DNA; MATHEMATICAL MODELS; YEAST;

GENOMIC CODE; NUCLEOSOMES; TRANSCRIPTION FACTOR BINDING;

GENES;

DNA BINDING PROTEIN; TRANSCRIPTION FACTOR;

DNA; EUKARYOTE; GENOMICS; PROTEIN; YEAST;

ARTICLE; DNA SEQUENCE; GENOME; NUCLEOSOME; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; TRANSCRIPTION INITIATION; YEAST;

EUKARYOTA;

EID: 33747500567     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature04979     Document Type: Article

References (44)

1. Richmond, T. J. & Davey, C. A. The structure of DNA in the nucleosome core. Nature 423, 145-150 (2003).
2. Satchwell, S. C., Drew, H. R. & Travers, A. A. Sequence periodicities in chicken nucleosome core DNA. J. Mol. Biol. 191, 659-675 (1986).
3. Widom, J. Role of DNA sequence in nucleosome stability and dynamics. Q. Rev. Biophys. 34, 269-324 (2001).
4. van Holde, K. E. Chromatin (Springer, New York, 1989).
5. Jenuwein, T. & Allis, C. D. Translating the histone code. Science 293, 1074-1080 (2001).
6. Kornberg, R. D. & Lorch, Y. Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell 98, 285-294 (1999).
7. Wyrick, J. J. et al. Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast. Nature 402, 418-421 (1999).
8. Trifonov, E. N. Sequence-dependent deformational anisotropy of chromatin DNA. Nucleic Acids Res. 8, 4041-4053 (1980).
9. Sekinger, E. A., Moqtaderi, Z. & Struhl, K. Intrinsic histone-DNA interactions and low nucleosome density are important for preferential accessibility of promoter regions in yeast. Mol. Cell 18, 735-748 (2005).
10. Anderson, J. D. & Widom, J. Poly(dA-dT) promoter elements increase the equilibrium accessibility of nucleosomal DNA target sites. Mol. Cell Biol. 21, 3830-3839 (2001).
11. Thåström, A. et al. Sequence motifs and free energies of selected natural and non-natural nucleosome positioning DNA sequences. J. Mol. Biol. 288, 213-229 (1999).
12. Ghaemmaghami, S. et al. Global analysis of protein expression in yeast. Nature 425, 737-741 (2003).
13. Cairns, B. R. Chromatin remodeling complexes: strength in diversity, precision through specialization. Curr. Opin. Genet. Dev. 15, 185-190 (2005).
14. Olson, W. K., Gorin, A. A., Lu, X. J., Hock, L. M. & Zhurkin, V. B. DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc. Natl Acad. Sci. USA 95, 11163-11168 (1998).
15. Wang, J. P. & Widom, J. Improved alignment of nucleosome DNA sequences using a mixture model. Nucleic Acids Res. 33, 6743-6755 (2005).
16. Dempster, A. P., Laird, N. M. & Rubin, D. B. Maximum likelihood from incomplete data via the EM algorithm. J. R. Stat. Soc. B 39, 1-39 (1977).
17. Lowary, P. T. & Widom, J. New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning. J. Mol. Biol. 276, 19-42 (1998).
18. Widlund, H. R. et al. Identification and characterization of genomic nucleosome-positioning sequences. J. Mol. Biol. 267, 807-817 (1997).
19. Rabiner, L. R. A tutorial on Hidden Markov Models and selected applications in speech recognition. Proc. IEEE 77, 257-286 (1989).
20. Harbison, C. T. et al. Transcriptional regulatory code of a eukaryotic genome. Nature 431, 99-104 (2004).
21. Li, S. & Smerdon, M. J. Nucleosome structure and repair of N-methylpurines in the GAL1-10 genes of Saccharomyces cerevisiae. J. Biol. Chem. 277, 44651-44659 (2002).
22. Weiss, K. & Simpson, R. T. High-resolution structural analysis of chromatin at specific loci: Saccharomyces cerevisiae silent mating type locus HMLα. Mol. Cell. Biol. 18, 5392-5403 (1998).
23. Weiss, K. & Simpson, R. T. Cell type-specific chromatin organization of the region that governs directionality of yeast mating type switching. EMBO J. 16, 4352-4360 (1997).
24. Moreira, J. M. & Holmberg, S. Nucleosome structure of the yeast CHA1 promoter: analysis of activation-dependent chromatin remodeling of an RNA-polymerase-II-transcribed gene in TBP and RNA pol II mutants defective in vivo in response to acidic activators. EMBO J. 17, 6028-6038 (1998).
25. Shimizu, M., Roth, S. Y., Szent-Gyorgyi, C. & Simpson, R. T. Nucleosomes are positioned with base pair precision adjacent to the α2 operator in Saccharomyces cerevisiae. EMBO J. 10, 3033-3041 (1991).
26. Kent, N. A., Tsang, J. S., Crowther, D. J. & Mellor, J. Chromatin structure modulation in Saccharomyces cerevisiae by centromere and promoter factor 1. Mol. Cell Biol. 14, 5229-5241 (1994).
27. Verdone, L., Camilloni, G., Di Mauro, E. & Caserta, M. Chromatin remodeling during Saccharomyces cerevisiae ADH2 gene activation. Mol. Cell Biol. 16, 1978-1988 (1996).
28. Almer, A., Rudolph, H., Hinnen, A. & Horz, W. Removal of positioned nucleosomes from the yeast PHO5 promoter upon PHO5 induction releases additional upstream activating DNA elements. EMBO J. 5, 2689-2696 (1986).
29. Lee, C. K., Shibata, Y., Rao, B., Strahl, B. D. & Lieb, J. D. Evidence for nucleosome depletion at active regulatory regions genome-wide. Nature Genet. 36, 900-905 (2004).
30. Bernstein, B. E., Liu, C. L., Humphrey, E. L., Perlstein, E. O. & Schreiber, S. L. Global nucleosome occupancy in yeast. Genome Biol. 5, R62 (2004).
31. Yuan, G. C. et al. Genome-scale identification of nucleosome positions in S. cerevisiae. Science 309, 626-630 (2005).
32. Guillemette, B. et al. Variant histone H2A.Z is globally localized to the promoters of inactive yeast genes and regulates nucleosome positioning. PLoS Biol. 3, e384 (2005).
33. Gasch, A. P. et al. Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell 11, 4241-4257 (2000).
34. Kim, J. & Iyer, V. R. Global role of TATA box-binding protein recruitment to promoters in mediating gene expression profiles. Mol. Cell Biol. 24, 8104-8112 (2004).
35. Ashburner, M. et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature Genet. 25, 25-29 (2000).
36. Hughes, T. R. et al. Functional discovery via a compendium of expression profiles. Cell 102, 109-126 (2000).
37. Ideker, T. et al. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292, 929-934 (2001).
38. Sudarsanam, P., Iyer, V. R., Brown, P. O. & Winston, F. Whole-genome expression analysis of snf/swi mutants of Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA 97, 3364-3369 (2000).
39. Casolari, J. M. et al. Genome-wide localization of the nuclear transport machinery couples transcriptional status and nuclear organization. Cell 117, 427-439 (2004).
40. Robert, F. et al. Global position and recruitment of HATs and HDACs in the yeast genome. Mol. Cell 16, 199-209 (2004).
41. Li, H., Rhodius, V., Gross, C. & Siggia, E. D. Identification of the binding sites of regulatory proteins in bacterial genomes. Proc. Natl Acad. Sci. USA 99, 11772-11777 (2002).
42. Basehoar, A. D., Zanton, S. J. & Pugh, B. F. Identification and distinct regulation of yeast TATA box-containing genes. Cell 116, 699-709 (2004).
43. Cui, Y. & Bustamante, C. Pulling a single chromatin fiber reveals the forces that maintain its higher-order structure. Proc. Natl Acad. Sci. USA 97, 127-132 (2000).
44. Thåstro̊m, A., Bingham, L. M. & Widom, J. Nucleosomal locations of dominant DNA sequence motifs for histone-DNA interactions and nucleosome positioning. J. Mol. Biol. 338, 695-709 (2004).