Prediction of nucleosome occupancy in Saccharomyces cerevisiae using position-correlation scoring function

Genomics

Volumn 98, Issue 5, 2011, Pages 359-366

  Xing, Yongqiang ^a,b   Zhao, Xiujuan ^a,b   Cai, Lu ^b  

^a INNER MONGOLIA UNIVERSITY   (China)

^b INNER MONGOLIA UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

Author keywords

Nucleosome positioning; Position weight matrix; Position correlation scoring function; Sequence bias

Indexed keywords

ALGORITHM; AREA UNDER THE CURVE; ARTICLE; CONTROLLED STUDY; CORRELATION COEFFICIENT; DNA SEQUENCE; FUNGAL GENE; GENETIC ANALYSIS; NONHUMAN; NUCLEOSOME; NUCLEOSOME OCCUPANCY; PERFORMANCE; POSITION CORRELATION SCORING FUNCTION; PRIORITY JOURNAL; RECEIVER OPERATING CHARACTERISTIC; SACCHAROMYCES CEREVISIAE; SCORING SYSTEM; VALIDATION STUDY;

ALGORITHMS; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DNA REPLICATION; DNA, FUNGAL; GENOME, FUNGAL; NUCLEOSOMES; REPLICATION ORIGIN; ROC CURVE; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS, DNA; TRANSCRIPTION, GENETIC;

SACCHAROMYCES CEREVISIAE;

EID: 80055091624     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2011.07.008     Document Type: Article

References (45)

1. Kornberg R.D. Structure of chromatin. Ann. Rev. Biochem. 1977, 46:931-954.
2. Richmond T.J., Davey C.A. The structure of DNA in the nucleosome core. Nature 2003, 423:145-150.
3. Athey B.D., Smith M.F., Rankert D.A., Williams S.P., Langmore J.P. The diameters of frozen-hydrated chromatin fibers increase with DNA linker length: evidence in support of variable diameter models for chromatin. J. Cell Biol. 1990, 111:795-806.
4. Mavrich T.N., et al. A barrier nucleosome model for statistical positioning of nucleosome throughout the yeast genome. Genome Res. 2008, 18:1073-1083.
5. Clapier C.R., Cairns B.R. The biology of chromatin remodeling complexes. Annu. Rev. Biochem. 2009, 78:273-304.
6. Lu Q., Wallrath L.L., Elgin S.C. Nucleosome positioning and gene regulation. J. Cell. Biochem. 1994, 55:83-92.
7. Thoma F., Bergman L.W., Simpson R.T. Nuclease digestion of circular TRP1ARS1 chromatin reveals positioned nucleosomes separated by nuclease-sensitive regions. J. Mol. Biol. 1984, 177:715-733.
8. Lee W., et al. A high-resolution atlas of nucleosome occupancy in yeast. Nat. Genet. 2007, 39:1235-1244.
9. Segal E., et al. A genomic code for nucleosome positioning. Nature 2006, 442:772-778.
10. Weiner A., Hughes A., Yassour M., Rando O.J., Friedman N. High-resolution nucleosome mapping reveals transcription-dependent promoter packaging. Genome Res. 2010, 20:90-100.
11. Field Y., et al. Distinct modes of regulation by chromatin encoded through nucleosome positioning signals. PLoS Comput. Biol. 2008, 4:e100216.
12. Zhang Y., et al. Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo. Nat. Struct. Mol. Biol. 2009, 16:847-852.
13. Mavrich T.N., et al. Nucleosome organization in the Drosophila genome. Nature 2008, 453:358-364.
14. Valouev A., et al. A high-resolution, nucleosome position map of C. elegans reveals lack of universal sequence-dictated positioning. Genome Res. 2008, 18:1051-1063.
15. Ozsolak F., Song J.S., Liu X.S., Fisher D.E. High-throughput mapping of the chromatin structure of human promoters. Nat. Biotechnol. 2007, 25:244-248.
16. Schones D.E., et al. Dynamic regulation of nucleosome positioning in the human genome. Cell 2008, 132:887-898.
17. Kaplan N., et al. Nucleosome sequence preferences influence in vivo nucleosome organization. Nat. Struct. Mol. Biol. 2010, 17:918-920.
18. Zhang Y., et al. Evidence against a genomic code for nucleosome positioning. Nat. Struct. Mol. Biol. 2010, 17:920-923.
19. Collings C.K., Fernandez A.G., Pitschka C.G., Hawkins T.B., Anderson J.N. Oligonucleotide sequence motifs as nucleosome positioning signals. PLoS One 2010, 5:e10933.
20. Anselmi C., Bocchinfuso G., De Santis P., Savino M., Scipioni A. Dual role of DNA intrinsic curvature and flexibility in determining nucleosome stability. J. Mol. Biol. 1999, 286:1293-1301.
21. Anselmi C., Bocchinfuso G., De Santis P., Savino M., Scipioni A. A theoretical model for the prediction of sequence-dependent nucleosome thermodynamic stability. Biophys. J. 2000, 79:601-603.
22. Chen K.F., et al. A novel DNA sequence periodicity decodes nucleosome positioning. Nucleic Acids Res. 2008, 36:6228-6236.
23. Chen K.F., et al. Sequence signature of nucleosome positioning in Caenorhabditis elegans. Genomics Proteomics Bioinform. 2010, 8:90-102.
24. Tillo D., Hughes T.R. G+C content dominates intrinsic nucleosome occupancy. BMC Bioinform. 2009, 10:442.
25. Fukushima A., et al. Periodicity in prokaryotic and eukaryotic genomes identified by power spectrum analysis. Gene 2002, 300:203-211.
26. Peckham H.E., et al. Nucleosome positioning signals in genomic DNA. Genome Res. 2007, 17:1170-1177.
27. Segal E., Widom J. Poly(dA:dT) tracts: major determinants of nucleosome organization. Curr. Opin. Struct. Biol. 2009, 19:65-71.
28. Rapoport A.E., Frenkel Z.M., Trifonov E.N. Nucleosome positioning pattern derived from oligonucleotide compositions of genomic sequences. J. Biomol. Struct. Dyn. 2011, 28:567-574.
29. Frenkel Z.M., Bettecken T., Trifonov E.N. Nucleosome DNA sequence structure of isochores. BMC Genomics 2011, 12:203.
30. Yuan G.C., Liu J.S. Genomic sequence is highly predictive of local nucleosome depletion. PLoS Comput. Biol. 2008, 4:e13.
31. Miele V., Vaillant C.D., Aubenton-Carafa Y. DNA physical properties determine nucleosome occupancy from yeast to fly. Nucleic Acids Res. 2009, 37:1746-3756.
32. Zhao X.J., Pei Z.Y., Liu J., Qin S., Cai L. Prediction of nucleosome DNA formation potential and nucleosome positioning using increment of diversity combined with quadratic discriminant analysis. Chromosome Res. 2010, 18:777-785.
33. Chen W., Luo L.F., Zhang L.R. The organization of nucleosomes around splice sites. Nucleic Acids Res. 2010, 38:2788-2798.
34. Kaplan N., et al. The DNA-encoded nucleosome organization of a eukaryotic genome. Nature 2009, 458:362-366.
35. Yuan G.C., et al. Genome-scale identification of nucleosome positions in S. cerevisiae. Science 2005, 309:626-630.
36. 70 promoters in Escherichia coli K-12. J. Theor. Biol. 2006, 242:135-141.
37. Li Q.Z., Zuo Y.C. Identification of TATA and TATA-less promoters in plant genomes by integrating diversity measure, GC-Skew and DNA geometric flexibility. Genomics 2011, 97:112-120.
38. Locke G., Tolkunova D., Moqtaderib Z., Struhlb K., Morozova A.V. High-throughput sequencing reveals a simple model of nucleosome energetics. Proc. Natl. Acad. Sci. 2010, 107:20998-21003.
39. Cui F., Zhurkin V.B. Structure-based analysis of DNA sequence patterns guiding nucleosome positioning in vitro. J. Biomol. Struct. Dyn. 2010, 27:821-841.
40. Yanagi K., Prive G.G., Dickerson R.E. Analysis of local helix geometry in three B-DNA decamers and eight dodecamers. J. Mol. Biol. 1991, 217:201-214.
41. Horz W., Altenburger W. Sequence specific cleavage of DNA by micrococcal nuclease. Nucleic Acids Res. 1981, 9:2643-2658.
42. Cui F., Zhurkin V.B. Distinctive sequence patterns in metazoan and yeast nucleosomes: implications for linker histone binding to AT-rich and methylated DNA. Nucleic Acids Res. 2009, 37:2818-2829.
43. Radwan A., Younis A., Luykx P., Khuri S. Prediction and analysis of nucleosome exclusion regions in the human genome. BMC Genomics 2008, 9:186.
44. Berbenetz N.M., Nislow C., Brown G.W. Diversity of eukaryotic DNA replication origins revealed by genome-wide analysis of chromatin structure. PLoS One 2010, 6:e1001092.
45. Eaton M.L., Galani K., Kang S., Bell S.P., MacAlpine D.M. Conserved nucleosome positioning defines replication origins. Genes Dev. 2010, 24:748-753.