Modeling interactions between adjacent nucleosomes improves genome-wide predictions of nucleosome occupancy

Bioinformatics

Volumn 25, Issue 12, 2009, Pages

  Lubliner, Shai ^a   Segal, Eran ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

CAENORHABDITIS ELEGANS; CONFERENCE PAPER; CONTROLLED STUDY; DNA PURIFICATION; IN VITRO STUDY; MATHEMATICAL ANALYSIS; NUCLEOSOME; PREDICTION; PRIORITY JOURNAL; PROCESS MODEL; PROTEIN INTERACTION; THERMODYNAMICS;

CHROMATIN; COMPUTATIONAL BIOLOGY; GENOME; MODELS, THEORETICAL; NUCLEOSOMES; THERMODYNAMICS;

EID: 66349114864     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp216     Document Type: Conference Paper

References (23)

1. Chodaparambil,J.V. et al. (2007) A charged and contoured surface on the nucleosome regulates chromatin compaction. Nat. Struct. Mol. Biol., 14, 1105-1107.
2. Cohanim,A.B. et al. (2005) Yeast nucleosome DNA pattern: deconvolution from genome sequences of S. cerevisae. J. Biomol. Struct. Dyn., 22, 687-694.
3. Cohanim,A.B. et al. (2006) Three sequence rules for chromatin. J. Biomol. Struct. Dyn., 23, 559-566.
4. Dorigo B et al. (2004) Nucleosome arrays reveal the two-start organization of the chromatin fiber. Science, 306, 1571-1573.
5. Field,Y. et al. (2008) Distinct modes of regulation by chromatin are encoded through nucleosome positioning signals. PLoS Comput. Biol., 4, e1000216.
6. Ioshikhes,I.P. et al. (1996) Nucleosome DNA sequence pattern revealed by multiple alignment of experimentally mapped sequences. J. Mol. Biol., 262, 129-139.
7. Ioshikhes,I.P. et al. (2006) Nucleosome positions predicted through comparative genomics. Nat. Genet., 38, 1210-1215.
8. Kaplan,N. et al. (2009) The DNA-encoded nucleosome organization of a eukaryotic genome. Nature, 458, 362-366.
9. Kato,M. et al. (2003) Dinucleosome DNA of human k562 cells: experimental and computational characterizations. J. Mol. Biol., 332, 111-125.
10. Kornberg RD, Lorch Y. (1999) Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell, 98, 285-294.
11. Lee,W. et al. (2007) A high-resolution atlas of nucleosome occupancy in yeast. Nat. Genet., 39, 1235-1244.
12. Luger,K. et al. (1997) Crystal structure of the nucleosome core particle at 2.8Å resolution. Nature, 389, 251-260.
13. Peckham,H.E. et al. (2007) Nucleosome positioning signals in genomic DNA. Genome Res., 17, 1170-1177.
14. Rabiner,L.R. (1989) A tutorial on Hidden Markov Models and selected applications in speech recognition. Proc. IEEE, 77, 257-286.
15. Routh,A. et al. (2008) Nucleosome repeat length and linker histone stoichiometry determine chromatin fiber structure. Proc. Natl Acad. Sci. USA, 105, 8872-8877.
16. Satchwell,S.C. et al. (1986) Sequence periodicities in chicken nucleosome core DNA. J. Mol. Biol., 191, 659-675.
17. Schalch,T. et al. (2005) X-ray structure of a tetranucleosome and its implications for the chromatin fibre. Nature, 436, 138-141.
18. Segal,E. et al. (2006) A genomic code for nucleosome positioning. Nature, 442, 772-778.
19. Valouev,A. et al. (2008)A high resolution, nucleosome position map of c. elegans reveals a lack of universal sequence-dictated positioning. Genome Res., 18, 1051-1063.
20. Wang,J.-P. et al. (2008) Preferentially quantized linker DNA lengths in Saccharomyces cerevisiae. PLoS Comput. Biol., 4, e1000175.
21. Widom,J. (1992) A relationship between the helical twist of DNA and the ordered positioning of nucleosomes in all eukaryotic cells. Proc. Natl Acad. Sci. USA, 89, 1095-1099.
22. Widom,J. (1996) Short-range order in two eukaryotic genomes: Relation to chromosome structure. J. Mol. Biol., 259, 579-588.
23. Yuan,G.C. and Liu,J.S. (2008) Genomic sequence is highly predictive of local nucleosome depletion. PLoS Comput. Biol., 4, e13.