Learning a weighted sequence model of the nucleosome core and linker yields more accurate predictions in Saccharomyces cerevisiae and Homo sapiens

PLoS Computational Biology

Volumn 6, Issue 7, 2010, Pages 17-

  Reynolds, Sheila M ^a   Bilmes, Jeff A ^a   Noble, William Stafford ^a,b  

^a University of Washington   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DYNAMIC PROGRAMMING; FORECASTING; GENE EXPRESSION; YEAST;

ACCURATE PREDICTION; BASIC-ELEMENTS; HOMO SAPIENS; NUCLEOSOME CORE; NUCLEOSOME POSITIONS; NUCLEOSOMES; PRECISE POSITIONING; S.CEREVISIAE; SEQUENCE MODELS; WEIGHTED SEQUENCES;

NUCLEOTIDES;

DINUCLEOTIDE; TRINUCLEOTIDE; CCCTC-BINDING FACTOR; DNA; FUNGAL DNA; REPRESSOR PROTEIN; TRANSCRIPTION FACTOR CTCF;

ACCURACY; ARTICLE; CHROMATIN STRUCTURE; CONTROLLED STUDY; DNA SEQUENCE; HUMAN; NONHUMAN; NUCLEOSOME; OSCILLATION; PREDICTION; RECEIVER OPERATING CHARACTERISTIC; SACCHAROMYCES CEREVISIAE; SCORING SYSTEM; ALU SEQUENCE; CHEMISTRY; CONFORMATION; DNA BASE COMPOSITION; GENETICS; NUCLEOTIDE SEQUENCE; REPRODUCIBILITY; SEQUENCE ALIGNMENT;

EUKARYOTA; HOMO SAPIENS; SACCHAROMYCES CEREVISIAE;

ALU ELEMENTS; BASE COMPOSITION; BASE SEQUENCE; DNA; DNA, FUNGAL; HUMANS; NUCLEIC ACID CONFORMATION; NUCLEOSOMES; REPRESSOR PROTEINS; REPRODUCIBILITY OF RESULTS; ROC CURVE; SACCHAROMYCES CEREVISIAE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

EID: 78049255935     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000834     Document Type: Article

References (51)

1. Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, et al. (2007) Highresolution profiling of histone methylations in the human genome. Cell 129: 823-837.
2. Zhang Y, Shin H, Song JS, Lei Y, Liu XS (2008) Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq. BMC Genomics 9.
3. Schones DE, Cui K, Cuddapah S, Roh TY, Barski A, et al. (2008) Dynamic regulation of nucleosome positioning in the human genome. Cell 132: 887-898.
4. Field Y, Kaplan N, Fondufe-Mittendorf Y, Moore IK, Sharon E, et al. (2008) Distinct modes of regulation by chromatin encoded through nucleosome positioning signals. PLoS Computational Biology 4: e1000216.
5. Trifonov EN, Sussman JL (1980) The pitch of chromatin DNA is reflected in its nucleotide sequence. Proceedings of the National Academy of Sciences of the United States of America 77: 3816-3820.
6. Lowary PT, Widom J (1998) New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning. Journal of Molecular Biology 276: 19-42.
7. Thåström A, Lowary P, Widlund HR, Cao H, Kubista M, et al. (1999) Sequence motifs and free energies of selected natural and non-natural nucleosome positioning DNA sequences. Journal of Molecular Biology 288: 213-229.
8. Satchwell SC, Drew HR, Travers AA (1986) Sequence periodicities in chicken nucleosome core DNA. Journal of Molecular Biology 191: 659-675.
9. Segal E, Fondufe-Mittendorf Y, Chen L, Thåström A, Field Y, et al. (2006) A genomic code for nucleosome positioning. Nature 44: 772-778.
10. Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, Tillo D, et al. (2009) The DNA-encoded nucleosome organization of a eukaryotic genome. Nature 548: 362-366.
11. Valouev A, Ichikawa J, Tonthat T, Stuart J, Ranade S, et al. (2008) A highresolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Research 18: 1051-1063.
12. Reynolds SM, Bilmes JA, Noble WS (2009) On the relationship between DNA periodicity and local chromatin structure. In: Research in Computational Molecular Biology. Berlin: Springer, volume 5541/2009 of Lecture Notes in Computer Science. pp 434-450.
13. Ioshikhes IP, Albert I, Zanton SJ, Pugh BF (2006) Nucleosome positions predicted through comparative genomics. Nature Genetics 38: 1210-5.
14. Mavrich TN, Ioshikhes IP, Venters BJ, Jiang C, Tomsho LP, et al. (2008) A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Research 18: 1073-83.
15. Yuan GC, Liu JS (2008) Genomic sequence is highly predictive of local nucleosome depletion. PLoS Computational Biology 4: e13.
16. Peckham HE, Thurman RE, Fu Y, Stamatoyannopoulos JA, Noble WS, et al. (2007) Nucleosome positioning signals in genomic DNA. Genome Research 17: 1170-1177.
17. Gupta S, Dennis J, Thurman RE, Kingston RE, Stamatoyannpoulos JA, et al. (2008) Predicting human nucleosome occupancy from primary sequence. PLoS Computational Biology 4: e1000134.
18. Lee W, Tillo D, Bray N, Morse RH, Davis RW, et al. (2007) A high-resolution atlas of nucleosome occupancy in yeast. Nature Genetics 39: 1235-1244.
19. Lubliner S, Segal E (2009) Modeling interactions between adjacent nucleosomes improves genome-wide predictions of nucleosome occupancy. Bioinformatics 25: 1348-1355.
20. Widom J (2001) Role of DNA sequence in nucleosome stability and dynamics. Quarterly Reviews of Biophysics 34: 269-324.
21. Bishop TC (2008) Geometry of the nucleosomal DNA superhelix. Biophysical Journal 95: 1007-1017.
22. Edayathumangalam RS, Weyermann P, Gottesfeld JM, Dervan PB, Luger K (2004) Molecular recognition of the nucleosomal "supergroove". Proceedings of the National Academy of Sciences of the United States of America 101: 6864-6869.
23. Schalch T, Duda S, Sargent DF, Richmond TJ (2005) X-ray structure of a tetranucleosome and its implications for the chromatin fibre. Nature 436: 138-141.
24. Robinson PJJ, Fairall L, Huynh VAT, Rhodes D (2006) EM measurements define the dimensions of the "30-nm" chromatin fiber: Evidence for a compact, interdigitated structure. Proceedings of the National Academy of Sciences of the United States of America 103: 6506-11.
25. Ghirlando R, Felsenfeld G (2008) Hydrodynamic studies on defined heterochromatin fragments support a 30-nm fiber having six nucleosomes per turn. Journal of Molecular Biology 376: 1417-1425.
26. Ioshikhes I, Bolshoy A, Derenshteyn K, Borodovsky M, Trifonov EN (1996) Nucleosome DNA sequence pattern revealed by multiple alignment of experimentally mapped sequences. Journal of Molecular Biology 262: 129-139.
27. Tolstorukov MY, Kharchenko PV, Goldman JA, Kingston RE, Park PJ (2009) Comparative analysis of H2A.Z nucleosome organization in the human and yeast genomes. Genome Research 19: 967-977.
28. Wang JPZ, Widom J (2005) Improved alignment of nucleosome DNA sequences using a mixture model. Nucleic Acids Research 33: 6743-6755.
29. Boser BE, Guyon IM, Vapnik VN (1992) A training algorithm for optimal margin classifiers. In: Haussler D, ed. 5th Annual ACM Workshop on COLT. Pittsburgh, PA: ACM Press. pp 144-152.
30. Keerthi S, DeCoste D (2005) A modified finite Newton method for fast solution of large scale linear SVMs. Journal of Machine Learning Research 6: 341-361.
31. Jin C, Zang C, Wei G, Cui K, Peng W, et al. (2009) H3.3/H2A.Z double variant-containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions. Nature Genetics 41: 941-945.
32. Henikoff S (2009) Labile H3.3+H2A.Z nucleosomes mark 'nucleosome-free regions'. Nature Genetics 41: 865-866.
33. Segal E, Widom J (2009) Poly(dA:dT) tracts: major determinants of nucleosome organization. Current Opinion in Structural Biology 19: 65-71.
34. Routh A, Sandin S, Rhodes D (2008) Nucleosome repeat length and linker histone stoichiometry determine chromatin fiber structure. Proceedings of the National Academy of Sciences of the United States of America 105: 8872-8877.
35. Wong H, Victor JM, Mozziconacci J (2007) An all-atom model of the chromatin fiber containing linker histones reveals a versatile structure tuned by the nucleosomal repeat length. PLoS ONE 2: e877.
36. van Holde KE (1989) Chromatin. Springer series in molecular biology. New York: Springer-Verlag.
37. Englander EW, Howard BH (1995) Nucleosome positioning by Human Alu Elements in Chromatin. Journal of Biological Chemistry 270: 10091-10096.
38. Grover D, Kannan K, Brahmachari SK, Mukerji M (2005) ALU-ring elements in the primate genomes. Genetica 124: 273-89.
39. Salih F, Salih B, Kogan S, Trifonov EN (2008) Epigenetic nucleosomes: Alu sequences and CG as nucleosome positioning element. Biomolecular Structure and Dynamics 26: 9-15.
40. Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O (2005) Repbase update, a database of eukaryotic repetitive elements. Cytogenetic and Genome Research 110: 462-467.
41. Fu Y, Sinha M, Peterson CL, Weng Z (2008) The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome. PLoS Genetics 4: e1000138.
42. Cuddapah S, Jothi R, Schones DE, Roh TY, Cui K, et al. (2009) Global analysis of the insulator binding protein CTCF in chromatin barrier regions revals demarcation of active and repressive domains. Genome Research 19: 24-32.
43. Wakaguri H, Yamashita R, Suzuki Y, Sugano S, Nakai K (2008) DBTSS: database of transcription start sites, progress report 2008. Nucleic Acids Research 36: D97-D101.
44. Vinogradov AE (2003) DNA helix: the importance of being GC-rich. Nucleic Acids Research 31: 1838-1844.
45. Kharchenko PV, Woo CJ, Tolstorukov MY, Kingston RE, Park PJ (2008) Nucleosome positioning in human HOX gene clusters. Genome Research 18: 1554-61.
46. Zhang Y, Moqtaderi Z, Rattner BP, Euskirchen G, Snyder M, et al. (2009) Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo. Nat Struct Mol Biol 16: 847-852.
47. DeLano WL (2002) The PYMOL molecular graphics system.
48. Porollo A, Meller J (2007) Versatile annotation and publication quality visualization of protein complexes using POLYVIEW-3D. BMC Bioinformatics 8: 316.
49. Berman HM, Henrick K, Nakamura H (2003) Announcing the worldwide Protein Data Bank. Nature Structural Biology 10: 980.
50. Davey CA, Sargent DF, Luger K, Maeder AW, Richmond TJ (2002) Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 Åresolution. Journal of Molecular Biology 319: 1097-1113.
51. Smit AFA, Hubley R, Green P (1996) Repeatmasker open-3.0. http://www.repeatmasker.org.