Prediction of nucleosome DNA formation potential and nucleosome positioning using increment of diversity combined with quadratic discriminant analysis

Chromosome Research

Volumn 18, Issue 7, 2010, Pages 777-785

  Zhao, Xiujuan ^a,b   Pei, Zhiyong ^b,c   Liu, Jia ^b   Qin, Sheng ^b   Cai, Lu ^b  

^a INNER MONGOLIA UNIVERSITY   (China)

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

^c INSTITUTE OF BOTANY   (China)

Author keywords

Increment of Diversity; Nucleosome DNA; Nucleosome Positioning; Quadratic Discriminant Analysis

Indexed keywords

DNA; NUCLEOSOME DNA; UNCLASSIFIED DRUG;

ACCURACY; ARTICLE; DISCRIMINANT ANALYSIS; DNA SEQUENCE; DROSOPHILA MELANOGASTER; EUKARYOTE; GENOME; HUMAN VERSUS NONHUMAN DATA; NUCLEOSOME; PRIORITY JOURNAL; QUADRATIC DISCRIMINANT ANALYSIS; RECEIVER OPERATING CHARACTERISTIC; SACCHAROMYCES CEREVISIAE; SENSITIVITY AND SPECIFICITY; SPECIES DIFFERENCE; STATISTICAL MODEL;

ALGORITHMS; ANIMALS; BASE COMPOSITION; COMPUTER SIMULATION; DISCRIMINANT ANALYSIS; DNA; DROSOPHILA MELANOGASTER; GENOME, FUNGAL; GENOME, HUMAN; GENOME, INSECT; HISTONES; HUMANS; NUCLEOSOMES; SACCHAROMYCES CEREVISIAE;

DROSOPHILA MELANOGASTER; EUKARYOTA; HOMO SAPIENS; SACCHAROMYCES CEREVISIAE;

EID: 78649938432     PISSN: 09673849     EISSN: 15736849     Source Type: Journal    
DOI: 10.1007/s10577-010-9160-9     Document Type: Article

References (47)

1. I Albert TN Mavrich LP Tomsho 2007 Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome Nature 446 572 576 1:CAS:528:DC%2BD2sXjsV2itbw%3D 10.1038/nature05632 17392789 (Pubitemid 46514724)
2. R Andersson S Enroth A Rada-Iglesias 2009 Nucleosomes are well positioned in exons and carry characteristic histone modifications Genome Res 19 1732 1741 1:CAS:528:DC%2BD1MXht1GjtbzL 10.1101/gr.092353.109 19687145
3. A Barski S Cuddapah K Cui 2007 High resolution profiling of histone methylations in the human genome Cell 129 823 837 1:CAS:528:DC%2BD2sXmtFKjsro%3D 10.1016/j.cell.2007.05.009 17512414 (Pubitemid 46802390)
4. BE Bernstein CL Liu EL Humphrey 2004 Global nucleosome occupancy in yeast Genome Biol 5 R62 10.1186/gb-2004-5-9-r62 15345046
5. GO Bryant V Prabhu M Floer 2008 Activator control of nucleosome occupancy in activation and repression of transcription PLoS Biol 6 12 e317 10.1371/journal.pbio.0060317
6. H Cao HR Widlund T Simonsson M Kubista 1998 TGGA repeats impair nucleosome formation J Mol Biol 281 253 260 1:CAS:528:DyaK1cXlsFSqsr8%3D 10.1006/jmbi.1998.1925 9698546 (Pubitemid 28360592)
7. W Chen LF Luo 2009 Classification of antimicrobial peptide using diversity measure with quadratic discriminant analysis J Microbiol Meth 78 94 96 1:CAS:528:DC%2BD1MXntVykt7s%3D 10.1016/j.mimet.2009.03.013
8. F Daenen F van Roy PJ De Bleser 2008 Low nucleosome occupancy is encoded around functional human transcription factor binding sites BMC Genomics 9 332 10.1186/1471-2164-9-332 18627598
9. RD Elizabeth MB Ashley GC Victor 2008 The role of insulator elements in large-scale chromatin structure in interphase Semin Cell Dev Biol 18 5 682 690
10. Y Field N Kaplan Y Fondufe-Mittendorf 2008 Distinct modes of regulation by chromatin encoded through nucleosome positioning signals PLoS Comput Biol 4 11 e1000216 10.1371/journal.pcbi.1000216 18989395
11. Y Field Y Fondufe-Mittendorf IK Moore 2009 Gene expression divergence in yeast is coupled to evolution of DNA-encoded nucleosome organization Nat Genet 41 438 445 1:CAS:528:DC%2BD1MXisVOrtbY%3D 10.1038/ng.324 19252487
12. ND Heintzman RK Stuart G Hon 2007 Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome Nat Genet 39 311 318 1:CAS:528:DC%2BD2sXitVOksbc%3D 10.1038/ng1966 17277777 (Pubitemid 46328487)
13. IP Ioshikhes I Albert SJ Zanton 2006 Nucleosome positions predicted through comparative genomics Nat Genet 38 10 1210 1215 1:CAS:528: DC%2BD28XhtVSns73J 10.1038/ng1878 16964265 (Pubitemid 44470369)
14. SM Johnson FJ Tan HL McCullough DP Riordan AZ Fire 2006 Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin Genome Res 16 1505 1516 1:CAS:528:DC%2BD28XhtlWgsrfN 10.1101/gr.5560806 17038564 (Pubitemid 44878489)
15. N Kaplan IK Moore Y Fondufe-Mittendorf 2008 The DNA-encoded nucleosome organization of a eukaryotic genome Nature 458 362 366 10.1038/nature07667 19092803
16. RD Kornberg Y Lorch 1997 Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome Cell 98 285 294 10.1016/S0092-8674(00) 81958-3
17. RR Laxton 1978 The measure of diversity J Theor Biol 70 1 51 67 1:STN:280:DyaE1c7ht1KnsQ%3D%3D 10.1016/0022-5193(78)90302-8 625122
18. CK Lee Y Shibata B Rao 2004 Evidence for nucleosome depletion at active regulatory regions genome-wide Nat Genet 36 900 905 1:CAS:528: DC%2BD2cXmtVOis7s%3D 10.1038/ng1400 15247917 (Pubitemid 39014111)
19. W Lee D Tillo N Bray RH Morse RW Davis 2007 A high-resolution atlas of nucleosome occupancy in yeast Nat Genet 39 1235 1244 1:CAS:528: DC%2BD2sXhtV2isL7E 10.1038/ng2117 17873876 (Pubitemid 47482684)
20. HD Liu JS Wu JM Xie XN Yang ZH Lu X Sun 2008 Characteristics of nucleosome core DNA and their applications in predicting nucleosome positions Biophys. J 94 1 8
21. K Luger AW Mäder RK Richmond 1997 Crystal structure of the nucleosome core particle at 2.8 A resolution Nature 389 251 260 1:CAS:528:DyaK2sXmtFGisrc%3D 10.1038/38444 9305837 (Pubitemid 27406632)
22. J Lv LF Luo 2008 Prediction for human transcription start site using diversity measure with quadratic discrimination Bioinformation 2 316 321
23. C Martinez-Campa P Politis JL Moreau N Kent 2004 Precise nucleosome positioning and the TATA box dictate requirements for the histone H4 tail and the bromodomain factor Bdf1 Mol Cell 15 1 69 81 1:CAS:528:DC%2BD2cXlvFeju74%3D 10.1016/j.molcel.2004.05.022 15225549 (Pubitemid 38850220)
24. TN Mavrich C Jiang IP Ioshikhes 2008 Nucleosome organization in the Drosophila genome Nature 453 358 362 1:CAS:528:DC%2BD1cXlvV2qtLY%3D 10.1038/nature06929 18408708 (Pubitemid 351693129)
25. V Miele C-D Vaillant Y Aubenton-Carafa 2009 DNA physical properties determine nucleosome occupancy from yeast to fly Nucleic Acids Res 37 11 1746 3756
26. P Milani G Chevereau C Vaillant 2009 Nucleosome positioning by genomic excluding-energy barriers Proc Natl Acad Sci USA 106 52 22257 22262 1:CAS:528:DC%2BC3cXmtlaiuw%3D%3D 10.1073/pnas.0909511106 20018700
27. AV Morozov K Fortney DA Gaykalova 2009 Using DNA mechanics to predict in vitro nucleosome positions and formation energies Nucleic Acids Res 37 14 4707 4722 1:CAS:528:DC%2BD1MXhtVWitLnN 10.1093/nar/gkp475 19509309
28. F Ozsolak JS Song XS Liu DE Fisher 2007 High-throughput mapping of the chromatin structure of human promoters Nat Biotechnol 25 244 248 1:CAS:528:DC%2BD2sXhtlOrsL4%3D 10.1038/nbt1279 17220878 (Pubitemid 46227125)
29. HE Peckham RE Thurman Y Fu JA Stamatoyannopoulos WS Noble 2007 Nucleosome positioning signals in genomic DNA Genome Res 17 1170 1177 1:CAS:528: DC%2BD2sXptVyhsL0%3D 10.1101/gr.6101007 17620451 (Pubitemid 47204860)
30. DK Pokholok CT Harbison S Levine 2005 Genome-wide map of nucleosome acetylation and methylation in yeast Cell 122 517 527 1:CAS:528: DC%2BD2MXpvVKntLc%3D 10.1016/j.cell.2005.06.026 16122420 (Pubitemid 41191151)
31. RM Raisner PD Hartley MD Meneghini 2008 Histone variant H2A.Z marks the 5′ ends of both active and inactive genes in euchromatin Cell 134 1 188 1:CAS:528:DC%2BD1cXoslyjtbo%3D 10.1016/j.cell.2008.06.046 (Pubitemid 351905754)
32. TJ Richmond CA Davey 2003 The structure of DNA in the nucleosome core Nature 423 145 150 1:CAS:528:DC%2BD3sXjsVOrtb0%3D 10.1038/nature01595 12736678 (Pubitemid 36569532)
33. SC Satchwell HR Drew A Travers 1986 Sequence periodicities in chicken nucleosome core DNA J Mol Biol 191 659 675 1:CAS:528:DyaL2sXivVertA%3D%3D 10.1016/0022-2836(86)90452-3 3806678 (Pubitemid 17185964)
34. T Schalch S Duda DF Sargent TJ Richmond 1997 X-ray structure of a tetranucleosome and its implications for the chromatin fibre Nature 436 138 141 10.1038/nature03686
35. DE Schones K Cui S Cuddapah, et al. 2008 Dynamic regulation of nucleosome positioning in the human genome Cell 132 5 887 898 1:CAS:528: DC%2BD1cXjs1ait7s%3D 10.1016/j.cell.2008.02.022 18329373 (Pubitemid 351312809)
36. E Segal Y Fondufe-Mittendorf L Chen 2006 A genomic code for nucleosome positioning Nature 442 772 778 1:CAS:528:DC%2BD28XotFKmtr4%3D 10.1038/nature04979 16862119 (Pubitemid 44258903)
37. E Segal J Widom 2009 Poly (dA:dT) tracts: major determinants of nucleosome organization Curr Opin Struct Biol 19 65 71 1:CAS:528: DC%2BD1MXit1Omsbw%3D 10.1016/j.sbi.2009.01.004 19208466
38. EA Sekinger Z Moqtaderi K Struhl 2005 Intrinsic histone-DNA interactions and low nucleosome density are important for preferential accessibility of promoter regions in yeast Mol Cell 18 735 748 1:CAS:528:DC%2BD2MXlslCjurw%3D 10.1016/j.molcel.2005.05.003 15949447 (Pubitemid 40804808)
39. L Tsai LF Luo 2000 A statistical mechanical model for predicting B-DNA curvature and flexibility J Theor Biol 207 177 194 1:STN:280: DC%2BD3M%2Fns1KjsQ%3D%3D 10.1006/jtbi.2000.2162 11034828
40. C Vaillant B Audit A Arneodo 2007 Experiments confirm the influence of genome long-range correlations on nucleosome positioning Phys Rev Lett 99 218 303 10.1103/PhysRevLett.99.218103 (Pubitemid 350159222)
41. A Weiner A Hughes M Yassour OJ Rando N Friedman 2010 High-resolution nucleosome mapping reveals transcription-dependent promoter packaging Genome Res 20 90 100 1:CAS:528:DC%2BC3cXls1Olsw%3D%3D 10.1101/gr.098509.109 19846608
42. HR Widlund PN Kuduvalli M Bengtsson 1999 Nucleosome structural features and intrinsic properties of the TATAAACGCC repeat sequence J Biol Chem 274 31847 31852 1:CAS:528:DyaK1MXnt12jsLw%3D 10.1074/jbc.274.45.31847 10542209 (Pubitemid 29522913)
43. JJ Wyrick 1999 Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast Nature 402 418 421 1:CAS:528: DyaK1MXnvVyrs74%3D 10.1038/46567 10586882
44. GC Yuan YJ Liu MF Dion 2005 Genome-scale identification of nucleosome positions in S. cerevisiae Science 309 626 630 1:CAS:528:DC%2BD2MXmsFChtr8%3D 10.1126/science.1112178 15961632 (Pubitemid 41033649)
45. GC Yuan JS Liu 2008 Genomic sequence is highly predictive of local nucleosome depletion PLoS Comput Biol 4 1 e13 10.1371/journal.pcbi.0040013 18225943 (Pubitemid 351230864)
46. LR Zhang LF Luo 2003 Splice site prediction with quadratic discriminant analysis using diversity measure Nucleic Acids Res 31 6214 6220 1:CAS:528:DC%2BD3sXos1anu70%3D 10.1093/nar/gkg805 14576308 (Pubitemid 37442349)
47. MQ Zhang 1997 Identification of protein coding regions in the human genome by quadratic discriminant analysis Proc Natl Acad Sci USA 94 565 568 1:CAS:528:DyaK2sXnslentg%3D%3D 10.1073/pnas.94.2.565 9012824 (Pubitemid 27053673)