title: Sequence-specific flexibility organization of splicing flanking sequence and prediction of splice sites in the human genome.
abstract: More and more reported results of nucleosome positioning and histone modifications showed that DNA structure play a well-established role in splicing. In this study, a set of DNA geometric flexibility parameters originated from molecular dynamics (MD) simulations were introduced to discuss the structure organization around splice sites at the DNA level. The obtained profiles of specific flexibility/stiffness around splice sites indicated that the DNA physical-geometry deformation could be used as an alternative way to describe the splicing junction region. In combination with structural flexibility as discriminatory parameter, we developed a hybrid computational model for predicting potential splicing sites. And the better prediction performance was achieved when the benchmark dataset evaluated. Our results showed that the mechanical deformability character of a splice junction is closely correlated with both the splice site strength and structural information in its flanking sequences.
authors.affiliation: The Key Laboratory of National Education Ministry for Mammalian Reproductive Biology and Biotechnology, Inner Mongolia University, Hohhot, 010021, China, yczuo@imu.edu.cn.
authors.forename: Yongchun
authors.initials: Y
authors.lastname: Zuo
authors.forename: Pengfei
authors.initials: P
authors.lastname: Zhang
authors.forename: Li
authors.initials: L
authors.lastname: Liu
authors.forename: Tao
authors.initials: T
authors.lastname: Li
authors.forename: Yong
authors.initials: Y
authors.lastname: Peng
authors.forename: Guangpeng
authors.initials: G
authors.lastname: Li
authors.forename: Qianzhong
authors.initials: Q
authors.lastname: Li
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000235:genetics*; D015894:Genome, Human; D006801:Humans; D009690:Nucleic Acid Conformation; D022821:RNA Splice Sites; D012326:RNA Splicing / Q000235:genetics*; D012372:ROC Curve
chemical_list: D022821:RNA Splice Sites; D004247:DNA
references.citation: Trends Plant Sci. 2003 Oct;8(10):468-71
references.pmid: 14557042
references.citation: Bioinformatics. 2005 Jan 1;21(1):10-9
references.pmid: 15308540
references.citation: Nucleic Acids Res. 2010 May;38(9):2788-98
references.pmid: 20097656
references.citation: Nucleic Acids Res. 1994 Sep 25;22(19):3854-60
references.pmid: 7937104
references.citation: Protein Pept Lett. 2010 Oct;17(10):1207-14
references.pmid: 20450487
references.citation: Trends Genet. 2001 Feb;17(2):100-7
references.pmid: 11173120
references.citation: PLoS One. 2012;7(11):e49040
references.pmid: 23189138
references.citation: J Theor Biol. 2006 Sep 7;242(1):135-41
references.pmid: 16603195
references.citation: Crit Rev Biochem Mol Biol. 1995;30(4):275-349
references.pmid: 7587280
references.citation: PLoS One. 2012;7(6):e38546
references.pmid: 22685582
references.citation: BMC Genomics. 2012 Sep 15;13:480
references.pmid: 22978521
references.citation: Nature. 2008 Jan 31;451(7178):591-5
references.pmid: 18235503
references.citation: Biopolymers. 1982 Jul;21(7):1469-72
references.pmid: 7115900
references.citation: Mol Biosyst. 2013 Apr 5;9(4):634-44
references.pmid: 23370050
references.citation: Anal Biochem. 2013 May 15;436(2):168-77
references.pmid: 23395824
references.citation: J Theor Biol. 2011 Mar 21;273(1):236-47
references.pmid: 21168420
references.citation: Mol Cell. 2010 Nov 24;40(4):571-81
references.pmid: 21095587
references.citation: J Theor Biol. 2010 Mar 21;263(2):203-9
references.pmid: 19961864
references.citation: Mol Cell. 2009 Feb 27;33(4):450-61
references.pmid: 19250906
references.citation: EMBO J. 2010 May 19;29(10):1629-36
references.pmid: 20407423
references.citation: FEBS Lett. 2012 Mar 23;586(6):934-8
references.pmid: 22449982
references.citation: PLoS One. 2012;7(10):e47843
references.pmid: 23144709
references.citation: Amino Acids. 2008 May;34(4):565-72
references.pmid: 18074191
references.citation: Trends Genet. 2012 Apr;28(4):147-54
references.pmid: 22397991
references.citation: Nucleic Acids Res. 2008 Apr;36(7):2379-94
references.pmid: 18299282
references.citation: Biochem J. 1984 Jul 1;221(1):27-31
references.pmid: 6466317
references.citation: J Theor Biol. 2013 Nov 21;337:71-9
references.pmid: 23988798
references.citation: J Proteomics. 2012 Dec 21;77:321-8
references.pmid: 23000219
references.citation: Biochem Biophys Res Commun. 2009 Dec 18;390(3):608-12
references.pmid: 19819222
references.citation: Bioinformatics. 2014 Jun 1;30(11):1522-9
references.pmid: 24504871
references.citation: Nat Struct Mol Biol. 2009 Sep;16(9):990-5
references.pmid: 19684600
references.citation: Genomics. 2011 Feb;97(2):112-20
references.pmid: 21112384
references.citation: Genome Res. 2012 Sep;22(9):1616-25
references.pmid: 22955974
references.citation: Genome Res. 2009 Oct;19(10):1732-41
references.pmid: 19687145
references.citation: Comput Biol Chem. 2010 Dec;34(5-6):320-7
references.pmid: 21106461
references.citation: Nucleic Acids Res. 2006 Jan 1;34(Database issue):D46-55
references.pmid: 16381912
references.citation: Nucleic Acids Res. 2006;34(21):6305-13
references.pmid: 17098928
references.citation: Trends Biochem Sci. 1989 Jun;14(6):212-3
references.pmid: 2763333
references.citation: PLoS One. 2013;8(2):e55844
references.pmid: 23409062
references.citation: PLoS One. 2013 Aug 27;8(8):e72234
references.pmid: 24015221
references.citation: Plant Physiol. 2013 Jun;162(2):1127-41
references.pmid: 23572549
references.citation: Biomed Res Int. 2013;2013:701317
references.pmid: 24371828
references.citation: PeerJ. 2013 Oct 03;1:e171
references.pmid: 24109555
references.citation: PLoS One. 2012;7(4):e35254
references.pmid: 22514724
references.citation: PLoS One. 2010 Jun 28;5(6):e11335
references.pmid: 20596258
references.citation: Comput Chem. 1999 Jun 15;23(3-4):191-207
references.pmid: 10404615
references.citation: Bioinformatics. 2014 Feb 15;30(4):472-9
references.pmid: 24318998
references.citation: Comput Biol Med. 2012 Apr;42(4):504-7
references.pmid: 22297432
references.citation: Biophys J. 1989 Aug;56(2):295-305
references.pmid: 2775828
references.citation: Cell. 2009 May 15;137(4):708-20
references.pmid: 19450518
references.citation: Theory Biosci. 2011 Jun;130(2):91-100
references.pmid: 21046474
references.citation: Proteins. 2001 May 15;43(3):246-55
references.pmid: 11288174
references.citation: Proc Natl Acad Sci U S A. 1998 Sep 15;95(19):11163-8
references.pmid: 9736707
references.citation: Bioinform Biol Insights. 2012;6:155-68
references.pmid: 22837642
references.citation: Mol Biosyst. 2013 Jun;9(6):1092-100
references.pmid: 23536215
references.citation: Int J Mol Sci. 2014 Jan 24;15(2):1746-66
references.pmid: 24469313
references.citation: Biochem Biophys Res Commun. 2008 Apr 4;368(2):379-81
references.pmid: 18230347
references.citation: PLoS One. 2011;6(6):e20592
references.pmid: 21698097
references.citation: Nucleic Acids Res. 2013 Apr 1;41(6):e68
references.pmid: 23303794
references.citation: Genome Biol. 2007;8(12):R263
references.pmid: 18072969
references.citation: Phys Biol. 2009 Jun 05;6(3):036012
references.pmid: 19502707
references.citation: Genome Res. 2002 Aug;12(8):1231-45
references.pmid: 12176931
references.citation: Biophys Chem. 1988 May;30(1):3-48
references.pmid: 3046672