Analysis of nucleosome positioning determined by DNA helix curvature in the human genome.
BACKGROUND
Nucleosome positioning has an important role in gene regulation. However, dynamic positioning in vivo casts doubt on the reliability of predictions based on DNA sequence characteristics. What role does sequence-dependent positioning play? In this paper, using a curvature profile model, nucleosomes are predicted in the human genome and patterns of nucleosomes near some key sites are investigated.


RESULTS
Curvature profiling revealed that in the vicinity of a transcription start site, there is also a nucleosome-free region. Near transcription factor binding sites, curvature profiling showed a trough, indicating nucleosome depletion. The trough of the curvature profile corresponds well to the high binding scores of transcription factors. Moreover, our analysis suggests that nucleosome positioning has a selective protection role. Target sites of miRNAs are occupied by nucleosomes, while single nucleotide polymorphism sites are depleted of nucleosomes.


CONCLUSIONS
The results indicate that DNA sequences play an important role in nucleosome positioning, and the positioning is important not only in gene regulation, but also in genetic variation and miRNA functions.
State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China.
Hongde
H
Liu
Xueye
X
Duan
Shuangxin
S
Yu
Xiao
X
Sun
D001483:Base Sequence / Q000235:genetics; D042002:Chromatin Assembly and Disassembly / Q000235:genetics / Q000502:physiology; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D015894:Genome, Human / Q000235:genetics*; D006801:Humans; D009690:Nucleic Acid Conformation; D009707:Nucleosomes / Q000378:metabolism*; D024363:Transcription Initiation Site
D009707:Nucleosomes; D004247:DNA
PLoS Comput Biol. 2008 Jan;4(1):e13
18225943
Proc Natl Acad Sci U S A. 2007 Oct 2;104(40):15635-40
17893337
Proc Natl Acad Sci U S A. 2004 Apr 20;101(16):6062-7
15075390
Cell. 2008 Jul 11;134(1):74-84
18614012
Nat Rev Genet. 2008 Jan;9(1):15-26
18059368
J Chem Inf Comput Sci. 2004 Jul-Aug;44(4):1228-37
15272830
Nat Genet. 2006 Oct;38(10):1210-5
16964265
PLoS Biol. 2008 Mar 18;6(3):e65
18351804
Nature. 2009 Mar 19;458(7236):362-6
19092803
Gene. 2005 Jun 6;352:57-62
15862762
Nat Struct Mol Biol. 2010 Feb;17(2):251-7
20118936
Genes Dev. 2008 Nov 15;22(22):3172-83
19056895
PLoS One. 2009 Nov 02;4(11):e7654
19888331
Nucleic Acids Res. 2001 Jan 1;29(1):308-11
11125122
J Mol Biol. 2004 Oct 29;343(4):891-901
15476808
Genome Res. 2008 Jul;18(7):1051-63
18477713
Nat Rev Genet. 2004 Apr;5(4):276-87
15131651
J Biomol Struct Dyn. 2008 Dec;26(3):273-82
18808193
Biophys J. 2008 Jun;94(12):4597-604
18326654
Proc Natl Acad Sci U S A. 2003 Oct 14;100(21):12247-52
14527995
Bioinformatics. 1999 Mar;15(3):187-93
10222405
Bioinformatics. 2008 Jun 15;24(12):1456-8
18445607
Biochemistry. 1989 Oct 31;28(22):8706-13
2605217
Nat Struct Mol Biol. 2009 Aug;16(8):847-52
19620965
Cell. 2008 Mar 7;132(5):887-98
18329373
Cell. 2005 Jan 14;120(1):15-20
15652477
Science. 2007 Jun 8;316(5830):1497-502
17540862
Curr Opin Genet Dev. 2005 Apr;15(2):200-5
15797203
Gene. 2002 Oct 30;300(1-2):203-11
12468102
Nat Biotechnol. 2007 Feb;25(2):244-8
17220878
Nucleic Acids Res. 2009 Aug;37(14):4707-22
19509309
Nat Rev Genet. 2009 Mar;10(3):161-72
19204718
Genome Res. 2008 Jul;18(7):1073-83
18550805
Cell. 2009 May 1;137(3):445-58
19410542
Nucleic Acids Res. 2008 Jun;36(11):3746-56
18487627
Nature. 2006 Aug 17;442(7104):772-8
16862119
BMC Genomics. 2008 Jul 15;9:332
18627598
Science. 2009 Jan 16;323(5912):401-4
19074313