Nucleosome rotational setting is associated with transcriptional regulation in promoters of tissue-specific human genes.
BACKGROUND
The position of a nucleosome, both translational along the DNA molecule and rotational between the histone core and the DNA, is controlled by many factors, including the regular occurrence of specific dinucleotides with a period of approximately 10 bp, important for the rotational setting of the DNA around the histone octamer.


RESULTS
We show that such a 10 bp periodic signal of purine-purine dinucleotides occurs in phase with the transcription start site (TSS) of human genes and is centered on the position of the first (+1) nucleosome downstream of the TSS. These data support a direct link between transcription and the rotational setting of the nucleosome. The periodic signal is most prevalent in genes that contain CpG islands that are expressed at low levels in a tissue-specific manner and are involved in the control of transcription.


CONCLUSIONS
These results, together with several lines of evidence from the recent literature, support a new model whereby the +1 nucleosome could be more efficiently disassembled from gene promoters by H3K56 acetylation marks if the periodic signal specifies an optimal rotational setting.
Hebert
Charles
C
Dyogen Group, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), 46 rue d'Ulm, CNRS UMR8197, INSERM U1024, 75005 Paris Cedex 05, France. charles.hebert@gmail.com
Roest Crollius
Hugues
H
D000107:Acetylation; D020029:Base Pairing / Q000235:genetics; D017124:Conserved Sequence; D018899:CpG Islands / Q000235:genetics; D004247:DNA / Q000235:genetics; D050881:E1A-Associated p300 Protein / Q000378:metabolism; D056890:Eukaryota / Q000235:genetics; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D016678:Genome / Q000235:genetics; D006657:Histones / Q000378:metabolism; D006801:Humans; D008239:Lysine / Q000378:metabolism; D008957:Models, Genetic; D009707:Nucleosomes / Q000235:genetics*; D009711:Nucleotides / Q000235:genetics; D009928:Organ Specificity / Q000235:genetics*; D011401:Promoter Regions, Genetic / Q000235:genetics*; D012319:RNA Polymerase II / Q000378:metabolism; D012399:Rotation; D024363:Transcription Initiation Site; D014158:Transcription, Genetic
D006657:Histones; D009707:Nucleosomes; D009711:Nucleotides; D004247:DNA; D050881:E1A-Associated p300 Protein; C494360:EP300 protein, human; D012319:RNA Polymerase II; D008239:Lysine
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W91-6
17478504
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W472-6
16845052
Genome Res. 2008 Jul;18(7):1051-63
18477713
Proc Natl Acad Sci U S A. 2004 Apr 20;101(16):6062-7
15075390
Proc Natl Acad Sci U S A. 2008 Jul 1;105(26):9000-5
18577595
Mol Cell Biol. 1992 Jun;12(6):2826-36
1534143
Nat Rev Genet. 2008 Jan;9(1):15-26
18059368
Cell. 2007 Feb 23;128(4):693-705
17320507
Nature. 2005 Jul 14;436(7048):294-8
16015338
Biopolymers. 1997;44(4):423-33
9782778
Cell. 2005 May 6;121(3):375-85
15882620
Nucleic Acids Res. 1980 Apr 11;8(7):1499-504
6253938
J Mol Biol. 1985 Dec 20;186(4):773-90
3912515
Nat Genet. 2008 Jul;40(7):897-903
18552846
Nature. 2009 May 7;459(7243):113-7
19270680
Gene. 2005 Jun 6;352:57-62
15862762
Chromosoma. 2009 Feb;118(1):1-10
18830703
Nature. 2007 Mar 29;446(7135):572-6
17392789
J Mol Biol. 2009 Mar 13;386(5):1411-22
19070622
Mol Cell Biol. 1986 Nov;6(11):3984-9
3099167
Proc Natl Acad Sci U S A. 1993 Sep 1;90(17):7923-7
8367444
Proc Natl Acad Sci U S A. 2006 Jan 31;103(5):1412-7
16432200
J Mol Biol. 2003 Sep 5;332(1):111-25
12946351
Mol Cell. 2009 Feb 27;33(4):417-27
19250903
J Cell Biol. 2000 Jul 10;150(1):265-73
10893273
Cell. 2007 May 18;129(4):823-37
17512414
J Biomol Struct Dyn. 2006 Aug;24(1):43-8
16780374
J Mol Biol. 2009 Jul 10;390(2):292-305
19427325
J Biol Chem. 2007 Jul 27;282(30):21901-12
17548348
Nucleic Acids Res. 2004 Sep 23;32(17):4969-78
15388799
Mol Cell Biol. 1998 Sep;18(9):5355-63
9710619
Mol Cell Biol. 1990 Nov;10(11):6041-5
2172790
Cell. 2008 Mar 7;132(5):887-98
18329373
Genome Res. 2009 Jun;19(6):967-77
19246569
Bioinformatics. 2005 Jun 1;21(11):2657-66
15797905
J Mol Biol. 2002 Jun 21;319(5):1097-113
12079350
Nature. 2003 May 8;423(6936):145-50
12736678
J Mol Biol. 1998 Aug 28;281(4):663-73
9710538
Genes Dev. 2003 Jun 1;17(11):1392-401
12782657
PLoS Comput Biol. 2008 Nov;4(11):e1000216
18989395
J Comput Biol. 2005 Jul-Aug;12(6):882-93
16108723
J Mol Biol. 1995 Oct 6;252(5):522-35
7563071
Nature. 2008 May 15;453(7193):358-62
18408708
Nucleic Acids Res. 2008 Jan;36(Database issue):D97-101
17942421
Cell. 2005 Oct 21;123(2):233-48
16239142
Nat Rev Genet. 2009 Mar;10(3):161-72
19204718
Curr Opin Struct Biol. 2006 Apr;16(2):213-20
16540311
Nature. 2006 Aug 17;442(7104):772-8
16862119
Nucleic Acids Res. 2005 Feb 16;33(3):934-45
15716311