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Results: 1 to 20 of 129

1.

Predicting nucleosome positions on the DNA: combining intrinsic sequence preferences and remodeler activities.

Teif VB, Rippe K.

Nucleic Acids Res. 2009 Sep;37(17):5641-55. doi: 10.1093/nar/gkp610. Epub 2009 Jul 22.

PMID:
19625488
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Remodelers organize cellular chromatin by counteracting intrinsic histone-DNA sequence preferences in a class-specific manner.

Moshkin YM, Chalkley GE, Kan TW, Reddy BA, Ozgur Z, van Ijcken WF, Dekkers DH, Demmers JA, Travers AA, Verrijzer CP.

Mol Cell Biol. 2012 Feb;32(3):675-88. doi: 10.1128/MCB.06365-11. Epub 2011 Nov 28.

PMID:
22124157
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Chromatin remodelers act globally, sequence positions nucleosomes locally.

Partensky PD, Narlikar GJ.

J Mol Biol. 2009 Aug 7;391(1):12-25. doi: 10.1016/j.jmb.2009.04.085. Epub 2009 May 18.

PMID:
19450608
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Multiple aspects of ATP-dependent nucleosome translocation by RSC and Mi-2 are directed by the underlying DNA sequence.

van Vugt JJ, de Jager M, Murawska M, Brehm A, van Noort J, Logie C.

PLoS One. 2009 Jul 23;4(7):e6345. doi: 10.1371/journal.pone.0006345.

PMID:
19626125
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Are nucleosome positions in vivo primarily determined by histone-DNA sequence preferences?

Stein A, Takasuka TE, Collings CK.

Nucleic Acids Res. 2010 Jan;38(3):709-19. doi: 10.1093/nar/gkp1043. Epub 2009 Nov 24.

PMID:
19934265
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Global remodeling of nucleosome positions in C. elegans.

Locke G, Haberman D, Johnson SM, Morozov AV.

BMC Genomics. 2013 Apr 26;14:284. doi: 10.1186/1471-2164-14-284.

PMID:
23622142
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

The core histone tail domains contribute to sequence-dependent nucleosome positioning.

Yang Z, Zheng C, Hayes JJ.

J Biol Chem. 2007 Mar 16;282(11):7930-8. Epub 2007 Jan 17.

PMID:
17234628
[PubMed - indexed for MEDLINE]
Free Article
8.

Structure-based analysis of DNA sequence patterns guiding nucleosome positioning in vitro.

Cui F, Zhurkin VB.

J Biomol Struct Dyn. 2010 Jun;27(6):821-41.

PMID:
20232936
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Control of nucleosome positions by DNA sequence and remodeling machines.

Schnitzler GR.

Cell Biochem Biophys. 2008;51(2-3):67-80. doi: 10.1007/s12013-008-9015-6. Epub 2008 Jun 10. Review.

PMID:
18543113
[PubMed - indexed for MEDLINE]
10.

DNA sequence- and conformation-directed positioning of nucleosomes by chromatin-remodeling complexes.

Rippe K, Schrader A, Riede P, Strohner R, Lehmann E, Längst G.

Proc Natl Acad Sci U S A. 2007 Oct 2;104(40):15635-40. Epub 2007 Sep 24.

PMID:
17893337
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Prediction of nucleosome positioning in genomes: limits and perspectives of physical and bioinformatic approaches.

De Santis P, Morosetti S, Scipioni A.

J Biomol Struct Dyn. 2010 Jun;27(6):747-64.

PMID:
20232931
[PubMed - indexed for MEDLINE]
12.

Changing the DNA landscape: putting a SPN on chromatin.

Formosa T.

Curr Top Microbiol Immunol. 2003;274:171-201. Review.

PMID:
12596908
[PubMed - indexed for MEDLINE]
13.

Mapping assembly favored and remodeled nucleosome positions on polynucleosomal templates.

Sims HI, Pham CD, Schnitzler GR.

Methods Mol Biol. 2012;833:311-36. doi: 10.1007/978-1-61779-477-3_19.

PMID:
22183602
[PubMed - indexed for MEDLINE]
14.

Sequence-dependent nucleosome positioning.

Chung HR, Vingron M.

J Mol Biol. 2009 Mar 13;386(5):1411-22. doi: 10.1016/j.jmb.2008.11.049. Epub 2008 Dec 3.

PMID:
19070622
[PubMed - indexed for MEDLINE]
15.

Nucleosome positioning and nucleosome stacking: two faces of the same coin.

Riposo J, Mozziconacci J.

Mol Biosyst. 2012 Apr;8(4):1172-8. doi: 10.1039/c2mb05407h. Epub 2012 Jan 23.

PMID:
22266567
[PubMed - indexed for MEDLINE]
16.

Nucleosome positioning in relation to nucleosome spacing and DNA sequence-specific binding of a protein.

Pusarla RH, Vinayachandran V, Bhargava P.

FEBS J. 2007 May;274(9):2396-410. Epub 2007 Apr 5.

PMID:
17419736
[PubMed - indexed for MEDLINE]
17.

Active nucleosome positioning beyond intrinsic biophysics is revealed by in vitro reconstitution.

Korber P.

Biochem Soc Trans. 2012 Apr;40(2):377-82. doi: 10.1042/BST20110730. Review.

PMID:
22435815
[PubMed - indexed for MEDLINE]
18.

Sequence-based prediction of single nucleosome positioning and genome-wide nucleosome occupancy.

van der Heijden T, van Vugt JJ, Logie C, van Noort J.

Proc Natl Acad Sci U S A. 2012 Sep 18;109(38):E2514-22. Epub 2012 Aug 20.

PMID:
22908247
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

The effect of nucleosome phasing sequences and DNA topology on nucleosome spacing.

Blank TA, Becker PB.

J Mol Biol. 1996 Jul 5;260(1):1-8.

PMID:
8676389
[PubMed - indexed for MEDLINE]
20.

Multiple sequence-directed possibilities provide a pool of nucleosome position choices in different states of activity of a gene.

Vinayachandran V, Pusarla RH, Bhargava P.

Epigenetics Chromatin. 2009 Mar 16;2(1):4. doi: 10.1186/1756-8935-2-4.

PMID:
19291282
[PubMed]
Free PMC Article
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