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Items: 1 to 20 of 101

1.

Nucleosome positions predicted through comparative genomics.

Ioshikhes IP, Albert I, Zanton SJ, Pugh BF.

Nat Genet. 2006 Oct;38(10):1210-5. Epub 2006 Sep 10.

PMID:
16964265
2.

Sequence-directed nucleosome-depletion is sufficient to activate transcription from a yeast core promoter in vivo.

Ichikawa Y, Morohashi N, Tomita N, Mitchell AP, Kurumizaka H, Shimizu M.

Biochem Biophys Res Commun. 2016 Jul 22;476(2):57-62. doi: 10.1016/j.bbrc.2016.05.063. Epub 2016 May 18.

3.

Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome.

Albert I, Mavrich TN, Tomsho LP, Qi J, Zanton SJ, Schuster SC, Pugh BF.

Nature. 2007 Mar 29;446(7135):572-6.

PMID:
17392789
4.

Experiments confirm the influence of genome long-range correlations on nucleosome positioning.

Vaillant C, Audit B, Arneodo A.

Phys Rev Lett. 2007 Nov 23;99(21):218103. Epub 2007 Nov 21.

PMID:
18233262
5.

Nucleosome free regions in yeast promoters result from competitive binding of transcription factors that interact with chromatin modifiers.

Ozonov EA, van Nimwegen E.

PLoS Comput Biol. 2013;9(8):e1003181. doi: 10.1371/journal.pcbi.1003181. Epub 2013 Aug 22.

6.
7.

A genomic code for nucleosome positioning.

Segal E, Fondufe-Mittendorf Y, Chen L, Thåström A, Field Y, Moore IK, Wang JP, Widom J.

Nature. 2006 Aug 17;442(7104):772-8. Epub 2006 Jul 19.

8.

A role for Snf2-related nucleosome-spacing enzymes in genome-wide nucleosome organization.

Gkikopoulos T, Schofield P, Singh V, Pinskaya M, Mellor J, Smolle M, Workman JL, Barton GJ, Owen-Hughes T.

Science. 2011 Sep 23;333(6050):1758-60. doi: 10.1126/science.1206097.

9.

Genome-Wide Analysis of Nucleosome Positions, Occupancy, and Accessibility in Yeast: Nucleosome Mapping, High-Resolution Histone ChIP, and NCAM.

Rodriguez J, McKnight JN, Tsukiyama T.

Curr Protoc Mol Biol. 2014 Oct 1;108:21.28.1-16. doi: 10.1002/0471142727.mb2128s108. Review.

10.

Distinct modes of regulation by chromatin encoded through nucleosome positioning signals.

Field Y, Kaplan N, Fondufe-Mittendorf Y, Moore IK, Sharon E, Lubling Y, Widom J, Segal E.

PLoS Comput Biol. 2008 Nov;4(11):e1000216. doi: 10.1371/journal.pcbi.1000216. Epub 2008 Nov 7.

11.

In vivo effects of histone H3 depletion on nucleosome occupancy and position in Saccharomyces cerevisiae.

Gossett AJ, Lieb JD.

PLoS Genet. 2012;8(6):e1002771. doi: 10.1371/journal.pgen.1002771. Epub 2012 Jun 21.

12.

New insights into two distinct nucleosome distributions: comparison of cross-platform positioning datasets in the yeast genome.

Feng J, Dai X, Xiang Q, Dai Z, Wang J, Deng Y, He C.

BMC Genomics. 2010 Jan 15;11:33. doi: 10.1186/1471-2164-11-33.

13.

Z curve theory-based analysis of the dynamic nature of nucleosome positioning in Saccharomyces cerevisiae.

Wu X, Liu H, Liu H, Su J, Lv J, Cui Y, Wang F, Zhang Y.

Gene. 2013 Nov 1;530(1):8-18. doi: 10.1016/j.gene.2013.08.018. Epub 2013 Aug 16.

PMID:
23958656
14.

Calculation of nucleosomal DNA deformation energy: its implication for nucleosome positioning.

Wang JY, Wang J, Liu G.

Chromosome Res. 2012 Oct;20(7):889-902. doi: 10.1007/s10577-012-9328-6. Epub 2012 Dec 5.

PMID:
23247720
15.

Distal chromatin structure influences local nucleosome positions and gene expression.

Jansen A, van der Zande E, Meert W, Fink GR, Verstrepen KJ.

Nucleic Acids Res. 2012 May;40(9):3870-85. doi: 10.1093/nar/gkr1311. Epub 2012 Jan 12.

16.

Nucleosome positioning signals in genomic DNA.

Peckham HE, Thurman RE, Fu Y, Stamatoyannopoulos JA, Noble WS, Struhl K, Weng Z.

Genome Res. 2007 Aug;17(8):1170-7. Epub 2007 Jul 9.

17.

A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome.

Mavrich TN, Ioshikhes IP, Venters BJ, Jiang C, Tomsho LP, Qi J, Schuster SC, Albert I, Pugh BF.

Genome Res. 2008 Jul;18(7):1073-83. doi: 10.1101/gr.078261.108. Epub 2008 Jun 12.

18.

Transcription factor binding site positioning in yeast: proximal promoter motifs characterize TATA-less promoters.

Erb I, van Nimwegen E.

PLoS One. 2011;6(9):e24279. doi: 10.1371/journal.pone.0024279. Epub 2011 Sep 9.

19.
20.

Genome-wide in vitro reconstitution of yeast chromatin with in vivo-like nucleosome positioning.

Krietenstein N, Wippo CJ, Lieleg C, Korber P.

Methods Enzymol. 2012;513:205-32. doi: 10.1016/B978-0-12-391938-0.00009-4.

PMID:
22929771

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