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Items: 1 to 20 of 85

1.

Nucleosome organization affects the sensitivity of gene expression to promoter mutations.

Hornung G, Oren M, Barkai N.

Mol Cell. 2012 May 11;46(3):362-8. doi: 10.1016/j.molcel.2012.02.019. Epub 2012 Mar 29.

2.

Evidence of association between nucleosome occupancy and the evolution of transcription factor binding sites in yeast.

Swamy KB, Chu WY, Wang CY, Tsai HK, Wang D.

BMC Evol Biol. 2011 May 31;11:150. doi: 10.1186/1471-2148-11-150.

3.

Stabilization of the promoter nucleosomes in nucleosome-free regions by the yeast Cyc8-Tup1 corepressor.

Chen K, Wilson MA, Hirsch C, Watson A, Liang S, Lu Y, Li W, Dent SY.

Genome Res. 2013 Feb;23(2):312-22. doi: 10.1101/gr.141952.112. Epub 2012 Nov 2.

4.

Chromatin mediation of a transcriptional memory effect in yeast.

Paul E, Tirosh I, Lai W, Buck MJ, Palumbo MJ, Morse RH.

G3 (Bethesda). 2015 Mar 5;5(5):829-38. doi: 10.1534/g3.115.017418.

5.

DNA physical properties determine nucleosome occupancy from yeast to fly.

Miele V, Vaillant C, d'Aubenton-Carafa Y, Thermes C, Grange T.

Nucleic Acids Res. 2008 Jun;36(11):3746-56. doi: 10.1093/nar/gkn262. Epub 2008 May 17.

6.

Gene expression divergence in yeast is coupled to evolution of DNA-encoded nucleosome organization.

Field Y, Fondufe-Mittendorf Y, Moore IK, Mieczkowski P, Kaplan N, Lubling Y, Lieb JD, Widom J, Segal E.

Nat Genet. 2009 Apr;41(4):438-45. doi: 10.1038/ng.324. Epub 2009 Mar 1.

7.

Two strategies for gene regulation by promoter nucleosomes.

Tirosh I, Barkai N.

Genome Res. 2008 Jul;18(7):1084-91. doi: 10.1101/gr.076059.108. Epub 2008 Apr 30.

8.

Interplay between nucleosomes and transcription factors at the yeast PHO5 promoter.

Svaren J, Hörz W.

Semin Cell Biol. 1995 Aug;6(4):177-83. Review.

PMID:
8562909
9.

The effect of an intervening promoter nucleosome on gene expression.

Parikh RY, Kim HD.

PLoS One. 2013 May 20;8(5):e63072. doi: 10.1371/journal.pone.0063072. Print 2013.

10.

Different roles for abf1p and a T-rich promoter element in nucleosome organization of the yeast RPS28A gene.

Lascaris RF, Groot E, Hoen PB, Mager WH, Planta RJ.

Nucleic Acids Res. 2000 Mar 15;28(6):1390-6.

11.

Intrinsic variability of gene expression encoded in nucleosome positioning sequences.

Choi JK, Kim YJ.

Nat Genet. 2009 Apr;41(4):498-503. doi: 10.1038/ng.319. Epub 2009 Mar 1.

PMID:
19252489
12.

Evolution of nucleosome occupancy: conservation of global properties and divergence of gene-specific patterns.

Tsui K, Dubuis S, Gebbia M, Morse RH, Barkai N, Tirosh I, Nislow C.

Mol Cell Biol. 2011 Nov;31(21):4348-55. doi: 10.1128/MCB.05276-11. Epub 2011 Sep 6.

13.

Divergence of nucleosome positioning between two closely related yeast species: genetic basis and functional consequences.

Tirosh I, Sigal N, Barkai N.

Mol Syst Biol. 2010 May 11;6:365. doi: 10.1038/msb.2010.20.

14.

Relating periodicity of nucleosome organization and gene regulation.

Wan J, Lin J, Zack DJ, Qian J.

Bioinformatics. 2009 Jul 15;25(14):1782-8. doi: 10.1093/bioinformatics/btp323. Epub 2009 May 15.

15.

Nucleosome organization in the vicinity of transcription factor binding sites in the human genome.

Nie Y, Cheng X, Chen J, Sun X.

BMC Genomics. 2014 Jun 19;15:493. doi: 10.1186/1471-2164-15-493.

16.

Chromatin remodelers clear nucleosomes from intrinsically unfavorable sites to establish nucleosome-depleted regions at promoters.

Tolkunov D, Zawadzki KA, Singer C, Elfving N, Morozov AV, Broach JR.

Mol Biol Cell. 2011 Jun 15;22(12):2106-18. doi: 10.1091/mbc.E10-10-0826. Epub 2011 Apr 20.

17.

Differential cofactor requirements for histone eviction from two nucleosomes at the yeast PHO84 promoter are determined by intrinsic nucleosome stability.

Wippo CJ, Krstulovic BS, Ertel F, Musladin S, Blaschke D, Stürzl S, Yuan GC, Hörz W, Korber P, Barbaric S.

Mol Cell Biol. 2009 Jun;29(11):2960-81. doi: 10.1128/MCB.01054-08. Epub 2009 Mar 23.

18.

Positioned and G/C-capped poly(dA:dT) tracts associate with the centers of nucleosome-free regions in yeast promoters.

Wu R, Li H.

Genome Res. 2010 Apr;20(4):473-84. doi: 10.1101/gr.103226.109. Epub 2010 Feb 4.

19.

Dynamic nucleosome organization at hox promoters during zebrafish embryogenesis.

Weicksel SE, Xu J, Sagerström CG.

PLoS One. 2013 May 9;8(5):e63175. doi: 10.1371/journal.pone.0063175. Print 2013.

20.

Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast.

Raveh-Sadka T, Levo M, Shabi U, Shany B, Keren L, Lotan-Pompan M, Zeevi D, Sharon E, Weinberger A, Segal E.

Nat Genet. 2012 May 27;44(7):743-50. doi: 10.1038/ng.2305.

PMID:
22634752

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