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Results: 1 to 20 of 109

1.

DNA transposon Hermes inserts into DNA in nucleosome-free regions in vivo.

Gangadharan S, Mularoni L, Fain-Thornton J, Wheelan SJ, Craig NL.

Proc Natl Acad Sci U S A. 2010 Dec 21;107(51):21966-72. doi: 10.1073/pnas.1016382107. Epub 2010 Dec 3.

PMID:
21131571
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Retrotransposon Ty1 integration targets specifically positioned asymmetric nucleosomal DNA segments in tRNA hotspots.

Mularoni L, Zhou Y, Bowen T, Gangadharan S, Wheelan SJ, Boeke JD.

Genome Res. 2012 Apr;22(4):693-703. doi: 10.1101/gr.129460.111. Epub 2012 Jan 4.

PMID:
22219510
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

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.

PMID:
16862119
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

The DNA-encoded nucleosome organization of a eukaryotic genome.

Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, Tillo D, Field Y, LeProust EM, Hughes TR, Lieb JD, Widom J, Segal E.

Nature. 2009 Mar 19;458(7236):362-6. doi: 10.1038/nature07667. Epub 2008 Dec 17.

PMID:
19092803
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

A nucleosomal surface defines an integration hotspot for the Saccharomyces cerevisiae Ty1 retrotransposon.

Baller JA, Gao J, Stamenova R, Curcio MJ, Voytas DF.

Genome Res. 2012 Apr;22(4):704-13. doi: 10.1101/gr.129585.111. Epub 2012 Jan 4.

PMID:
22219511
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Multipurpose transposon insertion libraries for large-scale analysis of gene function in yeast.

Kumar A.

Methods Mol Biol. 2008;416:117-29. doi: 10.1007/978-1-59745-321-9_8.

PMID:
18392964
[PubMed - indexed for MEDLINE]
7.

Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection.

Liu X, Lee CK, Granek JA, Clarke ND, Lieb JD.

Genome Res. 2006 Dec;16(12):1517-28. Epub 2006 Oct 19.

PMID:
17053089
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Insertional mutagenesis by a modified in vitro Ty1 transposition system.

Garraway LA, Tosi LR, Wang Y, Moore JB, Dobson DE, Beverley SM.

Gene. 1997 Oct 1;198(1-2):27-35.

PMID:
9370261
[PubMed - indexed for MEDLINE]
9.

Re-cracking the nucleosome positioning code.

Segal MR.

Stat Appl Genet Mol Biol. 2008;7(1):Article14. doi: 10.2202/1544-6115.1367. Epub 2008 Apr 21.

PMID:
18454729
[PubMed - indexed for MEDLINE]
10.

Identifying tagged transposon insertion sites in yeast by direct genomic sequencing.

Horecka J, Jigami Y.

Yeast. 2000 Jul;16(10):967-70.

PMID:
10870108
[PubMed - indexed for MEDLINE]
11.

Genome-wide mapping of nucleosomes in yeast using paired-end sequencing.

Cole HA, Howard BH, Clark DJ.

Methods Enzymol. 2012;513:145-68. doi: 10.1016/B978-0-12-391938-0.00006-9.

PMID:
22929768
[PubMed - indexed for MEDLINE]
12.

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
[PubMed - indexed for MEDLINE]
13.

Structural features based genome-wide characterization and prediction of nucleosome organization.

Gan Y, Guan J, Zhou S, Zhang W.

BMC Bioinformatics. 2012 Mar 26;13:49. doi: 10.1186/1471-2105-13-49.

PMID:
22449207
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

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
[PubMed - indexed for MEDLINE]
15.

Genome-wide transposon mutagenesis in Saccharomyces cerevisiae and Candida albicans.

Xu T, Bharucha N, Kumar A.

Methods Mol Biol. 2011;765:207-24. doi: 10.1007/978-1-61779-197-0_13.

PMID:
21815095
[PubMed - indexed for MEDLINE]
16.

Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo.

Zhang Y, Moqtaderi Z, Rattner BP, Euskirchen G, Snyder M, Kadonaga JT, Liu XS, Struhl K.

Nat Struct Mol Biol. 2009 Aug;16(8):847-52. doi: 10.1038/nsmb.1636. Epub 2009 Jul 20.

PMID:
19620965
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

The genome folding mechanism in yeast.

Kimura H, Shimooka Y, Nishikawa J, Miura O, Sugiyama S, Yamada S, Ohyama T.

J Biochem. 2013 Aug;154(2):137-47. doi: 10.1093/jb/mvt033. Epub 2013 Apr 24.

PMID:
23620598
[PubMed - indexed for MEDLINE]
18.

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.

PMID:
18989395
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Genome-wide mapping of nucleosomes in yeast.

Rando OJ.

Methods Enzymol. 2010;470:105-18. doi: 10.1016/S0076-6879(10)70005-7. Epub 2010 Mar 1.

PMID:
20946808
[PubMed - indexed for MEDLINE]
20.

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
[PubMed - indexed for MEDLINE]

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