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Literature DB >> 20683474

Evidence against a genomic code for nucleosome positioning. Reply to "Nucleosome sequence preferences influence in vivo nucleosome organization.".

Yong Zhang¹, Zarmik Moqtaderi, Barbara P Rattner, Ghia Euskirchen, Michael Snyder, James T Kadonaga, X Shirley Liu, Kevin Struhl.

Abstract

Entities: Chemical Disease Gene Species

Mesh：

Substances：
Histones
Nucleosomes

Year: 2010 PMID： 20683474 PMCID： PMC4742340 DOI： 10.1038/nsmb0810-920

Source DB: PubMed Journal: Nat Struct Mol Biol ISSN： 1545-9985 Impact factor: 15.369

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21 in total

1. Genome-scale identification of nucleosome positions in S. cerevisiae.

Authors: Guo-Cheng Yuan; Yuen-Jong Liu; Michael F Dion; Michael D Slack; Lani F Wu; Steven J Altschuler; Oliver J Rando
Journal: Science Date: 2005-06-16 Impact factor: 47.728

2. Sequence periodicities in chicken nucleosome core DNA.

Authors: S C Satchwell; H R Drew; A A Travers
Journal: J Mol Biol Date: 1986-10-20 Impact factor: 5.469

3. Statistical positioning of nucleosomes by specific protein-binding to an upstream activating sequence in yeast.

Authors: M J Fedor; N F Lue; R D Kornberg
Journal: J Mol Biol Date: 1988-11-05 Impact factor: 5.469

4. Sequence specific cleavage of DNA by micrococcal nuclease.

Authors: W Hörz; W Altenburger
Journal: Nucleic Acids Res Date: 1981-06-25 Impact factor: 16.971

5. Naturally occurring poly(dA-dT) sequences are upstream promoter elements for constitutive transcription in yeast.

Authors: K Struhl
Journal: Proc Natl Acad Sci U S A Date: 1985-12 Impact factor: 11.205

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

Authors: Travis N Mavrich; Ilya P Ioshikhes; Bryan J Venters; Cizhong Jiang; Lynn P Tomsho; Ji Qi; Stephan C Schuster; Istvan Albert; B Franklin Pugh
Journal: Genome Res Date: 2008-06-12 Impact factor: 9.043

7. Nucleosome reconstitution on plasmid-inserted poly(dA) . poly(dT).

Authors: A Prunell
Journal: EMBO J Date: 1982 Impact factor: 11.598

8. Single-molecule imaging of DNA curtains reveals intrinsic energy landscapes for nucleosome deposition.

Authors: Mari-Liis Visnapuu; Eric C Greene
Journal: Nat Struct Mol Biol Date: 2009-09-06 Impact factor: 15.369

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

Authors: Yong Zhang; Zarmik Moqtaderi; Barbara P Rattner; Ghia Euskirchen; Michael Snyder; James T Kadonaga; X Shirley Liu; Kevin Struhl
Journal: Nat Struct Mol Biol Date: 2009-07-20 Impact factor: 15.369

10. Evaluation of next generation sequencing platforms for population targeted sequencing studies.

Authors: Olivier Harismendy; Pauline C Ng; Robert L Strausberg; Xiaoyun Wang; Timothy B Stockwell; Karen Y Beeson; Nicholas J Schork; Sarah S Murray; Eric J Topol; Samuel Levy; Kelly A Frazer
Journal: Genome Biol Date: 2009-03-27 Impact factor: 13.583

21 in total

10. A functional evolutionary approach to identify determinants of nucleosome positioning: a unifying model for establishing the genome-wide pattern.

Authors: Amanda L Hughes; Yi Jin; Oliver J Rando; Kevin Struhl
Journal: Mol Cell Date: 2012-08-09 Impact factor: 17.970

Evidence against a genomic code for nucleosome positioning. Reply to "Nucleosome sequence preferences influence in vivo nucleosome organization.".

1. Genome-scale identification of nucleosome positions in S. cerevisiae.

2. Sequence periodicities in chicken nucleosome core DNA.

3. Statistical positioning of nucleosomes by specific protein-binding to an upstream activating sequence in yeast.

4. Sequence specific cleavage of DNA by micrococcal nuclease.

5. Naturally occurring poly(dA-dT) sequences are upstream promoter elements for constitutive transcription in yeast.

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

7. Nucleosome reconstitution on plasmid-inserted poly(dA) . poly(dT).

8. Single-molecule imaging of DNA curtains reveals intrinsic energy landscapes for nucleosome deposition.

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

10. Evaluation of next generation sequencing platforms for population targeted sequencing studies.

Review 1. Nucleosome positioning in Saccharomyces cerevisiae.

Review 2. Nucleosome mobility and the regulation of gene expression: Insights from single-molecule studies.

Review 3. Nucleosome positioning: bringing order to the eukaryotic genome.

4. A unified computational framework for modeling genome-wide nucleosome landscape.

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

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

7. Structural ensemble and microscopic elasticity of freely diffusing DNA by direct measurement of fluctuations.

Review 8. Understanding nucleosome dynamics and their links to gene expression and DNA replication.

9. Insights into Nucleosome Organization in Mouse Embryonic Stem Cells through Chemical Mapping.

10. A functional evolutionary approach to identify determinants of nucleosome positioning: a unifying model for establishing the genome-wide pattern.