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Literature DB >> 20946808

Genome-wide mapping of nucleosomes in yeast.

Abstract

The packaging of eukaryotic genomes into chromatin has wide-ranging influences on all DNA-templated processes, from DNA repair to transcriptional regulation. The repeating subunit of chromatin is the nucleosome, which comprises 147 bp of DNA wrapped around an octamer of proteins. Positioning of nucleosomes relative to underlying DNA is a key factor in the regulation of gene transcription by chromatin, as DNA sequences between nucleosomes are more accessible to regulatory factors than are DNA sequences within nucleosomes. Here, I describe protocols for mapping nucleosome positions across the yeast genome.

Entities: Chemical Disease Gene Mutation Species

Mesh：

Substances：
DNA, Fungal
Nucleosomes

Year: 2010 PMID： 20946808 PMCID： PMC4445963 DOI： 10.1016/S0076-6879(10)70005-7

Source DB: PubMed Journal: Methods Enzymol ISSN： 0076-6879 Impact factor: 1.600

20 in total

1. Modifying gene expression programs by altering core promoter chromatin architecture.

Authors: Stavros Lomvardas; Dimitris Thanos
Journal: Cell Date: 2002-07-26 Impact factor: 41.582

2. 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

3. Evolutionary footprints of nucleosome positions in yeast.

Authors: Stefan Washietl; Rainer Machné; Nick Goldman
Journal: Trends Genet Date: 2008-10-24 Impact factor: 11.639

4. Chromatin remodelling at promoters suppresses antisense transcription.

Authors: Iestyn Whitehouse; Oliver J Rando; Jeff Delrow; Toshio Tsukiyama
Journal: Nature Date: 2007-12-13 Impact factor: 49.962

5. Nucleosome positions predicted through comparative genomics.

Authors: Ilya P Ioshikhes; Istvan Albert; Sara J Zanton; B Franklin Pugh
Journal: Nat Genet Date: 2006-09-10 Impact factor: 38.330

6. Evidence for nucleosome depletion at active regulatory regions genome-wide.

Authors: Cheol-Koo Lee; Yoichiro Shibata; Bhargavi Rao; Brian D Strahl; Jason D Lieb
Journal: Nat Genet Date: 2004-07-11 Impact factor: 38.330

7. Nucleosome organization in the Drosophila genome.

Authors: Travis N Mavrich; Cizhong Jiang; Ilya P Ioshikhes; Xiaoyong Li; Bryan J Venters; Sara J Zanton; Lynn P Tomsho; Ji Qi; Robert L Glaser; Stephan C Schuster; David S Gilmour; Istvan Albert; B Franklin Pugh
Journal: Nature Date: 2008-04-13 Impact factor: 49.962

8. Chromatin decouples promoter threshold from dynamic range.

Authors: Felix H Lam; David J Steger; Erin K O'Shea
Journal: Nature Date: 2008-04-16 Impact factor: 49.962

9. 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

10. Genomic sequence is highly predictive of local nucleosome depletion.

Authors: Guo-Cheng Yuan; Jun S Liu
Journal: PLoS Comput Biol Date: 2007-12-13 Impact factor: 4.475

22 in total

Review 1. Nucleosome positioning in Saccharomyces cerevisiae.

Authors: An Jansen; Kevin J Verstrepen
Journal: Microbiol Mol Biol Rev Date: 2011-06 Impact factor: 11.056

Review 2. Nucleosome positioning in yeasts: methods, maps, and mechanisms.

Authors: Corinna Lieleg; Nils Krietenstein; Maria Walker; Philipp Korber
Journal: Chromosoma Date: 2014-12-23 Impact factor: 4.316

3. The histone H3-H4 tetramer is a copper reductase enzyme.

Authors: Narsis Attar; Oscar A Campos; Maria Vogelauer; Chen Cheng; Yong Xue; Stefan Schmollinger; Lukasz Salwinski; Nathan V Mallipeddi; Brandon A Boone; Linda Yen; Sichen Yang; Shannon Zikovich; Jade Dardine; Michael F Carey; Sabeeha S Merchant; Siavash K Kurdistani
Journal: Science Date: 2020-07-03 Impact factor: 47.728

Genome-wide mapping of nucleosomes in yeast.

1. Modifying gene expression programs by altering core promoter chromatin architecture.

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

3. Evolutionary footprints of nucleosome positions in yeast.

4. Chromatin remodelling at promoters suppresses antisense transcription.

5. Nucleosome positions predicted through comparative genomics.

6. Evidence for nucleosome depletion at active regulatory regions genome-wide.

7. Nucleosome organization in the Drosophila genome.

8. Chromatin decouples promoter threshold from dynamic range.

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

10. Genomic sequence is highly predictive of local nucleosome depletion.

Review 1. Nucleosome positioning in Saccharomyces cerevisiae.

Review 2. Nucleosome positioning in yeasts: methods, maps, and mechanisms.

3. The histone H3-H4 tetramer is a copper reductase enzyme.

4. Spt6 Is Required for the Fidelity of Promoter Selection.

5. H4K44 Acetylation Facilitates Chromatin Accessibility during Meiosis.

6. High-resolution genome-wide mapping of the primary structure of chromatin.

7. FACT is recruited to the +1 nucleosome of transcribed genes and spreads in a Chd1-dependent manner.

8. Standardized collection of MNase-seq experiments enables unbiased dataset comparisons.

9. Tup1 stabilizes promoter nucleosome positioning and occupancy at transcriptionally plastic genes.

10. Evolution of histone 2A for chromatin compaction in eukaryotes.