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Related Experiment Videos

Global nucleosome occupancy in yeast.

Bradley E Bernstein1, Chih Long Liu, Emily L Humphrey

  • 1Department of Chemistry and Chemical Biology, Bauer Center for Genomics Research, and Howard Hughes Medical Institute, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA. bbernstein@partners.org

Genome Biology
|September 4, 2004
PubMed
Summary
This summary is machine-generated.

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Nucleosome depletion in yeast promoters is linked to transcription factor binding sites, particularly Rap1 consensus sites. This suggests transcription factors play a key role in regulating chromatin accessibility for gene activation.

Area of Science:

  • Molecular Biology
  • Genomics
  • Chromatin Dynamics

Background:

  • Eukaryotic genomes are typically chromatin-associated.
  • The PHO5 promoter in yeast, when active, is largely nucleosome-free.
  • Systematic evaluation of nucleosome occupancy in yeast promoters was needed.

Purpose of the Study:

  • To systematically evaluate nucleosome occupancy in yeast promoters.
  • To identify factors correlating with nucleosome depletion.
  • To understand the role of transcription factor binding sites in chromatin structure.

Main Methods:

  • Immunoprecipitation of nucleosomal DNA.
  • Quantification of DNA enrichment using microarrays.
  • Validation by real-time PCR and micrococcal nuclease digestion.

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Main Results:

  • Nucleosome depletion occurs in promoters of active genes and those with conserved transcription factor binding motifs.
  • Rap1 consensus sites were uniquely identified in unbiased searches of depleted promoters.
  • Rap1 sites in ribosomal protein gene promoters showed depletion, which was reversed by rapamycin or removal of the sites.

Conclusions:

  • Transcription factor binding motifs are crucial for nucleosome depletion.
  • Collaborative action of multiple motifs promotes nucleosome exclusion.
  • Rap1 binding sites independently induce significant nucleosome depletion, potentially defining chromatin domains.