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Chromatin Immunoprecipitation (ChIP) of Histone Modifications from Saccharomyces cerevisiae
Published on: December 29, 2017
Perfect and imperfect nucleosome positioning in yeast
Hope A Cole1, V Nagarajavel, David J Clark
1Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute for Child Health and Development, National Institues of Health, MD 20892, USA.
Biochimica Et Biophysica Acta
|February 7, 2012
Summary
Nucleosomes in yeast chromatin generally form "position clusters" with multiple overlapping arrangements, rather than single fixed sites. Transcriptional activation disrupts these clusters, suggesting degeneracy in the nucleosome code.
Area of Science:
- Molecular Biology
- Genetics
- Chromatin Biology
Background:
- Nucleosomes typically adopt multiple overlapping positions on DNA in vitro, termed "position clusters".
- Previous work showed position clusters in specific yeast genes, but their genome-wide prevalence was unknown.
- The synthetic 601-sequence is an exception, enabling perfect in vitro nucleosome positioning.
Purpose of the Study:
- To investigate the genome-wide prevalence of nucleosome position clusters in yeast chromatin.
- To understand how position clusters and alternative nucleosomal arrays influence nucleosome occupancy profiles.
- To examine the impact of transcriptional activation on nucleosome positioning and the nucleosome code.
Main Methods:
- Genome-wide paired-end sequencing of nucleosomes in yeast.
- Analysis of nucleosome occupancy profiles.
- Comparison of nucleosome positioning in active versus inactive genes.
Main Results:
- Nucleosome position clusters are the general rule, not the exception, across yeast chromatin.
- Alternative nucleosomal arrays are formed within cell populations, contributing to observed occupancy profiles.
- Transcriptional activation disrupts nucleosome position clusters.
- Centromeric nucleosomes represent a rare case of perfect in vivo positioning, potentially due to specialized proteins and histone variants.
Conclusions:
- Nucleosome positioning in yeast is characterized by degeneracy, with multiple preferred sites.
- The observed degeneracy challenges simple models of the nucleosome code.
- Alternative nucleosomal arrays and position clusters are fundamental features of chromatin organization and regulation.
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