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Series GSE23711 Query DataSets for GSE23711
Status Public on May 19, 2011
Title Expression profiling of nhp6 mutants and wildtype yeast cells (Saccharomyces cerevisiae)
Platform organisms Schizosaccharomyces pombe; Saccharomyces cerevisiae
Sample organism Saccharomyces cerevisiae
Experiment type Expression profiling by array
Summary The basic unit of genome packaging is the nucleosome, and nucleosomes have long been proposed to restrict DNA accessibility both to damage and to transcription. However, nucleosome number in cells was considered fixed, and no condition was described where nucleosome number was reduced. We show here that mammalian cells lacking High Mobility Group Box 1 protein (HMGB1) contain a reduced amount of core, linker and variant histones, and a correspondingly reduced number of nucleosomes. Yeast nhp6 mutants lacking NHP6A and –B proteins, which are related to HMGB1, also have a reduced amount of histones and fewer nucleosomes. Nucleosome limitation in both mammalian and yeast cells increases the sensitivity of DNA to damage, increases transcription globally, and the relative expression of about 10% of genes. In yeast nhp6 cells the loss of more than one nucleosome in four does not affect the location of nucleosomes and their spacing, but nucleosomal occupancy. The decrease in nucleosomal occupancy is non-uniform, and our results can be modelled assuming that different nucleosomal sites compete for the available histones: sites with high affinity are almost always packaged into nucleosomes both in wt and nucleosome-depleted cells, whereas sites with low affinity are less frequently packaged in nucleosome-depleted cells. We suggest that by modulating the occupancy of nucleosomes histone availability may constitute a novel layer of epigenetic regulation.
Overall design This microarray experiment forms part of a larger study of the effects of nucleosome depletion on transcription
Using the Affymetrix Yeast Genome 2.0 Array, yeast nhp6 mutants (lacking NHP6A and NHP6B proteins) were compared to wildtype yeast cells (3 biological replicates per condition)
Contributor(s) Celona B, Weiner A, Di Felice F, Mancuso FM, Cesarini E, Rossi RL, Gregory L, Baban D, Lockstone H, Rossetti G, Pagani M, Bonaldi T, Ragoussis J, Friedman N, Camilloni G, Bianchi ME, Agresti A
Citation(s) 21738444
Submission date Aug 19, 2010
Last update date Feb 21, 2017
Contact name Jiannis Ragoussis
Organization name Wellcome Trust Centre For Human Genetics, University of Oxford
Lab Genomics Research Group
Street address Roosevelt Drive
City Oxford
ZIP/Postal code OX3 7BN
Country United Kingdom
Platforms (1)
GPL2529 [Yeast_2] Affymetrix Yeast Genome 2.0 Array
Samples (6)
GSM585193 Yeast_nhp6_mutant_replicate1
GSM585194 Yeast_nhp6_mutant_replicate2
GSM585195 Yeast_nhp6_mutant_replicate3
BioProject PRJNA130889

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE23711_RAW.tar 5.7 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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