Please note that we have stopped the regular imports of Gene Expression Omnibus (GEO) data into ArrayExpress. This may not be the latest version of this experiment.

E-GEOD-9771 - A comprehensive synthetic genetic interaction network governing yeast histone acetylation and deacetylation

Status
Released on 11 June 2008, last updated on 2 May 2014
Organism
Saccharomyces cerevisiae
Samples (88)
Array (1)
Protocols (28)
Description
Histone acetylation and deacetylation are among the principal mechanisms by which chromatin is regulated during transcription, DNA silencing, and DNA repair. We analyzed patterns of genetic interactions uncovered during comprehensive genome-wide analyses in yeast to probe how histone acetyltransferase (HAT) and histone deacetylase (HDAC) protein complexes interact. The genetic interaction data unveil an underappreciated role of HDACs in maintaining cellular viability, and led us to show that deacetylation of the histone variant Htz1p at lysine 14 is mediated by Hda1p. Studies of the essential nucleosome acetyltransferase of H4 (NuA4) revealed acetylation-dependent protein stabilization of Yng2p, a potential nonhistone substrate of NuA4 and Rpd3C, and led to a new functional organization model for this critical complex. We also found that DNA double-stranded breaks (DSBs) result in local recruitment of the NuA4 complex, followed by an elaborate NuA4 remodeling process concomitant with Rpd3p recruitment and histone deacetylation. These new characterizations of the HDA and NuA4 complexes demonstrate how systematic analyses of genetic interactions may help illuminate the mechanisms of intricate cellular processes. Keywords: genetic modification The 44 datasets in this Series profiled the genome-wide genetic interactions for query genes encoding either HAT and HDAC catalytic subunits or subunits of the associated protein complexes. Of the 32 query genes, 5 were essential and were tested as temperature-sensitive (ts) alleles at three or more temperatures. (ESA1 was also tested as a hypomorphic allele.) The other query genes were tested as null deletion alleles derived from the Yeast Knockout strain collection.
Experiment type
other 
Contacts
Daniel Yuan <dyuan@jhmi.edu>, Daniel S Yuan, Jef D Boeke, Jin-ying Lu, Joel S Bader, Xuewen Pan, Yan Qi, Yingming Zhao, Yu-yi Lin
Citation
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-9771.idf.txt
Sample and data relationshipE-GEOD-9771.sdrf.txt
Raw data (3)E-GEOD-9771.raw.1.zip, E-GEOD-9771.raw.2.zip, E-GEOD-9771.raw.3.zip
Processed data (1)E-GEOD-9771.processed.1.zip
Array designA-GEOD-1444.adf.txt
Links