Comment[ArrayExpressAccession] E-GEOD-9771 Public Release Date 2008-06-11 Investigation Title A comprehensive synthetic genetic interaction network governing yeast histone acetylation and deacetylation Comment[Submitted Name] A comprehensive synthetic genetic interaction network governing yeast histone acetylation and deacetylation Experiment 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. Date of Experiment Term Source Name EFO Term Source Version Term Source File http://www.ebi.ac.uk/efo/efo.owl Person Last Name Yuan Lin Qi Lu Pan Yuan Zhao Bader Boeke Person First Name Daniel Yu-yi Yan Jin-ying Xuewen Daniel Yingming Joel Jef Person Mid Initials S S D Person Email dyuan@jhmi.edu Person Affiliation Johns Hopkins Univ School of Medicine Person Phone 410-502-1877 Person Fax 401-502-1872 Person Address Molecular Biology and Genetics, Johns Hopkins Univ School of Medicine, 733 N. Broadway, Suite 351, Baltimore, MD, USA Person Roles submitter Person Roles Term Source REF Person Roles Term Accession Number Normalization Type Normalization Term Accession Number Normalization Term Source REF Replicate Type Replicate Term Accession Number Replicate Term Source REF Experimental Design Experimental Design Term Accession Number Experimental Design Term Source REF Quality Control Type Quality Control Term Accession Number Quality Control Term Source REF Protocol Name P-GSE9771-1 P-GSE9771-7 P-GSE9771-6 P-GSE9771-3 P-GSE9771-26 P-GSE9771-12 P-GSE9771-11 P-GSE9771-16 P-GSE9771-19 P-GSE9771-28 P-GSE9771-24 P-GSE9771-21 P-GSE9771-15 P-GSE9771-2 P-GSE9771-27 P-GSE9771-20 P-GSE9771-13 P-GSE9771-9 P-GSE9771-10 P-GSE9771-17 P-GSE9771-23 P-GSE9771-5 P-GSE9771-25 P-GSE9771-18 P-GSE9771-14 P-GSE9771-22 P-GSE9771-4 P-GSE9771-8 Protocol Description ID_REF =
VALUE = normalized log2 ratio (Cy3/Cy5) Images were acquired with a GenePix 4000B scanner. Labeled extracts were hybridized overnight to microarray slides at 42 degrees C. See PubMed ID 15994458. Genomic DNA was prepared by extraction with phenol-chloroform and ethanol-precipitated. See PubMed ID 15525520. Growth medium: -Nourseothricin (SC-His, -Leu-Arg+Canavanine+G418, -Ura) Growth temperature: 30 degrees C Growth medium: -Nourseothricin (SC-His, -Leu-Arg+Canavanine+G418, -Ura) Growth temperature: 29 degrees C Cells were obtained as a pool of heterozygous diploid Yeast Knockout strains that were sporulated and grown to yield MATa haploid progeny. See PubMed ID 16487579 for an overview and PubMed IDs 17189863 and 15525520 for detailed experimental protocols. Growth medium: +Nourseothricin (SC-His, -Leu-Arg+Canavanine+G418, -Ura) Growth temperature: 29 degrees C Cells were obtained as a pool of heterozygous diploid Yeast Knockout strains that were sporulated and grown to yield MATa haploid progeny. See PubMed ID 16487579 for an overview and PubMed IDs 17189863 and 15525520 for detailed experimental protocols. Growth medium: -Nourseothricin (SC-His, -Leu-Arg+Canavanine+G418, -Ura) Growth temperature: 31 degrees C Cells were obtained as a pool of heterozygous diploid Yeast Knockout strains that were sporulated and grown to yield MATa haploid progeny. See PubMed ID 16487579 for an overview and PubMed IDs 17189863 and 15525520 for detailed experimental protocols. Growth medium: +Nourseothricin (SC-His, -Leu-Arg+Canavanine+G418, -Ura) Growth temperature: 33 degrees C Cells were obtained as a pool of heterozygous diploid Yeast Knockout strains that were sporulated and grown to yield MATa haploid progeny. See PubMed ID 16487579 for an overview and PubMed IDs 17189863 and 15525520 for detailed experimental protocols. Growth medium: +Ura (SC-His, -Leu-Arg+Canavanine+G418) Growth temperature: 30 degrees C Growth medium: -Nourseothricin+Ura (SC-His, -Leu-Arg+Canavanine+G418) Growth temperature: 30 degrees C Cells were obtained as a pool of heterozygous diploid Yeast Knockout strains that were sporulated and grown to yield MATa haploid progeny. See PubMed ID 16487579 for an overview and PubMed IDs 17189863 and 15525520 for detailed experimental protocols. Growth medium: +Nourseothricin (SC-His, -Leu-Arg+Canavanine+G418, -Ura) Growth temperature: 34 degrees C Cells were obtained as a pool of heterozygous diploid Yeast Knockout strains that were sporulated and grown to yield MATa haploid progeny. See PubMed ID 16487579 for an overview and PubMed IDs 17189863 and 15525520 for detailed experimental protocols. Growth medium: +Nourseothricin (SC-His, -Leu-Arg+Canavanine+G418, -Ura) Growth temperature: 31 degrees C Cells were obtained as a pool of heterozygous diploid Yeast Knockout strains that were sporulated and grown to yield MATa haploid progeny. See PubMed ID 16487579 for an overview and PubMed IDs 17189863 and 15525520 for detailed experimental protocols. Growth medium: -Ura (SC-His, -Leu-Arg+Canavanine+G418) Growth temperature: 30 degrees C Cells were obtained as a pool of heterozygous diploid Yeast Knockout strains that were sporulated and grown to yield MATa haploid progeny. See PubMed ID 16487579 for an overview and PubMed IDs 17189863 and 15525520 for detailed experimental protocols. Growth medium: -Ura (SC-His, -Leu-Arg+Canavanine+G418) Growth temperature: 30 degrees C Growth medium: -Nourseothricin (SC-His, -Leu-Arg+Canavanine+G418, -Ura) Growth temperature: 33 degrees C Cells were obtained as a pool of heterozygous diploid Yeast Knockout strains that were sporulated and grown to yield MATa haploid progeny. See PubMed ID 16487579 for an overview and PubMed IDs 17189863 and 15525520 for detailed experimental protocols. Growth medium: +Nourseothricin (SC-His, -Leu-Arg+Canavanine+G418, -Ura) Growth temperature: 30 degrees C Cells were obtained as a pool of heterozygous diploid Yeast Knockout strains that were sporulated and grown to yield MATa haploid progeny. See PubMed ID 16487579 for an overview and PubMed IDs 17189863 and 15525520 for detailed experimental protocols. Growth medium: +Nourseothricin (SC-His, -Leu-Arg+Canavanine+G418, -Ura) Growth temperature: 28 degrees C Cells were obtained as a pool of heterozygous diploid Yeast Knockout strains that were sporulated and grown to yield MATa haploid progeny. See PubMed ID 16487579 for an overview and PubMed IDs 17189863 and 15525520 for detailed experimental protocols. Growth medium: -Nourseothricin (SC-His, -Leu-Arg+Canavanine+G418, -Ura) Growth temperature: 28 degrees C Cells were obtained as a pool of heterozygous diploid Yeast Knockout strains that were sporulated and grown to yield MATa haploid progeny. See PubMed ID 16487579 for an overview and PubMed IDs 17189863 and 15525520 for detailed experimental protocols. Growth medium: +Nourseothricin (SC-His, -Leu-Arg+Canavanine+G418, -Ura) Growth temperature: 32 degrees C Cells were obtained as a pool of heterozygous diploid Yeast Knockout strains that were sporulated and grown to yield MATa haploid progeny. See PubMed ID 16487579 for an overview and PubMed IDs 17189863 and 15525520 for detailed experimental protocols. Growth medium: +Nourseothricin+Ura (SC-His, -Leu-Arg+Canavanine+G418) Growth temperature: 30 degrees C Cells were obtained as a pool of heterozygous diploid Yeast Knockout strains that were sporulated and grown to yield MATa haploid progeny. See PubMed ID 16487579 for an overview and PubMed IDs 17189863 and 15525520 for detailed experimental protocols. Growth medium: +Ura (SC-His, -Leu-Arg+Canavanine+G418) Growth temperature: 30 degrees C Cells were obtained as a pool of heterozygous diploid Yeast Knockout strains that were sporulated and grown to yield MATa haploid progeny. See PubMed ID 16487579 for an overview and PubMed IDs 17189863 and 15525520 for detailed experimental protocols. Growth medium: +Nourseothricin (SC-His, -Leu-Arg+Canavanine+G418, -Ura) Growth temperature: 30 degrees C Growth medium: -Nourseothricin (SC-His, -Leu-Arg+Canavanine+G418, -Ura) Growth temperature: 32 degrees C Cells were obtained as a pool of heterozygous diploid Yeast Knockout strains that were sporulated and grown to yield MATa haploid progeny. See PubMed ID 16487579 for an overview and PubMed IDs 17189863 and 15525520 for detailed experimental protocols. Growth medium: -Nourseothricin (SC-His, -Leu-Arg+Canavanine+G418, -Ura) Growth temperature: 30 degrees C Cells were obtained as a pool of heterozygous diploid Yeast Knockout strains that were sporulated and grown to yield MATa haploid progeny. See PubMed ID 16487579 for an overview and PubMed IDs 17189863 and 15525520 for detailed experimental protocols. Growth medium: -Nourseothricin (SC-His, -Leu-Arg+Canavanine+G418, -Ura) Growth temperature: 34 degrees C Cells were obtained as a pool of heterozygous diploid Yeast Knockout strains that were sporulated and grown to yield MATa haploid progeny. See PubMed ID 16487579 for an overview and PubMed IDs 17189863 and 15525520 for detailed experimental protocols. UpTag and DnTag sequences were amplified from genomic DNA by asymmetric PCR using labeled primers. See PubMed ID 15994458. Paired image files were analyzed with the GenePix Pro software package (MDS Analytical Technologies, version 5.1). Feature intensities were quantified as the 'F532 Median - B532' or 'F635 Median - B635' values. The two channels were compared using the log2 ratio. Global intensity normalization factors were specific to the type of gene-specific probe (UpTag or DnTag) and were calculated as the log2 ratio of total signal intensity in features 1:6018 (UpTag) or 10972:16989 (DnTag). Ratios were ignored when intensities of the control features [635] were less than 400. Protocol Software Protocol Hardware Protocol Contact Protocol Type bioassay_data_transformation image_aquisition hybridization nucleic_acid_extraction grow grow grow grow grow grow grow grow grow grow grow grow grow grow grow grow grow grow grow grow grow grow labeling feature_extraction Protocol Term Source REF Protocol Term Accession Number Experimental Factor Name QUERY MUTATION Experimental Factor Type Query mutation Experimental Factor Term Source REF Experimental Factor Term Accession Number Publication Title A comprehensive synthetic genetic interaction network governing yeast histone acetylation and deacetylation. Publication Author List Lin YY, Qi Y, Lu JY, Pan X, Yuan DS, Zhao Y, Bader JS, Boeke JD PubMed ID 18676811 Publication DOI 10.1101/gad.1679508 Publication Status Publication Status Term Source REF Publication Status Term Accession Number Comment[SecondaryAccession] GSE9771 Comment[GEOLastUpdateDate] 2012-03-17 Comment[AEExperimentType] other Comment[GEOReleaseDate] 2008-06-10 Comment[ArrayExpressSubmissionDate] 2007-12-04 SDRF File E-GEOD-9771.sdrf.txt