Saccharomyces cerevisiae
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA103817 | ENA |
REPOSITORIES: ENA
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Project description:Spn1/Iws1 is an essential eukaryotic transcription elongation factor that is conserved from yeast to humans. Several studies have shown that Spn1 functions as a histone chaperone to control transcription, RNA splicing, genome stability, and histone modifications as an integral member of the RNA polymerase II elongation complex. However, the precise role of Spn1 is not understood, and there is little understanding of why it is essential for viability. To address these issues, we have isolated eight suppressor mutations that bypass the essential requirement for Spn1 in Saccharomyces cerevisiae. Unexpectedly, the suppressors identify several functionally distinct complexes and activities, including the histone chaperone FACT, the histone methyltransferase Set2, the Rpd3S histone deacetylase complex, the histone acetyltransferase Rtt109, the nucleosome remodeler Chd1, and a member of the SAGA co-activator complex, Sgf73. The identification of these distinct groups and their analysis suggests that there are multiple mechanisms by which Spn1 bypass can occur, including changes in histone acetylation and alterations of other histone chaperones. Thus, Spn1 may participate in multiple functions during transcription. Our results suggest that bypass of a subset of these functions allows viability in the absence of Spn1.
2022-05-16 | GSE202590 | GEO
Project description:ESA1 (essential SAS-family acetyltransferase) is the only known yeast histone acetyltransferase (HAT) required for cell viability. It is a member of the MYST (MOZ, YBF2/SAS3, SAS2, Tip60) family of HAT proteins and contains a conserved acetyltransferase domain in addition to a chromodomain. While ESA1âs HAT activity is important in processes such as deoxyribonucleic acid (DNA) repair, acetylation is likely not its essential function. Our lab has shown that mutants with a single point mutation in the active site cysteine are still viable even though their acetyltransferase abilities are abolished. Furthermore, chromatin immunoprecipitation assays have shown ESA1 distributed evenly along the length of chromatin, not localized to specific promoters as would be expected from a HAT protein involved in transcriptional regulation. As is the case for other HAT proteins, ESA1âs acetyltransferase activity is significant, but in processes such as DNA replication, DNA repair and cell cycle progression. The aim of this project is to determine the essential function of ESA1 - the catalytic subunit of the yeast HAT complex, NuA4 (nucleosome acetyltransferase of H4) â using a bypass suppression screen to identify suppressors of ESA1. It is proposed that suppressing mutations will alter a gene involved in the process that is the essential function of ESA1. Thus, identifying a suppressor that can bypass the need for ESA1 may provide insight into its essential function. Since ESA1 is an essential gene, a haploid esa1â strain in which wild-type ESA1 is provided on a centromeric plasmid was utilized. The bypass suppression screen resulted in suppressors of ESA1 that allowed esa1â cells to be viable even in the absence of the essential gene. These second site suppressors (sup-) of ESA1 each show the Mendelian segregation pattern of the suppressing gene and ESA1 in 2:2 ratios, implying they are single genes unlinked to ESA1. Microarray and nuclear morphology studies show abnormal gene expression and morphology of the esa1ï sup- cells, further implicating the suppressing mutation in DNA repair and replication processes. Investigating ESA1âs essential role and a probable conservation of function across species can provide a deeper understanding of the capabilities of HAT complexes. Experiment Overall Design: Eight samples were analyzed. The only variables are the ESA1 and SUP2 genes. WT (ESA1 SUP2), 2 replicates. Single mutant (ESA1 sup2-), 3 replicates. Double mutant (esa1 sup2-), 3 replicates.
2008-06-16 | E-GEOD-9840 | biostudies-arrayexpress
Project description:ESA1 (essential SAS-family acetyltransferase) is the only known yeast histone acetyltransferase (HAT) required for cell viability. It is a member of the MYST (MOZ, YBF2/SAS3, SAS2, Tip60) family of HAT proteins and contains a conserved acetyltransferase domain in addition to a chromodomain. While ESA1’s HAT activity is important in processes such as deoxyribonucleic acid (DNA) repair, acetylation is likely not its essential function. Our lab has shown that mutants with a single point mutation in the active site cysteine are still viable even though their acetyltransferase abilities are abolished. Furthermore, chromatin immunoprecipitation assays have shown ESA1 distributed evenly along the length of chromatin, not localized to specific promoters as would be expected from a HAT protein involved in transcriptional regulation. As is the case for other HAT proteins, ESA1’s acetyltransferase activity is significant, but in processes such as DNA replication, DNA repair and cell cycle progression. The aim of this project is to determine the essential function of ESA1 - the catalytic subunit of the yeast HAT complex, NuA4 (nucleosome acetyltransferase of H4) – using a bypass suppression screen to identify suppressors of ESA1. It is proposed that suppressing mutations will alter a gene involved in the process that is the essential function of ESA1. Thus, identifying a suppressor that can bypass the need for ESA1 may provide insight into its essential function. Since ESA1 is an essential gene, a haploid esa1∆ strain in which wild-type ESA1 is provided on a centromeric plasmid was utilized. The bypass suppression screen resulted in suppressors of ESA1 that allowed esa1∆ cells to be viable even in the absence of the essential gene. These second site suppressors (sup-) of ESA1 each show the Mendelian segregation pattern of the suppressing gene and ESA1 in 2:2 ratios, implying they are single genes unlinked to ESA1. Microarray and nuclear morphology studies show abnormal gene expression and morphology of the esa1- sup- cells, further implicating the suppressing mutation in DNA repair and replication processes. Investigating ESA1’s essential role and a probable conservation of function across species can provide a deeper understanding of the capabilities of HAT complexes. Keywords: Comparison of strains lacking essential ESA1 gene to those containing an ESA1 bypass suppressor.
2007-12-12 | GSE9840 | GEO
Project description:Gene expression variation was measured in 17 non-laboratory strains compared to the sequenced S288c lab strain Keywords: Gene expression comparisons in different yeast strains
2008-09-05 | GSE10268 | GEO
Project description:Total RNA from three replicate cultures of wild-type and mutant strains was isolated and the expression profiles were determined using Affymetrix arrays. Comparisons between the sample groups allow the identification of genes regulated by histone H2A^4-20 mutant. Experiment Overall Design: Comparison of genes whose mRNA levels are affected in a histone H2A^4-20 mutant yeast strain compared to wild-type yeast strain.
2008-06-15 | E-GEOD-7337 | biostudies-arrayexpress
Project description:Total RNA from three replicate cultures of wild-type and mutant strains was isolated and the expression profiles were determined using Affymetrix arrays. Comparisons between the sample groups allow the identification of genes regulated by the histone H2A K4,7G mutant. Experiment Overall Design: Comparison of genes whose mRNA levels are affected in a histone H2A K4,7G mutant yeast strain compared to wild-type yeast strain.
2008-06-15 | E-GEOD-7338 | biostudies-arrayexpress
Project description:Total RNA from three replicate cultures of wild-type and mutant strains was isolated and the expression profiles were determined using Affymetrix arrays. Comparisons between the sample groups allow the identification of genes regulated by H3 K4,79R mutant. Experiment Overall Design: Comparison of genes whose mRNA levels are affected in a histone H3 K4,79R mutant yeast strain compared to wild-type yeast strain.
2008-06-14 | E-GEOD-6319 | biostudies-arrayexpress
Project description:Total RNA from two replicate cultures of wild-type and mutant strains was isolated and the expression profiles were determined using Affymetrix arrays. Comparisons between the sample groups allow the identification of genes regulated by histone H3 K4,9,14,18,23,27,36,79G mutant. Experiment Overall Design: Comparison of genes whose mRNA levels are affected in a histone H3 K4,9,14,18,23,27,36,79G mutant yeast strain compared to wild-type yeast strain.
2009-01-14 | E-GEOD-10933 | biostudies-arrayexpress
Project description:The N-terminal tail of histone H2A shows evolutionary changes that parallel genome size and aid chromatin compaction. As genome size increases, so does the number of arginines. In contrast, serines corellate with small genomes. Examples for such changes are arginine in position 11 and serine in position 15. To test if these residues affect mRNA levels, we analysed gene expression profiles of S.cerevisiae strains containing either WT or mutant H2A. Yeast strains have endogenous histone H2A genes deleted and express plasmid born WT or mutant H2A. PolyA RNA of these strains was analyzed by single channel microarray hybridization. Three WT biological replicates provide the control. Two biological replicates of each of the mutants containing either R11, K11, carrying a deletion in S15 and the double mutant carrying both the deletion of S15 and an insertion of R11 are analysed.
2014-03-01 | E-GEOD-50440 | biostudies-arrayexpress
Project description:Histone H3 K36 trimethylation in wild-type BY4741 yeast strains
| PRJNA158265 | ENA