Saccharomyces cerevisiae W303
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ABSTRACT:
PROVIDER: PRJNA116685 | ENA |
REPOSITORIES: ENA
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Project description:This is the microarray data accompanying the aforementioned manuscript. Summary: The histone chaperone Vps75 forms a complex with, and stimulates the activity of, the histone acetyltransferase Rtt109. However, Vps75 can also be isolated on its own and might therefore play a role in histone-related cellular processes independently of Rtt109. Using the E-MAP approach, we compared the genetic interaction profiles for VPS75 and RTT109 and found that, whereas deletion of RTT109 behaved like DNA replication/repair mutants, vps75Δ genetically interacted with genes linked to transcriptional regulation. Further genetic and biochemical experiments indicated an intimate relationship with RNA polymerase II, and chromatin immunoprecipitation showed that Vps75 is recruited to activated genes in an Rtt109-independent manner. Expression microarray analysis identified a limited number of genes whose normal expression depends on VPS75. Interestingly, histone H2B dynamics at some of these genes were consistent with a role for Vps75 as a histone H2A/H2B eviction factor during transcription-associated nucleosome disassembly. Indeed, reconstitution of nucleosome disassembly using the ATP-dependent chromatin remodeler Rsc and Vps75 showed that these proteins can cooperate to remove H2A/H2B dimers from nucleosomes. Together, these results indicate a role for Vps75 in nucleosome dynamics during active transcription, and that this function is likely to be independent of the histone acetyltransferase Rtt109. Keywords: Array-based; Chip-chip
2009-04-11 | GSE15607 | GEO
Project description:S. cerevisiae Nucleosome mapping
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Project description:Chromatin-dependent binding of the S. cerevisiae HMGB protein Nhp6A affects nucleosome dynamics and transcription [Affymetrix]
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Project description:Dynamics of nucleosome positioning maturation following genomic replication
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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:A role for Snf2 related nucleosome spacing enzymes in genome-wide nucleosome organization
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Project description:A role for Snf2 related nucleosome spacing enzymes in genome-wide nucleosome organization
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Project description:These three replicates were analyzed in "Genomewide identification of Sko1 target promoters reveals a regulatory network that operates in response to osmotic stress in Saccharomyces cerevisiae. ", by Proft M, Gibbons FD, Copeland M, Roth FP, Struhl K; published in Eukaryot Cell. 2005 Aug;4(8):1343-52. A new analysis algorithm for Chip-chip data ('Chipper') is described in Genome Biology. Manuscript entitled "Chipper: discovering transcription-factor targets from chromatin immunoprecipitation microarrays using variance stabilization." by FD Gibbons, M Proft, K Struhl, and FP Roth. Accepted, no publication date as yet. Keywords: ChIP-chip
2005-09-21 | GSE3335 | GEO