Project description:Genomic events including gene regulation and chromatin status are controlled by transcription factors. Here we report that the Hsp90 molecular chaperone broadly regulates the transcription factor protein family. Our studies identified a biphasic use of Hsp90 in which early inactivation (15 min) of the chaperone triggered a wide reduction of DNA binding events along the genome with concurrent changes to chromatin structure. Long-term loss (6 h) of Hsp90 resulted in a decline of a divergent yet overlaying pool of transcription factors that produced a distinct chromatin pattern. Although both phases involve protein folding, the early point correlated with Hsp90 acting in a late folding step that is critical for DNA binding function whereas prolonged Hsp90 inactivation led to a significant decrease in the steady-state transcription factor protein levels. Intriguingly, despite the broad chaperone-impact on a variety of transcription factors, the operational influence of Hsp90 was at the level of chromatin with only a mild effect on gene regulation. Thus, Hsp90 selectively governs the transcription factor process overseeing local chromatin structure.

2019-10-23 | GSE139266 | GEO

Saccharomyces cerevisiae

Project description:Hog1 bypasses stress-mediated down-regulation of transcription by PolII redistribution and chromatin remodeling

| PRJNA177335 | ENA

Saccharomyces cerevisiae

Project description:Threonine-4 of the budding yeast RNAP II CTD couples transcription with Htz1-mediated chromatin remodeling

| PRJNA257690 | ENA

Saccharomyces cerevisiae Sko1-HA strain MAP37, W303-1A background

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

Saccharomyces cerevisiae

Project description:A library of yeast transcription factor motifs

| PRJNA113175 | ENA

DNaseI hypersensitivity mapping/DNaseI high-throughput sequencing (DHS-Seq) in Saccharomyces cerevisiae

Project description:We report the application of DHS-Seq and digital genomic footprinting to study chromatin changes and transcription factor-DNA binding upon long-term Hsp90 depletion utilizing the temperature-sensitive allele G170D. By generating about 86 and 85.6 million reads for wild type and mutant, we were able to reconstitute the chromatin accessibility and the transcription factor-DNA binding maps under regular conditions and under conditions where Hsp90 was long-term inactivated. We find that there is a global reduction of transcription factor binding sites with concurrent loss of open chromatin upon Hsp90 inactivation. This data was used in conjunction with our previous work involving DHS-Seq studies and short-term Hsp90 depletion (GEO GSE88875) to distinguish the affected transcription factor networks and the chromatin changes upon short- and long-term Hsp90 depletion. We identified two different modes of Hsp90 operation on transcription factor activities – short-term inactivation of Hsp90 altered transcription factor DNA binding activities, whereas long-term Hsp90 inactivation affected the steady-state levels of transcription factors. Overall, this study shows that Hsp90 regulates multiple transcription factor protein families and modulates chromatin architecture on a genome-wide scale.

2019-10-23 | GSE139268 | GEO

Saccharomyces cerevisiae

Project description:Genome-wide Analysis of Functional Sirtuin Chromatin Targets in Yeast

| PRJNA177035 | ENA