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| Status |
Public on Apr 11, 2009 |
| Title |
An Rtt109-independent role for Vps75 in transcription-associated nucleosome dynamics |
| Platform organism |
Saccharomyces cerevisiae |
| Sample organism |
Saccharomyces cerevisiae W303 |
| Experiment type |
Genome binding/occupancy profiling by genome tiling array
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| Summary |
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
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| Overall design |
ChIP-chip analysis of the distribution of Vps75 on budding yeast chromosomes. Experiment type: ChIP-chip = Chromatin immunoprecipitation (ChIP) followed by hybridization to a high-density oligonucleotide microarray (chip). Number of hybridizations performed: 2 ChIP-chip samples and 2 SUPernatant samples for each type of tiling array (whole genome and chromosome VI). Analysis: ChIP samples were normalized against SUPernatant fractions. Quality control: Confirmation of results by duplication of experiments and by hybridization to two different types of Saccharomyces cerevisiae tiling arrays (whole genome and chromosome VI). Also, whole cell extract, SUPernatant, and ChIP fractions were checked by Western blotting.
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| Contributor(s) |
Selth LA, Lorch Y, Ocampo-Hafalla MT, Mitter R, Shales M, Krogan NJ, Kornberg RD, Svejstrup JQ |
| Citation(s) |
19470761 |
| Submission date |
Apr 08, 2009 |
| Last update date |
Mar 21, 2012 |
| Contact name |
Luke Selth |
| E-mail(s) |
luke.selth@cancer.org.uk
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| Organization name |
Cancer Research UK
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| Street address |
Blanch Lane
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| City |
South Mimms |
| State/province |
Herts. |
| ZIP/Postal code |
EN6 3LD |
| Country |
United Kingdom |
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| Platforms (2) |
| GPL3722 |
ChromosomeVI tiling array (rikDACF) |
| GPL7249 |
[Sc03b_MF] Affymetrix GeneChip S. cerevisiae Tiling 1.0F Array |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA116685 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE15607_RAW.tar |
179.3 Mb |
(http)(custom) |
TAR (of CEL, TXT) |
| Processed data provided as supplementary file |
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