|
| Status |
Public on Nov 12, 2015 |
| Title |
Chromatin dynamics and the RNA exosome function in concert to regulate transcriptional homeostasis (ChIP-seq) |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
The histone variant H2A.Z is a hallmark of nucleosomes flanking the promoters of protein coding genes, and is often found in nucleosomes that also carry lysine 56- acetylated histone H3 (H3-K56Ac), a mark which promotes rapid replication- independent turnover of nucleosomes. Although H2A.Z and H3-K56Ac have been generally implicated in transcriptional activation, their exact contributions have remained elusive. Here we find that H3-K56Ac promotes RNA polymerase II occupancy at a large number of protein coding and noncoding loci, yet neither H3- K56Ac nor H2A.Z has a significant impact on steady state mRNA levels in yeast. Instead, broad effects of H3-K56Ac or H2A.Z on levels of both coding and noncoding RNAs (ncRNAs) are only revealed in the absence of the nuclear RNA exosome. H2A.Z is also necessary for expression of divergent, promoter-proximal ncRNAs in mouse embryonic stem cells, suggesting a conserved role for H2A.Z across eukaryotes. Finally, we show that H2A.Z functions with H3-K56Ac in chromosome folding, facilitating formation of chromosome interaction domains (CIDs). Our study suggests that H2A.Z and H3-K56Ac work in concert with the RNA exosome to control mRNA and ncRNA expression, perhaps in part by regulating higher order chromatin structures.
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| |
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| Overall design |
2 replicates of WT (CY1089), rtt109∆ (CY2210), rrp6∆ (CY2071) and one replicate of the W303 input (Sample 7). TableS5.xlsx contains the processed IP/input values for each ORF transcript.
|
| Web link |
http://www.sciencedirect.com/science/article/pii/S2211124715012000
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| |
|
| Contributor(s) |
Peterson CL |
| Citation(s) |
26586442 |
| Submission date |
Sep 03, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Craig L Peterson |
| E-mail(s) |
craig.peterson@umassmed.edu
|
| Phone |
508-856-5858
|
| Organization name |
University of Massachusetts Medical School
|
| Department |
Program in Molecular Medicine
|
| Street address |
373 Plantation Street
|
| City |
Worcester |
| State/province |
MASSACHUSETTS |
| ZIP/Postal code |
01605 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL13821 |
Illumina HiSeq 2000 (Saccharomyces cerevisiae) |
|
| Samples (7)
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| This SubSeries is part of SuperSeries: |
| GSE73145 |
Chromatin dynamics and the RNA exosome function in concert to regulate transcriptional homeostasis |
|
| Relations |
| BioProject |
PRJNA294675 |
| SRA |
SRP063297 |
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