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| Status |
Public on Jul 17, 2019 |
| Title |
The mRNA degradation factor Xrn1 regulates transcription elongation in parallel to Ccr4 |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
During the last decade several examples of coordination between gene transcription and mRNA degradation have been reported. mRNA imprinting by Rpb4 and 7 subunits of RNA polymerase II (RNAPII) and by the Ccr4-Not complex allows controlling its fate during transcription. Transcription regulation by mRNA degradation factors like Xrn1 constitutes a feedback loop that contributes to mRNA homeostasis. Mechanistic details of these phenomena are unclear. Most studies involve measurement of mRNA decay rates, usually by stressing procedures such as transcriptional shut-off or incorporation of modified nucleotides that can lead to biased results. In this work we have used the easily repressible yeast GAL1 gene to perform a genetic analysis of mRNA synthesis and degradation under physiological conditions. We combined this experimental approach with computational multi-agent modelling, testing different possibilities of Xrn1 and Ccr4-Not action in gene transcription. This double strategy brought us to conclude that Xrn1 regulates RNAPII backtracking in a Ccr4-independent manner. We validated this conclusion measuring TFIIS genome-wide recruitment to elongating RNAPII molecules. We found that xrn1∆ and ccr4∆ exhibited very different patterns of TFIIS/RNPAII which confirmed their differential role in controlling transcription elongation.
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| Overall design |
18 ChIP-seq samples: 2 IP and 1 Input; 3 strains; 2 replicates each.
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| Contributor(s) |
Begley V, Corzo D, Jordán-Pla A, Cuevas-Bermúdez A, Pérez-Aguado D, Machuca-Ostos M, Navarro F, Chávez MJ, Pérez-Ortín JE, Chávez S |
| Citation(s) |
31392315 |
| |
| Submission date |
Feb 26, 2019 |
| Last update date |
Oct 08, 2019 |
| Contact name |
Antonio Jordan |
| E-mail(s) |
[email protected]
|
| Organization name |
Universitat de Valencia
|
| Street address |
Doctor Moliner 50
|
| City |
Burjassot |
| State/province |
Valencia |
| ZIP/Postal code |
46100 |
| Country |
Spain |
| |
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| Platforms (1) |
| GPL13821 |
Illumina HiSeq 2000 (Saccharomyces cerevisiae) |
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| Samples (18)
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| Relations |
| BioProject |
PRJNA524296 |
| SRA |
SRP186872 |
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