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| Status |
Public on Jun 17, 2012 |
| Title |
Global analysis of mRNA decay intermediates in Saccharomyces cerevisiae |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
The general pathways of eukaryotic mRNA decay occur via deadenylation followed by 3’ to 5’ degradation or decapping, although some endonuclease sites have been identified in metazoan mRNAs. To determine the role of endonucleases in mRNA degradation in Saccharomyces cerevisiae, we mapped 5’ monophosphate ends on mRNAs in wild-type and dcp2∆ xrn1∆ yeast cells, wherein mRNA endonuclease cleavage products are stabilized. This led to three important observations. First, only few mRNAs that undergo low level endonucleotyic cleavage were observed suggesting that endonucleases are not a major contributor to yeast mRNA decay. Second, independent of known decapping enzymes, we observed low levels of 5’ monophosphates on some mRNAs suggesting that an unknown mechanism can generate 5' exposed ends, although for all substrates tested Dcp2 was the primary decapping enzyme. Finally, we identified debranched lariat intermediates from intron-containing genes, demonstrating a significant discard pathway for mRNAs during the second step of pre-mRNA splicing, which is a potential new step to regulate gene expression.
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| Overall design |
5' monophosphorylated ends of poly(A) RNA from wild-type and dcp2D xrn1D strains were identified in duplicates and triplicates, respectively.
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| |
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| Contributor(s) |
Harigaya Y, Parker R |
| Citation(s) |
22752303 |
| Submission date |
Nov 15, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Yuriko Harigaya |
| Organization name |
University of Colorado at Boulder
|
| Department |
Department of Chemistry and Biochemistry
|
| Lab |
Roy Parker Lab
|
| Street address |
3415 Colorado Ave, UCB 596
|
| City |
Boulder |
| State/province |
Colorado |
| ZIP/Postal code |
80303 |
| Country |
USA |
| |
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| Platforms (2) |
| GPL9377 |
Illumina Genome Analyzer II (Saccharomyces cerevisiae) |
| GPL13821 |
Illumina HiSeq 2000 (Saccharomyces cerevisiae) |
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| Samples (5)
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| Relations |
| BioProject |
PRJNA148473 |
| SRA |
SRP013460 |
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