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| Status |
Public on Jan 26, 2018 |
| Title |
The Cytoplasmic mRNA Decay Landscape of Arabidopsis Seedlings [small RNA-seq] |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
|
| Summary |
Cytoplasmic mRNA decay occurs through several pathways, but the contributions of these decay pathways to the degradation of specific mRNAs, and interactions between the pathways, are not well understood. We carried out a genome-wide analysis of mRNA decay rates using wild-type Arabidopsis and mutants with defects in mRNA decapping and SOV/DIS3L2. Decay rates and contributions of decapping and SOV to decay were estimated for 18,674 mRNAs using maximum likelihood modeling. Most mRNAs decayed by multiple pathways, few mRNAs degraded exclusively by mRNA decapping or SOV, and specific codon usage was linked to decay rates. Unexpected faster decay of transcripts in some genotypes was found to be independent of siRNAs; instead the data suggested an RNA buffering-like phenomenon in Arabidopsis, and that VCS (decapping) is essential for both this process and the decay of very unstable mRNAs.
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| |
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| Overall design |
Small RNA abundance measured in 5 day-old seedlings to compare to same time 0 decay rates in genome-wide decay dataset.
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| |
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| Contributor(s) |
Sieburth LE, Deshotel MJ, Sorenson R, Johnson K, Adler FR |
| Citation(s) |
29386391 |
| |
| Submission date |
Sep 01, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Leslie Ellen Sieburth |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Utah
|
| Department |
Biology
|
| Street address |
257 South 1400 East
|
| City |
Salt Lake City |
| State/province |
UT |
| ZIP/Postal code |
84124 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL17639 |
Illumina HiSeq 2500 (Arabidopsis thaliana) |
|
| Samples (12)
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| This SubSeries is part of SuperSeries: |
| GSE86361 |
The Cytoplasmic mRNA Decay Landscape of Arabidopsis Seedlings |
|
| Relations |
| BioProject |
PRJNA341505 |
| SRA |
SRP083969 |
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