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| Status |
Public on Sep 25, 2012 |
| Title |
Transcriptome-wide Analysis of Exosome Targets in the Budding Yeast Saccharomyces cerevisiae |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Other
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| Summary |
Purpose: The exosome plays major roles in RNA processing and surveillance but the in vivo target range and substrate acquisition mechanisms remain unclear. We applied an in vivo cross-linking technique coupled with deep sequencing (CRAC) that captures transcriptome-wide interactions between individual yeast exosome subunits and their targets in a living cell.
Methods: We apply CRAC to HTP-tagged proteins (HTP: His6 - TEV cleavage site - two copies of the z-domain of Protein A): Two nucleases (Rrp44, Rrp6) and two structural subunits (Rrp41, Csl4) of the yeast exosome. At least two independent experiments were performed in each case and analyzed separately. We performed CRAC on wild-type (WT) Rrp44 and two catalytic mutants, rrp44-endo (D91N, E120Q, D171N, D198N) and rrp44-exo (D551N). We further developed CRAC using cleavable proteins (split-CRAC) to compare endonuclease and exonuclease targets of Rrp44. Plasmids designed for split-CRAC contain a PreScission protease cleavage site (PP) inserted between aa 241 and 242 in the RRP44 ORF to allow in vitro cleavage of purified protein, and a His6 tag to select the respective cleaved fragment.
Results: Analysis of wild-type Rrp44 and catalytic mutants showed that both the CUT and SUT classes of noncoding RNA, snoRNAs and, most prominently, pre-tRNAs and other Pol III transcripts are targeted for oligoadenylation and exosome degradation. Unspliced pre-mRNAs were also identified as targets for Rrp44 and Rrp6. CRAC performed using cleavable proteins (split-CRAC) revealed that Rrp44 endonuclease and exonuclease activities cooperate on most substrates. Mapping oligoadenylated reads suggests that the endonuclease activity may release stalled exosome substrates. Rrp6 was preferentially associated with structured targets, which frequently did not associate with the core exosome. This indicates that substrates can follow multiple pathways to the nucleases.
Conclusion: Our study represents the first transcriptome-wide map of substrates for the yeast exosome nuclease complex.
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| Overall design |
Identification of targets for individual exosome subunits in wild-type and mutant yeast cells.
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| Contributor(s) |
Schneider C, Kudla G, Wlotzka W, Tuck A, Tollervey D |
| Citation(s) |
23000172, 25159613 |
| Submission date |
Aug 10, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Grzegorz Kudla |
| E-mail(s) |
gkudla@gmail.com
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| Phone |
+44 (0) 131 332 2471
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| Organization name |
University of Edinburgh
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| Department |
MRC HGU
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| Street address |
Crewe Road
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| City |
Edinburgh |
| ZIP/Postal code |
EH4 2XU |
| Country |
United Kingdom |
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| Platforms (2) |
| GPL13272 |
Illumina Genome Analyzer IIx (Saccharomyces cerevisiae) |
| GPL13821 |
Illumina HiSeq 2000 (Saccharomyces cerevisiae) |
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| Samples (16)
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| Relations |
| BioProject |
PRJNA172446 |
| SRA |
SRP014810 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE40046_RAW.tar |
4.3 Mb |
(http)(custom) |
TAR (of WIG) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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