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Transcriptome-wide Analysis of Exosome Targets
- Source :
- Molecular Cell; Vol 48, Molecular Cell, Schneider, C, Kudla, G, Wlotzka, W, Tuck, A & Tollervey, D 2012, ' Transcriptome-wide analysis of exosome targets ', Molecular Cell, vol. 48, no. 3, pp. 422-433 . https://doi.org/10.1016/j.molcel.2012.08.013
- Publication Year :
- 2012
- Publisher :
- Elsevier BV, 2012.
-
Abstract
- Summary The exosome plays major roles in RNA processing and surveillance but the in vivo target range and substrate acquisition mechanisms remain unclear. Here we apply in vivo RNA crosslinking (CRAC) to the nucleases (Rrp44, Rrp6), two structural subunits (Rrp41, Csl4) and a cofactor (Trf4) of the yeast exosome. Analysis of wild-type Rrp44 and catalytic mutants showed that both the CUT and SUT classes of non-coding 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 indicating that substrates follow multiple pathways to the nucleases.<br />Graphical Abstract Highlights ► The in vivo target range was identified for the exosome nuclease complex ► The endonuclease and exonuclease activities of Rrp44/Dis3 function cooperatively ► Comparison of Rrp6 and core exosome suggests multiple substrate recruitment pathways ► Pre-tRNA and other RNAs transcribed by Pol III emerge as major exosome targets
- Subjects :
- Exonuclease
Saccharomyces cerevisiae Proteins
Exosome complex
Saccharomyces cerevisiae
Biology
Exosome
Article
RNA polymerase III
03 medical and health sciences
0302 clinical medicine
Gene Expression Regulation, Fungal
RNA Precursors
RNA Processing, Post-Transcriptional
Small nucleolar RNA
Molecular Biology
030304 developmental biology
0303 health sciences
Binding Sites
Exosome Multienzyme Ribonuclease Complex
Gene Expression Profiling
Nuclear Proteins
RNA
RNA, Fungal
Cell Biology
Blotting, Northern
Molecular biology
Cell biology
Mutation
TRAMP complex
biology.protein
030217 neurology & neurosurgery
Protein Binding
Subjects
Details
- ISSN :
- 10972765
- Volume :
- 48
- Database :
- OpenAIRE
- Journal :
- Molecular Cell
- Accession number :
- edsair.doi.dedup.....29c6e12038cef8c96ee825cebbd3e870