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Transcriptome-wide Analysis of Exosome Targets

Lookup NU author(s): Dr Claudia SchneiderORCiD



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. Un-spliced 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.

Publication metadata

Author(s): Schneider C, Kudla G, Wlotzka W, Tuck A, Tollervey D

Publication type: Article

Publication status: Published

Journal: Molecular Cell

Year: 2012

Volume: 48

Issue: 3

Pages: 422-433

Print publication date: 01/11/2012

Date deposited: 10/06/2013

ISSN (print): 1097-2765

ISSN (electronic): 1097-4164

Publisher: Cell Press


DOI: 10.1016/j.molcel.2012.08.013


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Funder referenceFunder name
Darwin Trust of Edinburgh
077248Wellcome Trust
092076Wellcome Trust core funding
201142EC Program UNICELLSYS
UF100666Royal Society