Transcriptome-wide Analysis of Exosome Targets

• DOI: 10.1016/j.molcel.2012.08.013
• Publication Date: 2012-09-20T15:30:37Z
• Authors: Claudia Schneider; Grzegorz Kudla; Wiebke Wlotzka; Alex Tuck; David Tollervey
• Keywords: Exosome

SummaryThe exosome plays major roles in RNA processing and surveillance but the vivo target range substrate acquisition mechanisms remain unclear. Here we apply crosslinking (CRAC) to nucleases (Rrp44, Rrp6), two structural subunits (Rrp41, Csl4) a cofactor (Trf4) of yeast exosome. Analysis wild-type Rrp44 catalytic mutants showed that both CUT SUT classes non-coding RNA, snoRNAs and, most prominently, pre-tRNAs other Pol III transcripts are targeted for oligoadenylation degradation. Unspliced pre-mRNAs were also identified as targets Rrp6. CRAC performed using cleavable proteins (split-CRAC) revealed endonuclease exonuclease activities cooperate on substrates. Mapping oligoadenylated reads suggests activity may release stalled Rrp6 was preferentially associated with structured targets, which frequently did not associate core indicating substrates follow multiple pathways nucleases.Graphical abstractGraphical AbstractHighlights► The nuclease complex ► Rrp44/Dis3 function cooperatively Comparison recruitment Pre-tRNA RNAs transcribed by emerge