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Genome-wide analysis reveals distinct substrate specificities of Rrp6, Dis3, and core exosome subunits.

RNA (New York, N.Y.) (2010-02-27)
Daniel L Kiss, Erik D Andrulis
ABSTRACT

The RNA processing exosome complex was originally defined as an evolutionarily conserved multisubunit complex of ribonucleases responsible for the processing and/or turnover of stable RNAs. The exosome complex is also involved in the surveillance of mRNAs in both the nucleus and the cytoplasm, including nonsense-mediated decay (NMD) targets. The detailed mechanisms for how individual exosome subunits participate in each of these RNA metabolic pathways remains unclear. Here, we use RNAi to deplete exosome subunits, the exonucleases Rrp6 and Dis3, and an exosome cofactor in Drosophila melanogaster S2 tissue culture cells and assay the effects on global mRNA levels using gene expression microarrays. Consistent with the RNA degradative activities ascribed to the exosome, most mRNAs are increased. Notably, these stabilized mRNAs possess 3' untranslated regions that are longer than the representative transcriptomic average. Moreover, our results reveal substantial differences in the pools of affected mRNAs for each depleted subunit. For example, approximately 25% of the affected transcripts in Rrp6 depleted cells represent NMD substrates. While the affected mRNAs were dissimilar, they encode proteins that function in similar cellular pathways. We conclude that individual exosome subunits are largely functionally independent at the transcript level, but are interdependent on a transcriptomic level.

MATERIALS
Product Number
Brand
Product Description

Sigma-Aldrich
Anti-EXOSC2 antibody produced in rabbit, ~1.0 mg/mL, affinity isolated antibody
Sigma-Aldrich
Anti-EXOSC2 antibody produced in rabbit, affinity isolated antibody
Sigma-Aldrich
Anti-EXOSC2 antibody produced in rabbit, Prestige Antibodies® Powered by Atlas Antibodies, affinity isolated antibody, buffered aqueous glycerol solution
Sigma-Aldrich
Monoclonal Anti-EXOSC2 antibody produced in mouse, clone 4B6, purified immunoglobulin, buffered aqueous solution

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