Exosome cofactor hMTR4 competes with export adaptor ALYREF to ensure balanced nuclear RNA pools for degradation and export

Abstract

The exosome is a key RNA machine that functions in the degradation of unwanted RNAs. Here, we found that significant fractions of precursors and mature forms of mRNAs and long noncoding RNAs are degraded by the nuclear exosome in normal human cells. Exosome-mediated degradation of these RNAs requires its cofactor hMTR4. Significantly, hMTR4 plays a key role in specifically recruiting the exosome to its targets. Furthermore, we provide several lines of evidence indicating that hMTR4 executes this role by directly competing with the mRNA export adaptor ALYREF for associating with ARS2, a component of the cap-binding complex (CBC), and this competition is critical for determining whether an RNA is degraded or exported to the cytoplasm. Together, our results indicate that the competition between hMTR4 and ALYREF determines exosome recruitment and functions in creating balanced nuclear RNA pools for degradation and export.

ALYREF links 3′‐end processing to nuclear export of non‐polyadenylated mRNA s

“…In addition to SLBP and Lsm11, ALYREF was found to directly interact with ARS2 and CstF64 (Fan et al, 2017;Shi et al, 2017), which have been implicated in histone mRNA processing as well (Gruber et al, 2012;Romeo et al, 2014). We also provide evidence that U7-snRNP is important for 3 0 -end processingdependent ALYREF recruitment.…”

“…RNA immunoprecipitations were performed as previously described (Fan et al, 2017). Briefly, cells grown on 10-cm dishes were transfected with the corresponding siRNAs.…”

“…To increase resolution of the data, we identified clustered binding sites (Konig et al, 2010;Rossbach et al, 2014). Significantly, of the total 55 histone mRNAs that were easily detected in HeLa nuclei (Fan et al, 2017), clustered ALYREF binding sites were apparently and reproducibly detected on 52 ( Fig 1A). This binding was not due to the high abundance of histone mRNAs, as compared to those in nuclear total RNA-seq, histone reads were significantly more enriched in ALYREF iCLIP-seq ( Fig 1B).…”

Nuclear sorting of RNA

“…However, time can tip the scales again, since prolonged nuclear exposure may favor assembly, and activation, of decay factors (Schmid & Jensen, ). A key example of such battle of processes is the mutual competition between MTR4 and ALYREF for association with CBCA‐bound RNAs, the outcome of which plays a causative role in fate commitment (Fan et al, ; Giacometti et al, ; Schulze et al, ). This balance can be tipped to favor either pathway depending on the local environment, such as other export or decay factors already bound as a result of processing.…”

Exploiting the Hidden Treasure of Detained Introns

“…Interestingly, as illustrated in Figure 1A, IR can be further divided into two classes, one corresponding to those containing a premature termination codon (PTC), which elicits nonsense-mediated RNA decay (NMD) upon export to the cytoplasm, and the other corresponding to those retained in the nucleus, which are insensitive to NMD and collectively referred to as detained introns (DIs) (Boutz et al, 2015). DI-containing transcripts may be further spliced for nuclear export or degraded by the exosome (Fan et al, 2017). There must be specific cis -acting signals in nuclear-detained RNAs, which remain to be characterized.…”