The splicing factor SRSF3 is functionally connected to the nuclear RNA exosome for intronless mRNA decay

Nour El Houda Benbahouche,Antoine Corbin,Henri Gruffat,Fabrice Mure,Evelyne Manet,Edouard Bertrand

doi:10.1038/s41598-018-31078-1

Abstract

The RNA exosome fulfills important functions in the processing and degradation of numerous RNAs species. However, the mechanisms of recruitment to its various nuclear substrates are poorly understood. Using Epstein-Barr virus mRNAs as a model, we have discovered a novel function for the splicing factor SRSF3 in the quality control of nuclear mRNAs. We have found that viral mRNAs generated from intronless genes are particularly unstable due to their degradation by the nuclear RNA exosome. This effect is counteracted by the viral RNA-binding protein EB2 which stabilizes these mRNAs in the nucleus and stimulates both their export to the cytoplasm and their translation. In the absence of EB2, SRSF3 participates in the destabilization of these viral RNAs by interacting with both the RNA exosome and its adaptor complex NEXT. Taken together, our results provide direct evidence for a connection between the splicing machinery and mRNA decay mediated by the RNA exosome. Our results suggest that SRSF3 aids the nuclear RNA exosome and the NEXT complex in the recognition and degradation of certain mRNAs.

Highlights

In eukaryotic cells, functional mRNA expression is a multi-step process in which the DNA-encoded message is transcribed into a pre-mRNA molecule that undergoes numerous modifications such as 5′-end capping, splicing, 3′-end cleavage and polyadenylation, together with the assembly of diverse factors required for the formation of a messenger ribonucleoprotein particle[1,2]
ZCCHC8 has been shown to interact with the cap-binding complex (CBC) and several members of the SR protein family[21], and one study has reported that, in vitro, RBM7 interacts with the splicing factor 3b subunit 2 (SAP145) and the SRSF3 protein[26]
It has been extensively shown that the viral protein EB2, as well as its homologs from other herpesviruses - ICP27, UL69 and ORF57 - are involved in the cytoplasmic accumulation of viral mRNAs expressed from intronless genes

Summary

Introduction

Functional mRNA expression is a multi-step process in which the DNA-encoded message is transcribed into a pre-mRNA molecule that undergoes numerous modifications such as 5′-end capping, splicing, 3′-end cleavage and polyadenylation, together with the assembly of diverse factors required for the formation of a messenger ribonucleoprotein particle (mRNP)[1,2]. EB2 may serve as a bridge between viral RNAs and the cellular export complex (TREX), which is recruited to the 5 ́-end of cellular RNAs as a result of splicing[43] In this model, EB2, like homologous proteins from other herpesviruses, compensates for the absence of splicing of the viral mRNAs expressed from intronless genes, by recruiting the TREX complex. The interaction observed between EB2 and SR proteins like SRSF1 (ASF/SF2), SRSF3 (SRp20) and SRSF7 (9G8) is probably involved both in the modifications of specific cellular genes splicing and in the increase in nuclear mRNA export of viral mRNA expressed from intronless genes[46,47,48]. Our findings reveal an important novel function of the SR protein SRSF3, in the recognition and degradation of some mRNAs

Methods

Results

Conclusion