Coupling of alternative splicing and alternative polyadenylation

Abstract

RNA splicing and 3′-cleavage and polyadenylation (CPA) are essential processes for the maturation of RNA. There have been extensive independent studies of these regulated processing events, including alternative splicing (AS) and alternative polyadenylation (APA). However, growing evidence suggests potential crosstalk between splicing and 3′-end processing in regulating AS or APA. Here, we first provide a brief overview of the molecular machines involved in splicing and 3′-end processing events, and then review recent studies on the functions and mechanisms of the crosstalk between the two processes. On the one hand, 3′-end processing can affect splicing, as 3′-end processing factors and CPA-generated polyA tail promote the splicing of the last intron. Beyond that, 3′-end processing factors can also influence the splicing of internal and terminal exons. Those 3′-end processing factors can also interact with different RNA-binding proteins (RBPs) to exert their effects on AS. The length of 3′ untranslated region (3′ UTR) can affect the splicing of upstream exons. On the other hand, splicing and CPA may compete within introns in generating different products. Furthermore, splicing within the 3′ UTR is a significant factor contributing to 3′ UTR diversity. Splicing also influences 3′-end processing through the actions of certain splicing factors. Interestingly, some classical RBPs play dual roles in both splicing and 3′-end processing. Finally, we discuss how long-read sequencing technologies aid in understanding the coordination of AS-APA events and envision that these findings may potentially promote the development of new strategies for disease diagnosis and treatment.

1. Introduction

In eukaryotes, mRNA synthesis occurs within the cell nucleus, where nascent RNA undergoes a series of processing events to generate mature transcripts, including 5′ capping, splicing, and 3′-end processing. Each of these steps has alternative regulation, such as alternative splicing (AS) in skipping or including an exon and alternative polyadenylation (APA) in selectively choosing proximal or distal polyadenylation site (pPAS or dPAS), or even intronic polyadenylation site (iPAS). These regulatory mechanisms play crucial roles in shaping the final repertoire of mature transcripts, thereby contributing to the complexity of protein isoforms. Hence, both AS and APA contribute significantly to the mRNA diversification and differences in the proteome in many organisms [1,2].

Alternative splicing leads to variations in transcripts through exon skipping, inclusion, intron retention, and etc., determined by the selection of alternative splicing sites [1,3]. Meanwhile, the 3′-end formation in eukaryotes represents a pivotal step in mRNA maturation, involving the recognition of polyadenylation signals and subsequent cleavage and polyadenylation events [2,4]. These two processing events, the majority of which are co-transcriptional, have been studied independently. Contemporary research has revealed an intricate interplay between splicing and 3′-end processing mechanisms [5]. Notably, the coordination of these events is pertinent to APA and AS. This review starts with a brief introduction of the molecular machineries and processes of RNA splicing and 3′-end processing and aims to provide a comprehensive review of the progress on the coupling mechanisms between APA and AS.