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.

Keywords: RNA processing; RNA regulation; alternative polyadenylation; alternative splicing; crosstalk.

Figure 1

Schematic diagram illustrating the coupling between splicing and 3′-end processing The sequence signals of splicing (5′ or 3′ splicing site, ss) and 3′-end processing (PASs) are interleaving in many pre-mRNAs. The two processes are mutually regulated through multiple mechanisms, including dual-role RNA binding proteins (RBPs).

Figure 2

Regulation and mechanisms of 3′-end processing on alternative splicing (A) CFIm knockdown results in the formation of a short 3′ UTR transcript for Timp2, accompanied by retention of the last intron. (B) PABPN1 facilitates the splicing of a last intron with a weak 3′ splice site by recruiting RBM26/RBM27. (C) CPSF binding to the non-functional AAUAAA motif in the intron inhibits splicing of the cryptic exon. (D) Splicing factors and 3′-end processing factors interact on the terminal exon. (E) 3′-End processing factors, together with RBFOX2, NOVA2, HNRNPA1, and other RBPs, mediate exon inclusion and exclusion. (F) Elav promotes the usage of the long 3′ UTR of Dscam1, in coupled with the skipping of upstream exon 19.

Figure 3

Regulation and mechanisms of splicing on 3′-end processing (A) Splicing competes with intronic cleavage and polyadenylation to form IPA, SPI or lariat. (B) Schematic depiction of how increased 3′ UTR splicing may promote carcinogenesis. (C) U1 snRNP serves as a crucial factor in safeguarding pre-mRNA from premature cleavage and polyadenylation, thereby ensuring the production of full-length mRNA transcripts. (D) SRSF7 and SRSF3 exert opposing effects on APA. SRSF7 promotes the utilization of the proximal polyadenylation site, leading to the formation of a short 3′ UTR. Conversely, SRSF3 facilitates the use of the distal polyadenylation site, promoting the generation of a long 3′ UTR.

Figure 4

Dual-role RBPs in AS and APA (A) ELAV facilitates the expression of the eMIC-containing Drosophila Srrm234 isoform, which mediates microexon inclusion. (B) The MBNL protein exhibits a dual regulatory role in AS and APA. When the binding site of MBNL protein overlaps with the polyadenylation site, it impedes the recruitment of 3′-end processing factors, thereby influencing APA. Conversely, when MBNL protein binds to upstream of the polyadenylation site, it activates 3′-end processing at the downstream site, thereby modulating APA. (C) The splicing factors HNRNPC, PTBP1, and PCBP1 also modulate cleavage and polyadenylation.