Diverse regulation of 3′ splice site usage

Abstract

The regulation of splice site (SS) usage is important for alternative pre-mRNA splicing and thus proper expression of protein isoforms in cells; its disruption causes diseases. In recent years, an increasing number of novel regulatory elements have been found within or nearby the 3'SS in mammalian genes. The diverse elements recruit a repertoire of trans-acting factors or form secondary structures to regulate 3'SS usage, mostly at the early steps of spliceosome assembly. Their mechanisms of action mainly include: (1) competition between the factors for RNA elements, (2) steric hindrance between the factors, (3) direct interaction between the factors, (4) competition between two splice sites, or (5) local RNA secondary structures or longer range loops, according to the mode of protein/RNA interactions. Beyond the 3'SS, chromatin remodeling/transcription, posttranslational modifications of trans-acting factors and upstream signaling provide further layers of regulation. Evolutionarily, some of the 3'SS elements seem to have emerged in mammalian ancestors. Moreover, other possibilities of regulation such as that by non-coding RNA remain to be explored. It is thus likely that there are more diverse elements/factors and mechanisms that influence the choice of an intron end. The diverse regulation likely contributes to a more complex but refined transcriptome and proteome in mammals.

Exon Junction Complexes Suppress Spurious Splice Sites to Safeguard Transcriptome Integrity

“…A similar interference with the assembly of the early spliceosome has been reported for a diverse group of repressors of 3 0 SS usage, including PTB or Sxl (Izquierdo et al, 2005;Valcá rcel et al, 1993). Many of these factors compete with U2AF for binding to the pyrimidine tract, and therefore the inhibitory potential of the repressor depends on its binding strength to the 3 0 SS (Sohail and Xie, 2015). In contrast, the EJC has a clear competitive advantage over U2AF because its co-spliceosomal deposition ensures that cryptic or reconstituted SS are nearly immediately rendered inaccessible.…”

Splicing Enhancers at Intron–Exon Borders Participate in Acceptor Splice Sites Recognition

“…In line with that, 12% of exons have been shown to be U2AF-independent [25]. It is of note that even U2AF recognition may be further regulated by other proteins with affinity to the PPT that may either support or compete with U2AF binding (e.g., CELF, Sam68, and YB1; and hnRNP C, TDP43, PTB, respectively) [26,27].…”

Widespread separation of the polypyrimidine tract from 3’ AG by G tracts in association with alternative exons in metazoa and plants

“…Unlike the 3'SS consensus sequence where the Py and 3'AG are adjacent to each other separated by only two nucleotides 'NC', we have found a group of intron ends where they are separated further apart by RNA elements [3,4,17,18]. The first identified of these elements is CA-rich, called Ca ++ /calmodulin-dependent protein kinase IV (CaMKIV)-responsive RNA elements (CaRRE) to inhibit 3'SS usage through hnRNP L/LL [17,19,20].…”

“…We have shown previously that the REPA G tracts inhibits 3'SS usage by its trans-acting hnRNP H/F to interfere with U2AF65 binding [3,18], which is in a tight heterodimer with U2AF35[32]; thereby preventing their interaction with the Py and 3'AG, respectively [3,4]. Here they are also associated with more distant branch points from the 3'AG ( Fig.…”

“…Their sequences are constrained by a consensus but could be highly diverse among hundreds of species [1]. The diversity and flexibility may contribute to alternative pre-mRNA splicing as well as to the mutation effect in many diseases [2,3,4,5]. The majority of 3' splice sites are comprised of the branch point, polypyrimidine tract and 3' AG dinucleotides with a consensus (Y) 20 NCAGgt in humans based on the whole genome data [1].…”