Coevolutionary networks of splicing cis -regulatory elements

Abstract

Accurate and efficient splicing of eukaryotic pre-mRNAs requires recognition by trans-acting factors of a complex array of cis-acting RNA elements. Here, we developed a generalized Bayesian network to model the coevolution of splicing cis elements in diverse eukaryotic taxa. Cross-exon but not cross-intron compensatory interactions between the 5 splice site (5 ss) and 3 splice site (3 ss) were observed in human/mouse, indicating that the exon is the primary evolutionary unit in mammals. Studied plants, fungi, and invertebrates exhibited exclusively cross-intron interactions, suggesting that intron definition drives evolution in these organisms. In mammals, 5 ss strength and the strength of several classes of exonic splicing silencers (ESSs) evolved in a correlated way, whereas specific exonic splicing enhancers (ESEs), including motifs associated with hTra2, SRp55, and SRp20, evolved in a compensatory manner relative to the 5 ss and 3 ss. Interactions between specific ESS or ESE motifs were not observed, suggesting that elements bound by different factors are not commonly interchangeable. Thus, the splicing elements defining exons coevolve in a way that preserves overall exon strength, allowing specific elements to substitute for loss or weakening of others.C hoice of splice sites in nuclear pre-mRNA splicing involves a complex set of recognition events. Motifs at the 5Ј splice site (5Јss), the polypyrimidine tract (PPT) and 3Ј splice site (3Јss), and the branch point sequence (BPS) are required for splicing, but lack sufficient information content to define exon locations in most organisms (1). Auxiliary splicing regulatory elements (SREs), known as exonic splicing enhancers (ESEs), intronic splicing enhancers (ISEs), exonic splicing silencers (ESSs), and intronic splicing silencers (ISSs), are defined by their effects on adjacent splice sites, e.g., ESEs tend to promote inclusion and ESSs promote exclusion of the exons they reside in. SREs control splice site choice by recruitment of specific trans-acting factors to the pre-mRNA that function to either activate or repress splicing by interaction with other regulatory factors or core spliceosome components (reviewed in refs. 2 and 3).A prominent feature of splicing regulation is the elaborate network of interactions that occur among and between core and auxiliary splicing factors (4). Two general models have been proposed for early spliceosome assembly (5). In the intron definition model, intron-spanning interactions between factors recognizing the 5Јss and the downstream 3Јss occur initially; this model is supported for transcripts with large exons and small introns (6, 7). In the exon definition model, exon-spanning interactions between factors that recognize the 5Јss and factors bound at the upstream 3Јss lead to formation of exon definition complexes before rearrangements that yield intron-spanning spliceosomes. Exon definition is thought to predominate in splicing of mammalian internal exons, which are typically moderately sized (Ϸ50-250 bp) and often flan...

Splicing of designer exons informs a biophysical model for exon definition

“…The greater effect of the 5 ′ SS suggests a more critical role of its sequence, as has been suggested before (Xiao et al 2007). …”

“…It also allowed us to add multiple copies of an ESE while not adding any sequences that were not already present in a single ESE DE. It has been shown that the ESE strength or number inversely correlates with splice site strength in mammalian exons, i.e., ESEs can compensate for weak splice sites (Xiao et al 2007;Ke et al 2008). In addition, Hertel and Maniatis (1998) showed that the use of multiple downstream enhancer elements increased the use of a 3 ′ SS in an additive manner when tested in vitro .…”

Efficient backsplicing produces translatable circular mRNAs

“…Canonical splicing (i.e., linear splicing) of most metazoan introns requires a stepwise assembly of spliceosomal components in a cotranscriptional fashion (Kornblihtt et al 2013;Matera and Wang 2014), starting with a process called exon definition in which the 5 ′ ss and 3 ′ ss are recognized in pairs across exons through the interaction of U1 and U2 snRNPs (Fox-Walsh et al 2005;Xiao et al 2007). In a subsequent transition, U1 and U2 snRNPs undergo rearrangements to form an intron-spanning interaction known as intron definition complex (De Conti et al 2013).…”

Alternative splicing in spinal muscular atrophy underscores the role of an intron definition model

“…The intron definition model is often used to describe mechanism of splicing of large internal exons flanked by at least one small intron. 30,[35][36][37][38] Based on the wealth of information accumulated to date, we propose that splicing of SMN2 exon 7 is driven by the intron definition mechanism. Of note, much of the results described here pertain to the widely studied SMN intron 7, which is only 444-nt long.…”