Exon and intron definition in pre‐mRNA splicing

Abstract

One of the fundamental issues in RNA splicing research is represented by understanding how the spliceosome can successfully define exons and introns in a huge variety of pre-mRNA molecules with nucleotide-precision. Since its first description, researchers in this field have identified and characterized many fundamental elements and players capable of affecting the splicing process, both in a negative and positive manner. Indeed, it can be argued that today we know a great deal about the forces that make an exon, an exon and an intron, an intron. As will be discussed in this review, these decisions are a result of a complex combinatorial control resulting from many different factors/influences. Most importantly, these influences act across several levels of complexity starting from the relatively simple interaction between two consensus 5' and 3' splice sites to much more complex factors: such as the interplay between silencer or enhancer sequences, transcriptional processivity, genomic milieu, nucleosome positioning, and histone modifications at the chromatin level. Depending on local contexts, all these factors will act either antagonistically or synergistically to decide the exon/intron fate of any given RNA sequence. At present, however, what we still lack is a precise understanding of how all these processes add up to help the spliceosome reach a decision. Therefore, it is expected that future challenges in splicing research will be the careful characterization of all these influences to improve our ability to predict splicing choices in different organisms or in specific contexts.

Investigating Splicing Variants Uncovered by Next-Generation Sequencing the Alzheimer’s Disease Candidate Genes, CLU, PICALM, CR1, ABCA7, BIN1, the MS4A Locus, CD2AP, EPHA1 and CD33

“…A multitude of splicing regulatory proteins and ribonucleoproteins interact to precisely control splicing and influence the levels of different transcript isoforms created [39]. Many variants that disrupt splicing are found deep within exons and introns and affect splicing through the disruption of exonic or intronic splicing enhancers or silencers [40].…”

Selection on Position of Nonsense Codons in Introns

“…Intron length is strongly associated with intron-definition (for introns with fewer than 250 nucleotides) vs. exon-definition (for introns with more than 250 nucleotides) splicing (De Conti et al 2013). When a splicing error occurs, intron-definition splicing generally results in the retention of an intron, whereas exon-definition splicing generally results in exon skipping.…”

“…For the last intron, frame was determined by working backward from the stop codon. Fifth, it is not clear to us the appropriate way to compare across genes with a few vs. many introns, or those that vary in the proportion of introns that are short vs. long (see next section), which is important for intron definition (De Conti et al 2013).…”

“…We hypothesize that PTCs are selected to occur early in introns to promptly initiate NMD and reduce both the time taken for a ribosome to translate an aberrant mRNA containing unspliced introns and the length of the resulting aberrant proteins. Since selection is caused by the deleterious effects of having aberrantly spliced mRNAs, we expect our predictions to more likely hold for genes that are expressed at high levels, because they may produce more aberrant mRNAs, and introns with fewer than 250 nucleotides, where splicing errors more commonly lead to intron retention (Lim and Burge 2001;De Conti et al 2013).To test whether there is evidence that selection has acted to minimize the deleterious effects of failure to remove an intron from an mRNA by modifying the location of PTCs, we utilized data from seven model organisms: Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, Mus musculus, Saccharomyces cerevisiae, and Schizosaccharomyces pombe. These species have well-annotated genomes, reliable splicing information, and expression data, and thus represented all of the species with the necessary data to test our predictions.…”

“…We hypothesize that PTCs are selected to occur early in introns to promptly initiate NMD and reduce both the time taken for a ribosome to translate an aberrant mRNA containing unspliced introns and the length of the resulting aberrant proteins. Since selection is caused by the deleterious effects of having aberrantly spliced mRNAs, we expect our predictions to more likely hold for genes that are expressed at high levels, because they may produce more aberrant mRNAs, and introns with fewer than 250 nucleotides, where splicing errors more commonly lead to intron retention (Lim and Burge 2001;De Conti et al 2013).…”