Using positional distribution to identify splicing elements and predict pre-mRNA processing defects in human genes

Abstract

We present an intuitive strategy for predicting the effect of sequence variation on splicing. In contrast to transcriptional elements, splicing elements appear to be strongly position dependent. We demonstrated that exonic binding of the normally intronic splicing factor, U2AF65, inhibits splicing. Reasoning that the positional distribution of a splicing element is a signature of its function, we developed a method for organizing all possible sequence motifs into clusters based on the genomic profile of their positional distribution around splice sites. Binding sites for serine/arginine rich (SR) proteins tended to be exonic whereas heterogeneous ribonucleoprotein (hnRNP) recognition elements were mostly intronic. In addition to the known elements, novel motifs were returned and validated. This method was also predictive of splicing mutations. A mutation in a motif creates a new motif that sometimes has a similar distribution shape to the original motif and sometimes has a different distribution. We created an intraallelic distance measure to capture this property and found that mutations that created large intraallelic distances disrupted splicing in vivo whereas mutations with small distances did not alter splicing. Analyzing the dataset of human disease alleles revealed known splicing mutants to have high intraallelic distances and suggested that 22% of disease alleles that were originally classified as missense mutations may also affect splicing. This category together with mutations in the canonical splicing signals suggest that approximately one third of all disease-causing mutations alter pre-mRNA splicing. S plicing is catalyzed by the spliceosome, a riboprotein complex that rivals the ribosome in size and complexity. The ribosome has a large and small subunit whose assembly on the mRNA substrate corresponds to a functional switch from initiation to elongation. The spliceosome is composed of five subunits that appear to exist in at least four different stable configurations and, like the ribosomal subunits, transition between different assembled states corresponding to different stages of function (1-3). Mass spectroscopy has identified at least 300 RNA and protein components in this catalytic complex and studies have demonstrated heterogeneity in spliceosomal complexes isolated from different splicing substrates (4-6). The spliceosomal components that recognize the basic cis-elements of the splicing process are known. How the spliceosome assembles and reorganizes on these elements is also fairly well understood. However, several computational analyses estimate that these basic splicing elements contain at most half the information necessary for splice site recognition (7,8). The remaining information lies outside these splice sites presumably as enhancers or silencers.This information required to specify splicing presents a considerable mutational target-estimates of the fraction of disease mutations that affect splicing range from 15% (9) to 62% (10). Transcript analysis of genotyped cell lines has dis...

A sequence-based, deep learning model accurately predicts RNA splicing branchpoints

“…However, our predictions show a higher rate of A branchpoint nucleotides. While this could represent a "modal collapse" of our model or bias against C branchpoints in our training data, a strong bias to an A at the branchpoint is supported by a study of positional k-mer enrichment 12 . Additionally, the branchpoint nucleotide was not considered in the Taggart et.…”

Splicing inhibition of U2AF 65 leads to alternative exon skipping

“…U2AF 65 is also essential in vertebrate development (13,14). Its expression level is related to myotonic dystrophy, cystic fibrosis, and cancers (15,16).…”

Altérations de l’épissage et maladies rares

“…Les variants synonymes (des mutations ne modifiant pas l'acide aminé) étaient ainsi écartés, au même titre que les variants localisés en dehors des régions codantes. Il est maintenant établi qu'entre 15 % et 35 % des mutations connues pour être la cause d'une maladie génétique affecteraient l'épissage [11,12]. Sans a priori sur le fait qu'un variant génétique puisse être ou non une mutation causale d'une maladie génétique, certaines études estiment même à plus de 60 % la proportion de variants qui pourraient affecter l'épissage [13].…”