Confirming Predicted Allele-Specific mRNA Splicing

What is it about?

Splice isoform structure and abundancecan be affected by either noncoding or masquerading coding variants that alter the structure or abundance of transcripts.When these variants are common in the population, these nonconstitutive transcripts are sufficiently frequent so as to resemble naturally occurring, alternative mRNA splicing.Prediction of the effects of such variants has been shown to be accurate using information theory-based methods. Single nucleotide polymorphisms (SNPs) predicted to significantly alter natural and/or cryptic splice site strength were shown to affect gene expression. We explicitly predict and validate SNPs that influence mRNA structure and levels of expression of the genes containing them in immortalized lymphoblastoid cell lines and tumors. Since constitutive splicing mutations can arise at other locations within premRNA sequences that elicit cryptic splicing, we examined whether more common genomic polymorphisms might frequently affect the abundance and structure of splice isoforms.

Featured Image

Photo by National Cancer Institute on Unsplash

Photo by National Cancer Institute on Unsplash

Why is it important?

Accurate and comprehensive methods are needed for predicting impact of non-coding mutations, in particular splicing defects, which are prevalent in causing genetic disease. Allele-specific alternative splicing can affect disease susceptibility as well as modulate mRNA splicing associated with common phenotypic variability in the population. In this study, we evaluate effects of 22 SNPs that were predicted to impact mRNA splicing. We validate these predictions using cell lines from individuals with known genotypes (homozygous common, heterozygous, and homozygous rare for nearly all SNPs tested). We validate expression changes due to these SNPs by: q-RT-PCR, high resolution exon microarrays, and an RNAseq-based algorithm, Veridical, that detects effects of variants on normal splicing. Q-RT-PCR precisely quantitates relative abundance of exonic isoforms, microarray expression analysis indicates the distribution of expression levels at isoform-specific genomic locations among individuals with the same genotype, while Veridical is a digital expression method based on read counts in tumors containing these variants relative to controls, that identifies splicing outputs not detected by these other approaches. We find that predicted allele-specific alternative splicing is confirmed by each of these approaches and appears to be relatively common in human populations.

Perspectives