Allele‐specific mRNA Splicing in Human

Abstract

Polymorphisms and de novo mutations in the genome sequence determine the genetic contribution to human phenotype and disease. Many functionally significant variants, rather than altering an encoded protein, affect the regulation of transcription or posttranscriptional processing, including messenger ribonucleic acid (mRNA) splicing. The effects of these mutations can be difficult to determine, yet they make a substantial contribution to human disease and other phenotypes of medical significance, such as interindividual differences in responses to pharmaceuticals. Progress towards understanding the regulation of splicing, coupled with the advent of high‐throughput technologies for interrogating the transcriptome have given rise to new opportunities to investigate allelic differences in mRNA splicing.

Key Concepts

  • Splicing is a tightly regulated process that can be disrupted by sequence variants (polymorphisms or rare mutations).

  • Mutations and polymorphisms that affect mRNA splicing are thought to make a major contribution to human genetic diseases.

  • Alternatively spliced mRNA isoforms are detectable for the majority of human multiexon genes.

  • The contribution of sequence variants to the diversity of splice isoforms observed for a gene is often overlooked.

  • Sequence variants that affect splicing can disrupt splicing of constitutively spliced exons or affect the regulation of alternative splicing.

  • Variants with a quantitative effect on splicing are referred to as splicing quantitative trait loci (sQTLs).

  • Most examples of allele‐specific splicing involve differences in the relative abundance of isoforms, rather than the creation or loss of an isoform.

  • Because the balance of alternative splice isoforms is often evolutionarily conserved when the isoforms themselves are conserved, sQTLs of conserved isoforms may frequently have functional implications.

Keywords: alternative splicing; allele‐specific splicing; single nucleotide polymorphisms; genetic disease; pharmacogenetics

Figure 1.

Cis‐regulatory elements involved in splicing 1, donor site; 2, intronic splicing enhancers (ISE); 3, branch point; 4, intron splicing silencers (ISS); 5, acceptor site and polypyrimidine tract; 6, exon splicing enhancers (ESE) and 7, exon splicing silencers (ESS). For each cis‐regulatory element, the corresponding trans‐acting elements are shown directly above their corresponding cis‐regulatory elements.

Figure 2.

Detection of cis‐acting mutations that affect splicing. A hypothetical example of a splicing mutation that disrupts a splice acceptor leading to an exon skipping event is used to illustrate how it can be detected or predicted using different methods (a) ab initio prediction. (b) Primers can be designed that target the allele‐specific skipping event. Primers are shown as arrows in the figure. Gel electrophoresis can clearly indicate the skipping of the exon from the different alleles. (c) A minigene encompassing the splicing mutation and skipped exons can be designed to prove that the G to A mutation leads to aberrant splicing. (d) Exon arrays can be used to identify allele‐specific splicing. In the extreme example shown, the lack of an expression signal from the probe targeting the third exon in the lower sample points to complete skipping of the exon in this sample. If the samples are genotype differences and given sufficient numbers, differences in splicing can be associated with SNP alleles.

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Nembaware, V, and Seoighe, C(Sep 2009) Allele‐specific mRNA Splicing in Human. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0021764]