RNA Splicing and Alternative Splicing

Splicing is the process that removes introns from a pre-mRNA and joins the remaining exons into a continuous coding sequence. When the same pre-mRNA can be spliced in more than one way—alternative splicing—a single gene can give rise to multiple distinct mRNAs and proteins, vastly expanding the coding capacity of the genome and providing a major layer of gene regulation.

Definition

RNA splicing is the removal of introns and ligation of exons in a pre-mRNA to form a mature coding sequence; alternative splicing is the regulated use of different splice sites so that one gene yields multiple mRNA and protein isoforms.

Scope

This topic covers the chemistry and machinery of pre-mRNA splicing by the spliceosome, the patterns and regulation of alternative splicing, its contribution to proteome diversity, and self-splicing introns as catalytic precedents. It treats splicing as a regulatory and structural topic within molecular biology and is reference-educational, not clinical guidance.

Core questions

• How does the spliceosome recognise exon-intron boundaries and catalyse intron removal?
• How does alternative splicing let one gene encode many proteins?
• What signals and regulatory proteins control which splice sites are used?
• How do splicing errors and dysregulation contribute to disease?

Key concepts

• Introns and exons
• Spliceosome (small nuclear ribonucleoproteins)
• 5' and 3' splice sites and branch point
• Exon skipping and alternative splice-site choice
• Splicing regulatory proteins (e.g. SR and hnRNP families)
• Isoform diversity and proteome expansion
• Self-splicing introns

Key theories

Catalytic RNA in splicing

The discovery that a group I intron can excise itself without protein established that RNA can catalyse the phosphoryl-transfer chemistry of splicing, foreshadowing the RNA-centred catalytic core of the spliceosome.

Mechanisms

Most pre-mRNA splicing is carried out by the spliceosome, a large dynamic complex of small nuclear ribonucleoproteins and proteins that assembles on each intron, recognises the 5' splice site, branch point, and 3' splice site, and catalyses two transesterification reactions that excise the intron as a lariat and join the flanking exons. Which sites are chosen is not fixed: regulatory proteins binding to enhancer and silencer sequences bias the machinery toward including or skipping particular exons, producing alternative isoforms in a cell-type- and developmental-stage-specific manner. Across vertebrate genomes, alternative splicing is pervasive and a major source of transcriptome and proteome diversity. The chemistry of splicing has a catalytic-RNA precedent in self-splicing introns, which remove themselves without the spliceosome.

Clinical relevance

Mutations that disrupt splice sites or splicing regulators cause or modify many genetic diseases and cancers, and splice-modulating molecules have become a therapeutic strategy. This entry presents that biology as educational background and is not a basis for individual diagnosis or treatment.

History

The late-1970s discovery that genes are split into exons and introns implied a mechanism to remove the introns, and the spliceosome was subsequently characterised as the machine responsible. The recognition that splicing can occur in alternative patterns turned it from a mere maturation step into a central regulatory mechanism, and genome-wide studies later showed how extensively vertebrate transcriptomes exploit it. The earlier finding of self-splicing introns showed that the underlying chemistry can be RNA-catalysed.

Key figures

• Phillip Sharp
• Richard Roberts
• Thomas Cech
• Adrian Krainer
• Benjamin Blencowe

Seminal works

• kruger-1982
• nilsen-2010
• barbosa-morais-2012

Frequently asked questions

What is the difference between splicing and alternative splicing?

Splicing removes introns and joins exons to form a mature mRNA; alternative splicing is when the same pre-mRNA is spliced in more than one way, so one gene can produce several different mRNA and protein isoforms.

What machine carries out most pre-mRNA splicing?

The spliceosome, a large complex of small nuclear ribonucleoproteins and associated proteins that recognises splice sites and catalyses intron removal.