RNA Processing and Splicing

How a raw primary transcript is capped, spliced, and tailed into a mature messenger RNA — and how alternative splicing expands the protein output of a genome.

Definition

RNA processing is the set of modifications that mature a primary transcript, principally 5' cap addition, intron removal by splicing, and 3' cleavage and polyadenylation; splicing is the precise excision of introns and ligation of exons carried out by the spliceosome.

Scope

This topic covers the co- and post-transcriptional modifications that convert a eukaryotic primary transcript into a functional mRNA: 5' capping, removal of introns and joining of exons by the spliceosome, and 3' cleavage and polyadenylation. It also covers alternative splicing as a source of protein diversity. Processing of non-coding RNAs is noted but developed further in the RNA biology area.

Core questions

• Why are eukaryotic genes interrupted by introns, and how are these removed?
• What modifications protect and define the ends of an mRNA?
• How does the spliceosome recognise exon–intron boundaries accurately?
• How does alternative splicing let one gene encode several proteins?

Key theories

Split-gene organisation

Eukaryotic protein-coding sequences are interrupted by introns that are transcribed but removed from the mature mRNA, a discovery that established that genes and their final transcripts are not colinear.

Alternative splicing as a diversity generator

By joining different combinations of exons from the same primary transcript, alternative splicing allows a single gene to specify multiple distinct proteins, greatly expanding proteome complexity.

Mechanisms

As transcription proceeds, the nascent transcript receives a modified 5' cap that protects it and aids later steps. Introns are removed by the spliceosome, a complex of small nuclear ribonucleoproteins that recognises splice-site sequences, brings the intron ends together, and catalyses two transesterification reactions that excise the intron as a lariat and join the flanking exons. The 3' end is generated by cleavage at a polyadenylation signal followed by addition of a poly(A) tail. Regulated use of alternative splice sites produces different mature mRNAs from one transcript.

Clinical relevance

Mutations that disrupt splice sites or splicing factors cause numerous genetic diseases, and splicing-directed therapies have been developed for some of them; presented as significance rather than as clinical guidance.

History

The 1977 discovery of split genes by Sharp's and Roberts's groups overturned the assumption of colinear genes and mRNAs and launched the study of splicing; the spliceosome and alternative splicing were subsequently characterised, work recognised by the 1993 Nobel Prize in Physiology or Medicine.

Key figures

• Phillip Sharp
• Richard Roberts

Seminal works

• berget1977
• lodish2016

Frequently asked questions

What is the difference between an intron and an exon?

Introns are intervening sequences removed from the primary transcript during splicing; exons are the segments retained and joined together in the mature mRNA.

Why is the 5' cap important?

It protects the mRNA from degradation and is recognised by the machinery that exports and later translates the message.