- Introns are removed by the process of RNA splicing, which occurs only in cis on an individual RNA molecule.
- Only mutations in exons can affect protein sequence, but mutations in introns can affect processing of the RNA and therefore prevent production of protein.
How does the existence of introns change our view of the gene? Following splicing, the exons are always joined together in the same order in which they lie in DNA. So the colinearity of gene and protein is maintained between the individual exons and the corresponding parts of the protein chain.
Figure 2.2 shows that the order of mutations in the gene remains the same as the order of amino acid replacements in the protein. But the distances in the gene do not correspond at all with the distances in the protein. Genetic distances, as seen on a recombination map, have no relationship to the distances between the corresponding points in the protein. The length of the gene is defined by the length of the initial (precursor) RNA instead of by the length of the messenger RNA.
All the exons are represented on the same molecule of RNA, and their splicing together occurs only as an intramolecular reaction. There is usually no joining of exons carried by different RNA molecules, so the mechanism excludes any splicing together of sequences representing different alleles. Mutations located in different exons of a gene cannot complement one another; thus they continue to be defined as members of the same complementation group.
Mutations that directly affect the sequence of a protein must lie in exons. What are the effects of mutations in the introns? Since the introns are not part of the messenger RNA, mutations in them cannot directly affect protein structure. However, they can prevent the production of the messenger RNA—for example, by inhibiting the splicing together of exons. A mutation of this sort acts only on the allele that carries it. So it fails to complement any other mutation in that allele, and constitutes part of the same complementation group as the exons.
Mutations that affect splicing are usually deleterious. The majority are single base substitutions at the junctions between introns and exons. They may cause an exon to be left out of the product, cause an intron to be included, or make splicing occur at an aberrant site. The most common result is to introduce a termination codon that results in truncation of the protein sequence. About 15% of the point mutations that cause human diseases are caused by disruption of splicing (for review see Faustino and Cooper, 2003).
Eukaryotic genes are not necessarily interrupted. Some correspond directly with the protein product in the same manner as prokaryotic genes. In yeast, most genes are uninterrupted. In higher eukaryotes, most genes are interrupted; and the introns are usually much longer than exons, creating genes that are very much larger than their coding regions (for review see Breathnach and Chambon, 1981).