Splicing out introns

Capping and tailing work on the ends of a pre-mRNA. Splicing works on the middle: it cuts pieces out of the RNA and stitches the rest back together.

Genes in pieces

In many eukaryotic protein-coding genes, the coding sequence is broken up by stretches of DNA that are transcribed but never translated. These interrupting stretches are introns. The pieces that stay in the mature mRNA are exons, the expressed regions that carry the coding sequence. Removing the introns and joining the exons together is RNA splicing, or simply splicing.

How common introns are depends on the organism. Most protein-coding genes in animals and flowering plants have at least one. They are less common in single-celled eukaryotes such as yeast, and rare in bacteria and archaea.

Check yourselfIs an intron’s sequence found in the gene’s DNA? In the pre-mRNA? In the mature mRNA?

It’s in the DNA and in the pre-mRNA, because introns are transcribed. It isn’t in the mature mRNA, because splicing removed it.

How the spliceosome works

Introns are removed with precision by the spliceosome, a large complex built from several snRNPs (pronounced “snurps”). Each snRNP is a small RNA bound to a set of proteins.

Three short sequences mark each intron for removal: the 5′ splice site at its boundary with the exon before it, the 3′ splice site at its boundary with the exon after it, and the branch site inside the intron.

The cutting and joining aren’t done by a protein. An RNA within one of the snRNPs catalyzes them, so that RNA is a ribozyme, the kind of RNA catalyst you met in Chapter 4.

Check yourselfWhich part of the spliceosome actually cuts the pre-mRNA and joins the exons?

An RNA molecule within one of its snRNPs. It acts as a ribozyme, catalyzing the cuts at the splice sites and the joining of the exons.

Alternative splicing

Splicing can be regulated, so the same pre-mRNA can be spliced in more than one way. This is alternative splicing, which Chapter 4 introduced as one reason two cells with the same genes can make different proteins. Each combination of exons codes a polypeptide with a somewhat different amino acid sequence, so one gene can produce two or more polypeptides.

Complex eukaryotes use alternative splicing to make different versions of a protein in different cell types or at different stages of development. It enlarges the proteome without enlarging the genome.

Check yourselfLiver cells and muscle cells make two different polypeptides from the same gene. Is their DNA different? What explains it?

The DNA is the same. The gene’s pre-mRNA is alternatively spliced, keeping a different set of exons in each cell type, so each mature mRNA codes a different polypeptide.

Self-splicing RNAs

A few rRNAs and tRNAs in certain species also contain introns, but no spliceosome removes them. Instead, these RNAs are self-splicing: part of the RNA itself acts as a ribozyme, cutting out its own intron and joining its exons.