portion of exon 2 exon 1 exon 3 exon 1 6–22), and these components are transferred directly from the polymerase to the
RNA as the RNA emerges from the polymerase. This strategy helps the cell keep track of introns and exons: for example, the snRNPs that assemble at a 5ʹ splice site are initially presented only with the single 3ʹ splice site that emerges next from the polymerase; the potential sites further downstream have not yet been synthe sized. The coordination of transcription with splicing is especially important in preventing inappropriate exon skipping.
A strategy called “exon definition” also helps cells choose the appropriate splice sites. Exon size tends to be much more uniform than intron size, averaging about 150 nucleotide pairs across a wide variety of eukaryotic organisms (Figure 6–31). Through exon definition, the splicing machinery can seek out the relatively homogeneously sized exon sequences. As RNA synthesis proceeds, a group of additional components (most notably SR proteins, so-named because they con help to mark off each 3ʹand 5ʹ splice site, starting at the 5ʹ end of the RNA (Figure 6–32). These proteins, in turn, recruit U1 snRNA, which marks the downstream exon boundary, and U2 snRNA, which specifies the upstream one. By specifically marking the exons in this way and thereby taking advantage of the relatively uni form size of exons, the cell increases the accuracy with which it deposits the initial splicing components on the nascent RNA and thereby avoids “near miss” splice sites. How the SR proteins discriminate exon sequences from intron sequences is not understood in detail; however, it is known that some of the SR proteins bind preferentially to specific RNA sequences in exons, termed splicing enhancers.
In principle, since any one of several different codons can be used to code for a given amino acid, there is freedom to evolve the exon nucleotide sequence so as to form a binding site for an SR protein, without necessarily affecting the amino acid sequence that the exon specifies.
Both the marking of exon and intron boundaries and the assembly of the spli ceosome begin on an RNA molecule while it is still being elongated by RNA poly merase at its 3ʹ end. However, the actual chemistry of splicing can take place later.
This delay means that intron sequences are not necessarily removed from a pre mRNA molecule in the order in which they occur along the RNA chain.
Figure 6–30 Two types of splicing errors.
(A) Exon skipping. (B) Cryptic splice-site selection. Cryptic splicing signals are nucleotide sequences of RNA that closely resemble true splicing signals and are sometimes mistakenly used by the spliceosome.
Figure 6–31 Variation in intron and exon lengths in the human, worm, and fly genomes. (A) Size distribution of exons.
(B) Size distribution of introns. Note that exon length is much more uniform than intron length. (Adapted from International Human Genome Sequencing Consortium, Nature 409:860–921, 2001. With permission from Macmillan Publishers Ltd.) percentage of introns percentage of exons 100 200 300 400 500 600 700 800 900 1000 <100 100–2000 2000–5000 5000–30,000 >30,000 exon length (nucleotide pairs) intron length (nucleotide pairs)