Figure 6–32 The exon definition hypothesis. According to this idea,  SR proteins bind to each exon sequence in the pre-mRNA and thereby help to guide the snRNPs to the proper intron/ exon boundaries. This demarcation of exons by the SR proteins occurs cotranscriptionally, beginning at the CBC (cap-binding complex) at the 5ʹ end. It has been proposed that a group of proteins known as the heterogeneous nuclear ribonucleoproteins (hnRNPs) may preferentially associate with intron sequences, further helping the spliceosome distinguish introns from exons. (Adapted from R. Reed, Curr. Opin. Cell Biol. 12:340–345, 2000. With permission from Elsevier.) splicing plays important roles in the development of cystic fibrosis, frontotemporal dementia, Parkinson’s disease, retinitis pigmentosa, spinal muscular atrophy, myotonic dystrophy, premature aging, and cancer. It has been estimated that of the many point mutations that cause inherited human diseases, 10% produce aberrant splicing of the gene containing the mutation.
The plasticity of RNA splicing also means that the cell can easily regulate the pattern of RNA splicing. Earlier in this section we saw that alternative splicing can give rise to different proteins from the same gene and that this is a common strategy to enhance the coding potential of genomes. Some examples of alternative splicing are constitutive; that is, the alternatively spliced mRNAs are produced continuously by cells of an organism. However, in many cases, the cell regulates the splicing patterns so that different forms of the protein are produced at different times and in different tissues (see Figure 6–26). In Chapter 7, we return to this issue to discuss some specific examples of regulated RNA splicing.
When the spliceosome was first discovered, it puzzled molecular biologists. Why do RNA molecules instead of proteins perform important roles in splice-site recognition and in the chemistry of splicing? Why is a lariat intermediate used rather than the apparently simpler alternative of bringing the 5ʹand 3ʹ splice sites together in a single step, followed by their direct cleavage and rejoining? The answers to these questions reflect the way in which the spliceosome has evolved.
As discussed briefly in Chapter 1 (and in more detail in the final section of this chapter), it is likely that early cells used RNA molecules rather than proteins as their major catalysts and that they stored their genetic information in RNA rather than in DNA sequences. RNA-catalyzed splicing reactions presumably had critical roles in these early cells. As evidence, some self-splicing RNA introns (that is, intron sequences in RNA whose splicing out can occur in the absence of proteins or any other RNA molecules) remain today—for example, in the nuclear rRNA genes of the ciliate Tetrahymena, in a few bacteriophage T4 genes, and in some mitochondrial and chloroplast genes. In these cases, the RNA molecule folds into a specific three-dimensional structure that brings the intron/exon junctions together and catalyzes the two transesterification reactions. A self-splicing intron sequence can be identified in a test tube by incubating a pure RNA molecule that contains the intron sequence and observing the splicing reaction. Because the basic chemistry of some self-splicing reactions is so similar to pre-mRNA splicing, it has been proposed that the much more involved process of pre-mRNA splicing evolved from a simpler, ancestral form of RNA self-splicing.
RNA-Processing Enzymes Generate the 3ʹ End of Eukaryotic mRNAs