The splicing codes

The first step of epigenesis transforms primary transcripts into messenger RNAs by removing some RNA strings (called introns) and by joining together the remaining pieces (the exons). This is a true assembly, because exons are assembled into messengers, and we need therefore to find out if it is a catalyzed assembly (like transcription) or a codified assembly (like translation).
In the first case the cutting-and-sealing operations, collectively known as splicing, would require only a catalyst (comparable to RNA-polymerase), whereas in the second case they would need a catalyst and a set of adaptors (comparable to ribosome and tRNAs).
This suggests immediately that splicing is a codified process because it is implemented by structures that are very similar to those of protein synthesis. The splicing catalysts, known as spliceosomes, are huge molecular machines with molecular weights in the range of ribosome figures, and employ small molecular structures, known as snRNAs or snurps, which are comparable to tRNAs (Figure 4-5) (Maniatis and Reed, 1987; Steitz, 1988). The key point, however, is that the comparison goes much deeper than a mere similarity, because snRNAs, like tRNAs, have properties that fully qualify them as adaptors. They bring together, in a single molecule, two independent recognition processes, one for the beginning and one for the end af an intron, thus creating a specific correspondence between the world of transcripts and the world of messengers (Figure 4-6).
The two recognition steps are independent not only because there is a physical distance between them, but above all because the first step could be associated with different types of the second one, as demonstrated by the cases of alternative splicing (Figures 4-7).
The choice of the beginning and of the end of an intron, furthermore, is the operation that actually defines the introns and gives them a meaning. Without a complete set of such operations, primary transcripts could be transformed arbitrarily into messengers, and again biological specificity would be lost.
In RNA splicing, in conclusion, we find the three basic characteristics of the codes: