RNA Processing

There are three main types of RNA processing events: trimming one or both of the ends of the primary transcript to the mature RNA length; removing internal RNA sequences by a process called RNA splicing; and modifying RNA nucleotides either at the ends of an RNA or within the body of the RNA. We will briefly examine each of these and then discuss how they are applied to the various types of cellular RNAs.

Almost all RNAs have extra sequences at one or both ends of the primary transcripts that must be removed. The removal of individual nucleotides from the ends of the RNA strand is carried out by any of several ribonucleases (enzymes that cut RNA), called exoribonucleases. An entire section of RNA sequence can be removed by cleavage in the middle of an RNA strand. The enzymes responsible for the cleavage in this location are called endoribonucleases. Each of these ribonucleases is targeted so that it only cleaves particular RNAs at particular places.

The principal steps in processing various types of RNAs in eukaryotic nuclei. RNA sequences that are in the mature RNAs are indicated in blue while RNA sequences that are removed during processing are in black. Small "x's" indicate sites of internal modifications of RNAs. The various steps do not necessarily occur in the order shown.

RNA splicing is similar to trimming in that it removes extra RNA sequences, but it is different because the sequence is removed from the middle of an RNA and the two flanking pieces are joined together again (see figure). The part of the RNA that is removed is called an intron, whereas the two pieces that are joined together, or spliced, are called exons. Just as with the cleavage enzymes, the splicing machinery recognizes particular sites within the RNA, in this case the junctions between exons and introns, and cleaves and rejoins the RNA at those positions.

Modification of RNA nucleotides can occur at the ends of an RNA molecule or at internal positions. Modification of the ends can protect the RNA from degradation by exoribonucleases and can also act as a signal to guide the transport of the molecule to a particular subcellular compartment. Some internal modifications, particularly of tRNAs and rRNAs, are necessary for these RNAs to carry out their functions in protein synthesis. Some internal modifications of mRNAs change the sequence of the message and so change the amino acid sequence of the protein coded for by the mRNA. This process is called RNA editing. As with the other types of RNA processing, the enzymes that modify RNAs are directed to specific sites on the RNA.