RNA Processing

RNA processing is to generate a mature mRNA (for protein genes) or a functional tRNA or rRNA from the primary transcript.  In this section, we discuss first the processing of pre-mRNA and then processing of pre-rRNA and pre-tRNA.

Processing of pre-mRNA involves the following steps:

• Capping - add 7-methylguanylate (m⁷G) to the 5' end.
• Polyadenylation - add a poly-A tail to the 3' end.
• Splicing - remove introns and join exons.

In some cases, RNA editing is also involved.

Figure 5-A-1.  The procedure of RNA processing for protein genes.

5'-Capping

Capping occurs shortly after transcription begins.   The chemical structure of the "cap" is shown in the following figure, where m⁷G is linked to the first nucleotide by a special 5'-5' triphosphate linkage.  In most organisms, the first nucleotide is methylated at the 2'-hydroxyl of the ribose.  In vertebrates, the second nucleotide is also methylated.

Figure 5-A-2.  Modifications at the 5' end.

3'-Polyadenylation

A stretch of adenylate residues are added to the 3' end.  The poly-A tail contains ~ 250 A residues in mammals,  and ~ 100 in yeasts.

Figure 5-A-3.  Polyadenylation at the 3' end.  The major signal for the 3' cleavage is the sequence AAUAAA.  Cleavage occurs at 10-35 nucleotides downstream from the specific sequence.   A second signal is located about 50 nucleotides downstream from the cleavage site.   This signal is a GU-rich or U-rich region.

Processing of pre-rRNA and pre-tRNA

The newly transcribed pre-rRNA is a cluster of three rRNAs: 18S, 5.8S and 28S in mammals.  They must be separated to become functional.  Pre-rRNA is synthesized in the nucleolus.  The U3 snRNA, other U-rich snRNAs, and their associated proteins in the nucleolus are involved in the cleavage of the pre-rRNA.

5S rRNA is synthesized in the nucleoplasm.  It does not require any processing.   After 5S rRNA is synthesized, it will enter the nulceolus to combine with 28S and 5.8S rRNAs, forming the large subunit of the ribosome.

Pre-tRNA requires extensive processing to become a functional tRNA.  Four types of modifications are involved:

1. Removing an extra segment (~ 16 nucleotides) at the 5' end by RNase P.
2. Removing an intron (~ 14 nucleotides) in the anticodon loop by splicing.
3. Replacing two U residues at the 3'end by CCA, which is found in all mature tRNAs.
4. Modifying some residues to characteristic bases, e.g., inosine, dihydrouridine and pseudouridine.

Review Articles:

tRNA Splicing - J. Biol. Chem., 1998.

The trials and travels of tRNA - Genes and Development, 1999.