Capping - The first modification occurs at the 5' end of the pre-mRNA. A GTP residue is added in reverse orientation and forms, together with the first two nucleotides of the chain, a structure known as a cap (Figure 28.30). The cap is "decorated" by the addition of methyl groups to the N-7 position of the guanine and to one or two sugar hydroxyl groups of the cap nucleotides. The cap structure serves to position the mRNA on the ribosome for translation.
Splicing - After being capped, the pre-mRNA becomes complexed with a number of small nuclear ribonucleoprotein particles (snRNPs), which are themselves complexes of small nuclear RNAs (snRNAs) and special splicing enzymes. The snRNP--pre--mRNA complex is called a spliceosome. snRNAs recognize and bind intron--exon splice sites by means of complementary sequences (Figure 28.31). Table 28.6 shows some representative splice site sequences and the consensus sequences common to most introns. Excision of a single intron involves assembling and disassembling a spliceosome. Figure 28.32 and Figure 28.33 depict possible chemical and molecular aspects of the process. The sequence of reactions can be summarized as follows:
1. It begins with the attachment of the U1 snRNP to the G site at the 5' end of the intron.
2. The U2 snRNP then attaches at the branch site.
3. Assembly of the spliceosome continues, including the addition of several more snRNPs,
4. The lariat loop in the intron is formed and the two exons are joined. Splicing has now been accomplished, and the products--a ligated mRNA and a looped intron--are released. As the spliceosome disintegrates, the looped intron is degraded, and the mRNA is exported from the nucleus.
Alternative
Splicing - Some gene transcripts may
be spliced in different ways, in different tissues of an organism
or at different developmental stages. Alternative splicing
of the heavy chains of immunoglobulins (see here)
results in proteins that may or may not carry a hydrophobic membrane-binding
domain. Another example of alternative
splicing is shown in Figure 28.34.
The protein 
-tropomyosin is used in different
kinds of contractile systems in various cell types (see here) . A single gene is transcribed,
but the specific splicing patterns in different tissues provide
a variety of -tropomyosins. There are three positions
at which alternative choices can be made for which exon to splice
in. The choice of splice site appears to be determined by a cell-specific
protein that interacts with the spliceosome. The economy of alternative
splicing, given the size of the genome is significant.
RNA editing - RNA editing is a process affecting mitochondrial mRNAs of some unicellular eukaryotes, which involves insertion or deletion of uridine residues into messages during the processing steps. Apparently, the insertions are made by a kind of reverse splicing mechanism, and only at certain points. Small RNAs, called guide RNAs, are required for the process. A quite different type of editing involves deamination of adenosine to inosine in mRNA. Neither alternative splicing nor editing formally contradicts the basic concept that gene sequence carries the cell's information, because the sites for splicing and editing are themselves contained in the DNA, as are the sequences of the small nuclear RNAs and the guide RNAs.