Prokaryotic DNA transcription produces messenger RNA, which is necessary for transfer from the cell nucleus to the cytoplasm where translation occurs. In contrast, eukaryotic DNA transcription takes place in a cell's nucleus and produces what is called a primary RNA transcript or pre-messenger RNA. Before eukaryotic products of transcription can be moved into the cytoplasm, they must undergo modifications that allow them to become mature messenger RNA. Splicing is the name given to the reaction that removes unnecessary segments of the primary RNA transcript, called introns. The removal of the introns produces mRNA (see the figure, below). Messenger RNA contains only exons, those portions of the primary RNA transcript that will be translated into a protein.
Unlike the sequence of an exon, intron sequences are unimportant. Only small portions of an intron sequence are preserved. These portions, located near the end of each intron, serve to identify a sequence as an intron, identifying the sequence for removal. There are intron identifying portions:
- The 5' splice site, consisting of a guanine next to a uracil base at the 5' end of the intron.
- The 3' splice site, consisting of an adenine next to a guanine at the 3' end of an intron.
- The branch point A, located about 30 nucleotides from the 3' end, consisting of just one adenine.
With the help of the spliceosome, a multi-component protein, the splicing reaction occurs in two steps. The spliceosome contains five small nuclear ribonucleoproteins (snRNPS, pronounced "snurps"). They are called U1, U2, U4, U5, and U6. Each snRNP contains protein components that are critical for the splicing reaction. U1 binds directly to the 5' splice site via complementary base pairing. U1 then recruits U2, which forms a complex with branch point A. U4 and U6 work in concert to form a "pre-splicing complex" and U5 helps to hold the exons in place between the first and second steps in the splicing reaction. Once the splicing reactions have occurred and the exons have been joined, the resulting mRNA is freed from the spliceosome machinery and the different snRNP components are recycled for further use.
In addition to the post-transcriptional modifications already discussed (5' cap, poly A tail addition, and splicing), a fourth type of modification can be made: RNA editing. RNA editing is a modification that changes the mRNA sequence and as a result alters the protein produced by that mRNA. Editing can occur in two ways. First, by changing one nucleotide to another, and second by inserting or deleting a nucleotide or nucleotides.