Figure 6–47 A model for an mRNA production factory. mRNA production is made more efficient in the nucleus by an aggregation of the many components needed for transcription and pre-mRNA processing, thereby producing a specialized biochemical factory. In (A), a postulated scaffold protein holds various components in the proximity of a transcribing RNA polymerase. Other key components are bound directly to the RNA polymerase tail, which likewise serves as a scaffold (see Figure 6–22), but for simplicity these are not shown here. In (B), a large number of such scaffolds have been brought together to form an aggregate that is highly enriched in the many components needed for the synthesis and processing of pre-mRNAs. Such a scaffold model can account for the several thousand sites of active RNA transcription and processing typically observed in the nucleus of a mammalian cell, each of which has a diameter of roughly 100nm and is estimated to contain, on average, about 10 RNA polymerase II molecules in addition to many other proteins. (C) Here, mRNA production factories and DNA replication factories have been visualized in the same mammalian cell by briefly incorporating differently modified nucleotides into each nucleic acid and detecting the RNA and DNA produced using antibodies, one (green) detecting the newly synthesized DNA and the other (red) detecting the newly synthesized RNA. (C, from D.G. Wansink et al., J. Cell Sci. 107:1449–1456, 1994. With permission from The Company of Biologists.) granule clusters—which contain stockpiles of RNA processing components—are often observed next to these sites of transcription, as though poised to replenish supplies. We can thus view the nucleus as organized into subdomains, with snRNPs, snoRNPs, and other nuclear components moving among them in an orderly fashion according to the needs of the cell.
Before the synthesis of a particular protein can begin, the corresponding mRNA molecule must be produced by transcription. Bacteria contain a single type of RNA polymerase (the enzyme that carries out the transcription of DNA into RNA). An mRNA molecule is produced after this enzyme initiates transcription at a promoter, synthesizes the RNA by chain elongation, stops transcription at a terminator, and releases both the DNA template and the completed mRNA molecule. In eukaryotic cells, the process of transcription is much more complex, and there are three RNA polymerases—polymerase I, II, and III—that are related evolutionarily to one another and to the bacterial polymerase.
RNA polymerase II synthesizes eukaryotic mRNA. This enzyme requires a set of additional proteins, both the general transcription factors, and specific transcriptional activator proteins, to initiate transcription on a DNA template. It requires still more proteins (including chromatin remodeling complexes and histone-modifying enzymes) to initiate transcription on its chromatin templates inside the cell.
During the elongation phase of transcription, the nascent RNA undergoes three types of processing events: a special nucleotide is added to its 5ʹ end (capping), intron sequences are removed from the middle of the RNA molecule (splicing), and the 3ʹ end of the RNA is generated (cleavage and polyadenylation). Each of these processes is initiated by proteins that travel along with RNA polymerase II by binding to sites on its long, extended C-terminal tail. Splicing is unusual in that many of its key steps are carried out by specialized RNA molecules rather than proteins. Only properly processed mRNAs are passed through nuclear pore complexes into the cytosol, where they are translated into protein.
For many genes, RNA, rather than protein, is the final product. In eukaryotes, these genes are usually transcribed by either RNA polymerase I or RNA polymerase