Figure 6–22 eukaryotic RNA polymerase II as an “RNA factory.” As the polymerase transcribes DNA into RNA, it carries RNA-processing proteins on its tail that are transferred to the nascent RNA at the appropriate time. The tail contains 52 tandem repeats of a seven-amino-acid sequence, and there are two serines in each repeat. The capping proteins first bind to the RNA polymerase tail when it is phosphorylated on Ser5 of the heptad repeat late in the process of transcription initiation (see Figure 6–15). This strategy ensures that the RNA molecule is efficiently capped as soon as its 5ʹ end emerges from the RNA polymerase. As the polymerase continues transcribing, its tail is extensively phosphorylated on the Ser2 positions by a kinase associated with the elongating polymerase and is eventually dephosphorylated at Ser5 positions. These further modifications attract splicing and 3ʹ-end processing proteins to the moving polymerase, positioning them to act on the newly synthesized RNA as it emerges from the RNA polymerase. There are many RNA-processing enzymes, and not all travel with the polymerase. For RNA splicing, for example, the tail carries only a few critical components; once transferred to an RNA molecule, they serve as a nucleation site for the remaining components.
When RNA polymerase II finishes transcribing a gene, it is released from DNA, soluble phosphatases remove the phosphates on its tail, and it can reinitiate transcription. Only the fully dephosphorylated form of RNA polymerase II is competent to begin RNA synthesis at a promoter.
a reverse linkage (5ʹ to 5ʹ instead of 5ʹ to 3ʹ), and a third (a methyl transferase) adds a methyl group to the guanosine (Figure 6–23). Because all three enzymes bind to the RNA polymerase tail phosphorylated at the Ser5 position—the modification added by TFIIH during transcription initiation— they are poised to modify the 5ʹ end of the nascent transcript as soon as it emerges from the polymerase.
The 5ʹ-methyl cap signifies the 5ʹ end of eukaryotic mRNAs, and this landmark helps the cell to distinguish mRNAs from the other types of RNA molecules present in the cell. For example, RNA polymerases I and III produce uncapped RNAs during transcription, in part because these polymerases lack a CTD. In the nucleus, the cap binds a protein complex called CBC (cap-binding complex), which, as we discuss in subsequent sections, helps a future mRNA be further processed and exported. The 5ʹ-methyl cap also has an important role in the translation of mRNAs in the cytosol, as we discuss later in the chapter.
5˜ end of nascent RNA transcript
As discussed in Chapter 4, the protein-coding sequences of eukaryotic genes are typically interrupted by noncoding intervening sequences (introns). Discovered 5˜ 3˜ in 1977, this feature of eukaryotic genes came as a surprise to scientists, who had been, until that time, familiar only with bacterial genes, which typically consist of a continuous stretch of coding DNA that is directly transcribed into mRNA. In marked contrast, eukaryotic genes were found to be broken up into small pieces of coding sequence (expressed sequences or exons) interspersed with much longer intervening sequences or introns; thus, the coding portion of a eukaryotic gene is often only a small fraction of the length of the gene (Figure 6–24).