Transcription elongation phase

Fig. 1.32. Phosphorylation of the C-terminal domain of RNA polymerase II and the beginning of transcription. The transition from the initiation complex to actual begin of transcription is regulated via phosphorylation of the C-terminal domain (CTD) of RNA polymerase II. In the above model it is assumed that initially a complex is formed between TFIID and a holoenzyme of RNA polymerase consisting of RNA polymerase II and associated factors (mediators, SRB proteins) and the basal transcription factors. Phosphorylation of the C-terminal domain effects the dissociation of the RNA polymerase from the initation complex and the transition to the elongation phase. A protein kinase, which is part of TFIIH, is responsible for the phosphorylation. The nature of the signal that induces phosphorylation of RNA polymerase II remains unknown. SRB suppressor of RNA polymerase B. After Koleske and Young (1995).

Unlike DNA polymerase, RNA polymerase does not require a primer to initiate synthesis. Initiation occurs when RNA polymerase binds at specific DNA sequences called promoters (described below). The 5 -triphos-phate group of the first residue in a nascent (newly formed) RNA molecule is not cleaved to release PPj, but instead remains intact throughout the transcription process. During the elongation phase of transcription, the growing end of the new RNA strand base-pairs temporarily with the DNA template to form a short hybrid... 

RNA Strand Initiation and Promoter Clearance TFIIH has an additional function during the initiation phase. A kinase activity in one of its subunits phosphorylates Pol II at many places in the CTD (Fig. 26-9). Several other protein kinases, including CDK9 (cyclin-dependent kinase 9), which is part of the complex pTEFb (positive transcription elongation/actor b), also phosphorylate the... 

CTD. This causes a conformational change in the overall complex, initiating transcription. Phosphorylation of the CTD is also important during the subsequent elongation phase, and it affects the interactions between the transcription complex and other enzymes involved in processing the transcript (as described below). 

During synthesis of the initial 60 to 70 nucleotides of RNA, first TFIIE and then TFIIH is released, and Pol II enters the elongation phase of transcription. 

The extent of methylation of a gene is correlated with its ability to transcribe. Given that DNA methylation usually reduces transcription, two important, closely related questions remain unanswered How is methylation regulated in vivo How does methylation interfere with transcription Since methylation is known not to interfere with the elongation phase of RNA synthesis, it seems likely that methylation blocks initiation. The binding of polymerase and other regulatory proteins at the initiation locus is sensitive to modification of these nucleotides. The precise inhibition mechanisms, however, await further elucidation. 

Eukaryotic cells contain at least four different DNA-dependent RNA polymerases. Their localization, cellular transcripts, and susceptibility to the cyclic octapeptide a-amanitin (derived from poisonous mushrooms) are shown in Table 11.3. a-Amanitin blocks the elongation phase of RNA synthesis. Although the structures of these enzymes are much more complex than that of the prokaryotic RNA polymerase, the basic mechanism is very similar to that of the prokaryotic enzyme. 

The drug rifampin binds to bacterial RNA polymerases and is a useful experimental inhibitor of initiation of transcription. It binds to the P subunit of RNA polymerase, blocking the transition from the chain initiation phase to the elongation phase it is an inhibitor of chain initiation but not of elongation. Actinomycin D also inhibits initiation but does so by binding to DNA. These drugs have limited clinical use because of their toxicity. 

Eukaryotic cells have three types of RNA polymerases. Binding of RNA polymerase II to its promoters requires an array of proteins called transcription factors. Elongation factors participate in the elongation phase of transcription. The largest subunit of Pol II has a long carboxyl-terminal domain, which is phosphorylated during the initiation and elongation phases. 

Backtracking of Pol II during the elongation phase can lead to transcriptional pausing and arrest. Pausing and arrest are blocks to transcription that... 

The elongation phase of transcription is affected by the presence or absence of specific protein factors, called elongation factors, such as GreA and GreB for E. coli RNA Pol and TFllS for eukaryotic RNA Pol 11. The stimulation of transcriptional elongation is attributed, at least in part, to the elongation factor-associated 3 — 5 hydrolytic activity which enables the stalled RNA Pol complex to retract from the transcription barriers (e.g., pause sites) and to repeat the forward synthesis, eventually overcoming the barriers. 

Transcription exhibits three phases initiation, elongation, and termination. All are dependent upon distinct DNA czV-elements and can be modulated by distinct tranS jzim protein factors. 

LIKE TRANSCRIPTION, PROTEIN SYNTHESIS CAN BE DESCRIBED IN THREE PHASES INITIATION, ELONGATION, TERMINATION... 

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