Literature review of the conversion of RNA into DNA.

With particular emphasis on the biochemistry, discuss the machinery involved in the transcriptional process.

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...y increase the affinity of TBP for the TATA box (Imbalzano et al., 1994). Regulatory proteins have been shown to bind TFIIB and prevent it from associating with TBP, thereby affecting transcription (Colgan et al., 1995). TFIIB also plays a role in recruiting Pol II for eventual transcription (Huh et al., 1999). As well, recruitment of Pol II by TFIIB determines the correct transcriptional start site (Li et al., 1994).
After the formation of this pre-initiation complex, Pol II binds to another transcription factor, TFIIF, and then this complex is recruited by the pre-initiation complex of TFIIA/TBP/TFIIB (Nogales 2000). After binding of the Pol II/TFIIF complex the DNA wraps around the polymerase, which aids in transcription initiation (Robert et al., 1998; Kuhlman et al., 1999).
TFIIE and TFIIH are the next factors to join the growing complex giving a basal complex with a total mass of nearly 2 megadaltons (Dvir et al., 2001). TFIIE interacts with TBP and TFIIF and it also binds to Pol II (Maxon et al., 1994). TFIIE also plays a role in recruiting TFIIH to the basal complex, thus completing the pre-initiation steps. TFIIH functions to unwind the DNA template at the transcriptional start site in an ATP-dependent fashion (Roy et al., 1994). Apart from the role in transcription, TFIIH can also repair DNA damage by a nucleotide-excision based pathway (Wang et al., 1994). TFIIH is the only general transcription factor that binds into the basal complex that has an enzymatic activity (Drapkin and Reinberg, 1994).
A mutation in a subunit results in a less stable complex. If the complex cannot bind stably to the TATA box and Pol II the transcription rate will be decreased (Bangur et al., 1997). Most of these mechanisms are based on independent in vitro models. The timing of the complex assembly is inferred from these studies. As a result, the timing of the coming together of the subunits has not been fully elucidated. Understanding the timing of the binding will give more insight into the level of control in transcription.

After the basal complex is complete, the next step in transcription is elongation. Before this takes place, Pol II must escape from the promoter region. Following formation of the initiation complex the transcription factors release from the complex and can go on to other promoter areas or even be reused for that particular gene (Zawel et al., 1995). TBP remains bound to the TATA box consensus sequence while the other general transcription factors are released from the basal complex. After Pol II initiates transcription, about 9-13 bases downstream of the transcriptional start site, there is a good chance of arrest of this growing chain unless Pol II becomes "escape competent" (Dvir et al., 1996). Being escape competent means release of the appropriate attached general transcription factors allowing Pol II to move downstream along the DNA template. After TFIIB is released it re-associates with TFIID and can then recruit another Pol II (Zawel et al., 1995). TFIIE releases after the tenth nucleotide is added and TFIIH releases once Pol II reaches the +30 location (Zawel et al., 1995). Once these factors are released Pol II escapes and can elongate the growing RNA strand by the addition of ribonucleotides. Before the 30th nucleotide is added Pol II can stall, aborting transcription. Elongation depends on Pol II escape by the polymerase getting past +30 (Zawel et al., 1995).
As Poll II moves along the template strand, a ribonucleotide is added to the growing nascent (new) strand of pre-mRNA. The template strand (anti-sense strand) of DNA is the strand read by Pol II and the sense strand is the other strand, which is ignored by Pol II. The nascent strand is the exact sequence of the sense strand of DNA but uracil is present in the nascent strand in place of thymine.
While the RNA transcript is growing there is a great deal of control mediated by several transcription factors (Reines et al., 1996; Kim et al., 2001). The arrest of Pol II during transcription is mediated by positive elongation factors (P-TEFs) and negative elongation factors (N-TEFs). During the early stages of transcript elongation, N-TEFs can stop Pol II whereas P-TEFs allow Pol II to continue transcription (Dvir et al., 1996). This stalling of the transcriptional process by N-TEFs may be a mechanism that allows for processing of environmental cues that regulate gene transcription. While Pol II is stalled the transcript remains as a short oligonucleotide until a cue from a P-TEF re-initiates elongation.
Most of the data on the control of elongation has been derived from in vitro model systems where the rate of elongation is considerably slower than it is in vivo (Ucker and Yamamoto, 1984). In vivo, Pol II can add nucleotides at the rate of over 2000 per minute, but under in vitro conditions this rate drops to ~300 nucleotides per minute (Ucker and Yamamoto, 1984). Pol II pauses several times during the in vitro elongation process and this contributes to the slower rate. This data indicates both the importance of the general transcription factors for ensuring a fast rate of transcription and suggests that the in vitro system, as it is currently understood, must still be missing some element(s) compared with the in vivo system that prevents Pol II from pausing.
There are two different types of P-TEFs that are classified according to their proposed function. The transcription factors TFIIF, SIII, ELL and ELL2 all aid transcription by modifying the Km and increasing the Vmax of the enzymatic activity of Pol II (Shilatifard, 1998). The other type includes P-TEFb, SII, and heat shock factor 1 (HSF1), which increase transcription by other methods aimed at preventing arrest of Pol II (Reines, 1996; Shilatifard, 1998).
TFIIF binds to Pol II early on during assembly of the initiation steps and remains bound to Pol II during the elongation step. The other factors SIII, ELL and ELL2 stop the pausing of the Pol II, which occurs at numerous points along the DNA template (Shilatifard, 1998). Suppression of ...