Transcription by RNA polymerase

Buratowski, S. The basics of basal transcription by RNA Polymerase II. Cell 77 1-3, 1994. 

Chen D, Ma H, Hong H, Koh SS, Huang SM, Schurter BT, Aswad DW, Stallcup MR (1999) Regulation of transcription by a protein methyltransferase. Science 284 2174-2177 Chubb JR, Boyle S, Perry P, Bickmore WA (2002) Chromatin motion is constrained by association with nuclear compartments in human cells. Curr Biol 12 439-445 Croston GE, Kadonaga JT (1993) Role of chromatin structure in the regulation of transcription by RNA polymerase II. Curr Opin Cell Biol 5 417-423... 

Table 1.L General initiation factors of transcription by RNA polymerase II After Roeder (1996). TAF TATA box binding protein associated factor TBP TATA box binding protein RNA Pol II RNA polymerase II...

Roeder, R.G. The role of general initiation factors in transcription by RNA polymerase II (1996) Trends Biochem. Sd. 21, 327-555... 

Examples of proteins that are specifically phosphorylated during the cell cycle are the lamins. Hyperphosphorylation of the lamins leads to disintegration of the nuclear lamina. Myosin in actin-myosin filaments is also specifically phosphorylated during mitosis. Other M-phase-specific phosphorylations occur at transcription factor TFIIIB, leading to inhibition of transcription by RNA polymerase III. Phosphorylation of TAP proteins (see 1.4.2.3) is also involved in general inhibition of banscription. 

MECHANISM FIGURE 26-1 Transcription by RNA polymerase in E. coli. For synthesis of an RNA strand complementary to one of two DNA strands in a double helix, the DNA is transiently unwound, (a) About 17 bp are unwound at any given time. RNA polymerase and the bound transcription bubble move from left to right along the DNA as shown facilitating RNA synthesis. The DNA is unwound ahead and rewound behind as RNA is transcribed. Red arrows show the direction in which the DNA must rotate to permit this process. As the DNA is rewound, the RNA-DNA hybrid is displaced and the RNA strand extruded. The RNA polymerase is in close contact with the DNA ahead of the transcription bubble, as well as with the separated DNA strands and the RNA within and immediately behind the bubble. A channel in the protein funnels new nucleoside triphosphates (NTPs) to the polymerase active site. The polymerase footprint encompasses about 35 bp of DNA during elongation. 

Fig. 2. Transcription by RNA polymerase. In each step the incoming ribonucleotide selected is that which can base-pair with the next base of the DNA template strand. In the diagram, the incoming nucleotide is rUTP to base-pair with the A residue of the template DNA. A 3 5 phosphodiester bond is formed, extending the RNA chain by one nucleotide, and pyrophosphate is released. Overall the RNA molecule grows in a 5 to 3 direction.

Fig. 3. Initiation of transcription by RNA polymerase II. TFIID binds to the TATA box followed in order by the binding of TFIIA, TFIIB and a pre-formed complex of TFIIF. RNA polymerase II. Subsequently TFIIE, TFIIH and TFIIJ bind in order and transcription then starts about 25 bp downstream from the TATA box. Note that the placement of the various factors in this diagram is arbitrary their exact positions in the complex are not yet known.

Yes. For this to occur, transcription by RNA polymerase would proceed through the segment of duplex DNA in opposite directions and from different promoters. Each strand of the duplex DNA would be functioning as both coding and template strands, but for two different RNA transcripts. 

Mauger E, Scott PH. 2004. Mitogenic stimulation of transcription by RNA polymerase III. Biochem Soc Trans 32 ... 

R. J. White and S.P. Jackson. 1992. The TATA-binding protein A central role in transcription by RNA polymerases 1,11 and 111 Trends Genet. 8 284-288. (PubMed)... 

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