Transcription factors and elongation of RNA chains in eukaryotes

Content
Expression of Gene : Protein Synthesis 2.  Transcription in Prokaryotes and Eukaryotes
Transcription in prokaryotes 
Single RNA polymerase in E. coli
Promoter sites for initiation of transcription in prokaryotes
Initiation and elongation of RNA synthesis in prokaryotes
'Inchworm model' for elongation of transcript
Elongation arrest vs termination of transcription
Termination and antitermination of mRNA synthesis in prokaryotes
Transcription in eukaryotes 
Multiple RNA polymerases in eukaryotes
Promoter, enhancer and silencer sites for initiation of transcription in eukaryotes
Transcription factors and initiation of RNA synthesis in eukaryotes
Formation of preinitiation (transcription) complex with RNA polymerase II (Pol II)
Structure and role of TFIID and other transcription factors (TBP, TAFs)
TFIIB domains for interaction with TFIID/TATA complex
Phosphorylation of CTD of a subunit of Pol II
Formation of pre-initiation complex with Pol I and Pol III
Separate DNA binding and transcription activation domains
Transcription factors and elongation of RNA chains in eukaryotes
Chromatin structure and transcription
Transcription in mitochondria
Transcription of vertebrate mtDNA
Transcription of yeast and plant mtDNA
Transcription in chloroplasts


Transcription factors and elongation of RNA chains in eukaryotes
Certain accessory proteins of transcription, called the 'elongation factors', enhance the overall activity of RNA polymerase II, leading to increase in elongation rate. Atleast two such proteins (transcription factors) are known (i) The transcription factor TFIIF accelerates RNA chain growth relatively uniformly, in concert with RNA polymerase II or Pol II. (ii) The transcription factor TFIIS (also called SII) helps elongation of RNA chain, by relieving the obstructions in the path of such elongation. TFIIS is known to function by first causing hydrolytic cleavage at 3' ends of RNA chains, which are stuck and can not elongate. Thus, RNA polymerase moves backwards (hydrolytic cleavage) under the direction of TFIIS before it moves forward through the block to elongation (Fig. 32.27). It is possible that hydrolytic activity resides in Pol II and is enhanced by TFIIS (second largest subunit of Pol II has regions of homology with bacterial ribonuclease; see Fig. 32.12).

Prokaryotic elongation factors, Gre A and Gre B (discovered in 1992-93) also cause hydrolytic cleavage at 3' end of nascent RNA in E. coli.
 
The role of TFIIS in elongation of RNA chain (see text for details).
Fig. 32.27. The role of TFIIS in elongation of RNA chain (see text for details).

Functional regions of the second largest subunit of RNA polymerase II of Drosophila. Solid bar shows similarity with barnase and other bacterial RNAses; A to I are regions having homology with prokaryotic RNA polymerase.
Fig. 32.12. Functional regions of the second largest subunit of RNA polymerase II of Drosophila. Solid bar shows similarity with barnase and other bacterial RNAses; A to I are regions having homology with prokaryotic RNA polymerase.

Termination of RNA synthesis in eukaryotes AAUAAA sequence and 'snurp' in post-transcriptional cleavage. In eukaryotes, the actual termination of RNA polymerase II activity during transcription may take place through termination sites similar to those found in prokaryotes (the nature of individual termination sites in not known). But these termination sites are believed to be present away (sometimes upto one kilobase away) from the site of the 3' end of mRNA. Obviously 3' end of mRNA will be generated due to post-transcriptional cleavage. This cleavage, at the end, is believed to be achieved by what is popularly called 'snurp' (small nuclear RNA-protein complex). 'Snurp' used for post-transcription cleavage has not been identified so far but is believed to be certainly different than the U1 snurp, which is believed to be involved in intron splicing in split genes (see Expression of Gene : Protein Synthesis 3.  RNA Processing (RNA Splicing, RNA Editing and Ribozymes)). Moreover, a sequence 5'AAUAAA 3' has been found just on the 5' side of poly(A) addition site in several eukaryotic mRNAs (e.g. αand βglobins in mouse and ovalbumin in chicken). We will notice in the next topic that poly(A) tail is added to 3' end of eukaryotic mRNA after processing of precursor mRNA. The sequence 5'AAUAAA3' in mRNA 3' end seems to be common in eukaryotic mRNA and mutations in this sequence cause elongation of mRNA. This will suggest that this sequence contains the signal for endonucleolytic post-transcriptional cleavage. This sequence, therefore, is not involved in the termination of the synthesis of mRNA, but helps in generating 3' end later through endonuclease cleavage, in which snurp helps in an unknown manner.