User:Jordan Scott/Sandbox RNA polII: Difference between revisions

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== General Transcription Factors ==
== General Transcription Factors ==


In both eukaryotes and prokaryotes, the basic mechanism for initiating transcription is the same: protein factors selectively bind to promoter regions on DNA. Prokaryotes use sigma factors while eukaryotes use a complex of 6 general transcription factors(GTFs). The combination of all the transcription factors bound to the DNA promoter region, in complex with RNAP II, is known as the preinitiation complex. This complex is necessary for an accurate initiation. The formation of the PIC occurs in an ordered pathway, beginning with the TATA box which is a promoter region on DNA at position -27.
In both eukaryotes and prokaryotes, the basic mechanism for initiating transcription is the same: protein factors selectively bind to promoter regions on DNA. Prokaryotes use sigma factors while eukaryotes use a complex of 6 general initiation factors(GIFs). The combination of all the transcription factors bound to the DNA promoter region, in complex with RNAP II, is known as the preinitiation complex. This complex is necessary for an accurate initiation. The formation of the PIC occurs in an ordered pathway, beginning with the TATA box which is a promoter region on DNA at position -27.


Process of PIC formation:
Process of PIC formation:


Source: https://www.pnas.org/content/94/1/151. <scene name='82/824648/Tfiid-tbp/3'>TFIID</scene> is highly conserved among eukaryotes. It recognizes and binds the TATA box. This is facillitated by a subunit named the TATA-binding protein (TBP). This subunit also causes slight deformations in the helix which may be important for further binding of the PIC units.  
Source: https://www.pnas.org/content/94/1/151.
1. <scene name='82/824648/Tfiid-tbp/3'>TFIID</scene> is highly conserved among eukaryotes. It recognizes and binds the TATA box. This is facilitated by a subunit named the TATA-binding protein (TBP). This subunit also causes slight deformations in the helix which may be important for further binding of the PIC units.  


2. <scene name='82/824648/Tfiib/3'>TFIIB</scene> and <scene name='82/824648/Tfiia/3'>TFIIA</scene> and interact with TBP and are recruited to the promoter.
2. <scene name='82/824648/Tfiib/3'>TFIIB</scene> is the second to join the PIC. It is thought to be responsible for stabilizing the TBP/DNA complex and insuring proper directionality . If the orientation is wring unfavorable interactions form. Mutagenesis studies also suggest that it works as a bridge between TFIID and pol II.


3. <scene name='82/824648/Tfiif/5'>TFIIF</scene> binds directly to RNAP II and escorts it to the promoter while TFIIB helps the complex bind correctly.  
3. <scene name='82/824648/Tfiif/5'>TFIIF</scene> binds directly to RNAP II and escorts it to the promoter while TFIIB helps the complex bind correctly.  


4. <scene name='82/824648/Tfiie/4'>TFIIE</scene> and <scene name='82/824648/Tfiih/3'>TFIIH</scene> are sequentually recruited which completes the <scene name='82/824648/Pic/3'>PIC</scene>.  
4. <scene name='82/824648/Tfiie/4'>TFIIE</scene> and <scene name='82/824648/Tfiih/3'>TFIIH</scene> are sequentially recruited which completes the <scene name='82/824648/Pic/3'>PIC</scene>.


5.<scene name='82/824648/Tfiia/3'>TFIIA</scene> is a co-activator that helps regulate PIC assembly. It serves as an enhancer and stabilizes the early complexes. It allows for inhibitory effect to be reduced and activators to be more effective. 




Once the <scene name='82/824648/Pic/3'>PIC</scene> is formed, <scene name='82/824648/Rnap_ii/1'>RNAP II</scene> initiates RNA synthesis and produces a short transcript. When RNAP II becomes phosphorylated, it releases some of the GTFs from the complex and moves away from the promoter. TFIID stays bound to the promoter and can reinitiate transcription. The transcription factors are replaced by a new six-protein complex call the Elongator. TFIIF and TFIIH both remain associated with RNAP II during elongation.  
Once the <scene name='82/824648/Pic/3'>PIC</scene> is formed, <scene name='82/824648/Rnap_ii/1'>RNAP II</scene> initiates RNA synthesis and produces a short transcript. When RNAP II becomes phosphorylated, it releases some of the GTFs from the complex and moves away from the promoter. TFIID stays bound to the promoter and can reinitiate transcription and hlep with successive transcription. The transcription factors are replaced by a new six-protein complex call the Elongator. TFIIF and TFIIH both remain associated with RNAP II during elongation.




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