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

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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)<ref name="txn"/>. 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)<ref name="txn"/>. 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:


https://www.rcsb.org/structure/5VVS Use this for scene making




1. <scene name='86/862225/Tfiid/5'>TFIID</scene> is highly conserved among eukaryotes. It recognizes and binds the TATA region of DNA. This is facilitated by a subunit named the TATA-binding protein (TBP) that has antiparralel beta-sheet that provides a large surface for minor groove interactions. This subunit binding also causes major deformations in the helix which may be important for further binding of the PIC units by creating a more compact protein-DNA complex. As the complex begins to form the TBP-TATA complex remains unchanged. Its shape resembles that of a saddle sitting on the DNA. <ref name="txn"/>  
1. <scene name='86/862225/Tfiid/7'>TFIID</scene> is highly conserved among eukaryotes. It recognizes and binds the TATA region of DNA. This is facilitated by a subunit named the TATA-binding protein (TBP) that has antiparralel beta-sheet that provides a large surface for minor groove interactions. This subunit binding also causes major deformations in the helix which may be important for further binding of the PIC units by creating a more compact protein-DNA complex. As the complex begins to form the TBP-TATA complex remains unchanged. Its shape resembles that of a saddle sitting on the DNA. <ref name="txn"/>  


2. <scene name='86/862225/Tfiib/1'>TFIIB</scene> is the second to join the PIC. It is thought to be responsible for stabilizing the TBP/DNA complex and tethering the TFIID-DNA complex to RNAP I. It is also important in specifying the the TSS. In vitro studies have shown that accurate initiation can occur with only TFIID, TFIIB, and RNAP II suggesting that these two subunits serve to position RNAP. . Mutagenesis studies also suggest that it works as a spacer between TFIID and pol II. It may also function to ensure correct directionality. IF TBP binds the wrog end of TATA, TFIIB would have unfavorable interactions with TFB. <ref name="txn"/>  
2. <scene name='86/862225/Tfiib/2'>TFIIB</scene>> is the second to join the PIC. It is thought to be responsible for stabilizing the TBP/DNA complex and tethering the TFIID-DNA complex to RNAP I. It is also important in specifying the the TSS. In vitro studies have shown that accurate initiation can occur with only TFIID, TFIIB, and RNAP II suggesting that these two subunits serve to position RNAP. . Mutagenesis studies also suggest that it works as a spacer between TFIID and pol II. It may also function to ensure correct directionality. IF TBP binds the wrog end of TATA, TFIIB would have unfavorable interactions with TFB. <ref name="txn"/>  


3. <scene name='86/862225/Tfiif/1'>TFIIF</scene> binds directly to RNAP II and forms a very stable complex. It then escorts RNAP II to the promoter TFIIF also increases specificity and efficiency of transcription. It also acts similarly to bacterial sigma factor by inhibiting and reversing RNAP II binding to nonpromoter sites. (F)TFIIF is a hetero-dimer of 30 and 70 kDa. <ref name="txn"/>  
3. <scene name='86/862225/Tfiif/2'>TFIIF</scene> binds directly to RNAP II and forms a very stable complex. It then escorts RNAP II to the promoter TFIIF also increases specificity and efficiency of transcription. It also acts similarly to bacterial sigma factor by inhibiting and reversing RNAP II binding to nonpromoter sites. TFIIF is a hetero-dimer of 30 and 70 kDa. <ref name="txn"/>  


4.<scene name='86/862225/Tfiie/3'>TFIIE</scene> is required to begin transcription even though RNAP II is bound to DNA before TFIIE binds. Once bound it recruits TFIIH. TfIIE is  an α2β2 heterotetramer of 35 and 56 kDA. <ref name="txn"/>
4.<scene name='86/862225/Tfiie/6'>TFIEE</scene> is required to begin transcription even though RNAP II is bound to DNA before TFIIE binds. Once bound it recruits TFIIH. TfIIE is  an α2β2 heterotetramer of 35 and 56 kDA. <ref name="txn"/>


5.<scene name='86/862225/Tfiih/1'>TFIIH</scene> supports catalytic activity such as DNA ATPase, DNA helicase, and a kinase that phosphorylates the CTD of RPB1.<ref name="txn"/>(F) Some of its subunits are also components of DNA repair machinery. It is the last TF to bind and completes the <scene name='82/824648/Pic/3'>PIC</scene>.  
5.<scene name='86/862225/Tfiih/2'>TFIIH</scene> supports catalytic activity such as DNA ATPase, DNA helicase, and a kinase that phosphorylates the CTD of RPB1.<ref name="txn"/>(F) Some of its subunits are also components of DNA repair machinery. It is the last TF to bind and completes the <scene name='82/824648/Pic/3'>PIC</scene>.  


6.<scene name='82/824648/Tfiia/3'>TFIIA</scene> is a co-activator that helps regulate PIC assembly. It was initially thought to be essential for activity.  It binds to and stabilizes the early complexes. It also neutralizes transcription repressors. The mechanism is unknown but it is thought to either increase TBP affinity for DNA or displace repressors. (f)TFIIA binds to the N-terminal of TBP. It lies upstream, of TATA where it can interact with promoter and enhancer elements.<ref name="txn"/>  
6.<scene name='86/862225/Tfiia/2'>TFIAA</scene> is a co-activator that helps regulate PIC assembly. It was initially thought to be essential for activity.  It binds to and stabilizes the early complexes. It also neutralizes transcription repressors. The mechanism is unknown but it is thought to either increase TBP affinity for DNA or displace repressors. TFIIA binds to the N-terminal of TBP. It lies upstream, of TATA where it can interact with promoter and enhancer elements.<ref name="txn"/>  


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 help 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.   
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 help 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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