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ITBP = TATA binding protein with the residues responsible for binding to the DNA (in purple spacefill)

1NIK= RNA Polymerase by itself

IR5U= Binding of RNA Polymerase to TFIIB (white)

RNA Polymerase :

There are 3 different types of RNA polymerase however, they are very similar in DNA sequences.

RNA polymerase I (Pol I): Transcribes ribosomal RNA (rRNA) and can be found in the nucleolus.  The transcriptional site contains a TATA-like sequence promoter, which is refer to as the ribosomal initiator element (RLNR).  Present upstream of this promoter (150-200 bp) is an upstream promoter element (UPE).  Binding of the RLNR and UPE aids in the recruitment of Pol I.

RNA polymerase II (Pol II ): Transcribes mRNA, which mostly codes for proteins. Pol II can be found in the nucleus of cells and fully functional Pol II is a 12-subunit protein. The association and disassociaton between Rpb7 and Rpb4 forms a heterodimer and associates reversibly with the core (10-subunit).  Pol II core alone can’t not start or participate in initiation but can be found in elongation.  Rpb7 interacts with both Rpb1 and Rpb6 and contains a ribonucleoprotein fold and oligonucleotide-binding fold.  The Rpb4/Rpb7 heterodimer was able to bind single stranded DNA and RNA and studies suggest that it interacts with RNA from the groove.  Due to its interactions with the groove, this suggests that Rpb4/Rpb7 has a possible role in the assembly of the initiation complex.  The heterodimer is located adjacent to the site of TFIIB and studies show that the heterodimer’s interaction with transcription factor IIB (TFIIB) increases the affinity towards the TATA box.  The N terminus of Rpb1 was shown to interact with Pol II forming part of the linker between the carboxyl terminal domain (CTD) and the body of Pol II.  CTD is also required for binding of the Mediator to Pol II [4].

RNA polymerase III (Pol III): Transcribes transfer RNA (tRNA) and other small RNA's. Pol III is considered a housekeeping gene and is less regulated then Pol II.

General Process:

Promoters: Initiation occurs at a consensus sequence known as the TATA box.  The TATA box is a repeated sequence of TATA and is located at -30 or -100, or 30 or 100 nucleotides upstream of the transcription start point (+1).  The TATA box is usually paired with an initiator sequence located between positions -3 to +5 called the initiator element (INR) and increases transcriptional activity. The INR determines the exact start site due to the large variable distances that other promoter elements lie.  Recruitment of transcription factors (TFII) aids in recognition and the completion of the initiation complex.  DPE (downstream core promoter element) may be found at +28 or +32 downstream of the start site but can also be found in genes that lack a TATA box. Other promoters such as the CAAT box or the GC box increases transcription activity. In addition, Mediators (regulatory signal transducters) also aid in specificity and binding of Pol II to a promoter. 

First, TFIIB is recognized and bound to Pol II by the zinc ribbon present on the N-terminal domain (NTD).  TFIID binds to the TATA box with the TBP (TATA-binding protiein) present on TFIID.  Binding to the DNA by TFIID bends the TATA box around allowing TFIIB to bind to the TBP-TATA box complex on the C terminal domain (CTD).  Next TFIIA interacts and binds to the DNA and TFIID stabilizing the interactions. TFIIF enters the complex and interacts with non-template DNA strand to speed up the polymerization process. TFIIE enters the complex and couples the Pol II promoter interaction along with recruiting TFIIH.  TFIIE helps open and close the ‘jaw-like” structure on Pol II to enable movement down the DNA strand.  TFIIH then enters the complex and has 3 main functions.  TFIIH is responsible for binding specifically to the template strand to ensure that the correct strand of DNA is transcribed.  The second function is the ATPase/Helicase activity  to separates the DNA. Lastly, TFIIH has kinase activity that can phosphorylate the CTD of Pol II.  With all these TFII’s and the Pol II this complex is called the initiation complex. Binding of TFIIB gives a space of 25 base pairs between the TATA box and the transcription start site, which, serves as a spacer and is vital [5] [6]

Additional notes on TFIIB: TFIIB also determines the location of the transcription start site.  This determination is considered a two-step process starting with TFIIB CTD binding to the TBP-TATA box complex and the TFIIB zinc ribbon binding to Pol II.  There is also evidence to support that TFIIB may aid in unwinding DNA prior to transcription initiation [7].

Enhancers: The binding of enhances (upstream activating sequences (UAS’s)) are required for gene –specific activation and recruitment of the Pol II.  The TBP or TBP-associated factors (TAF’s) component of the TFIID complex, and the 20 subunit Mediator complex, which associates with the Pol II core, to form the completed Pol II enzyme.  However, no TAF’s are universally required for transcription.  Srb4 and Srb6 are required for Pol II transcription in the Mediator complex. However, Pol II is not required for Mediators to bind to the enhancers.  For example, Mediators are able to associate with GAL UAS independently of Pol II [8]. 

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