RNA Polymerase II Holoenzyme and Transcription Factors

Abstract

The transcription, which is the RNA (ribonucleic acid) biosynthesis, constitutes a tightly regulated multistep process involving the spatial and temporal recruitment of numerous protein complexes. The three main steps of the process are transcription initiation with the formation of the transcription preinitiation complex (PIC), elongation and termination. All these steps have in common the enzymatic activity of the protein complex known as the RNA polymerase II (RNAPII), which is an enzyme giving rise to the promoter‐specific protein complex called RNAPII holoenzyme. The composition of RNAPII holoenzyme (dependent on the extraction/purification process and the origin of the material) varies from laboratory to laboratory, but always includes RNAPII, general transcription factors (GTFs), protein mediators such as the suppressor of RNA polymerase B mutations (SRBs), histone acethyl transferase (HAT) and chromatin remodelling factors. This article focuses on the structure of RNAPII and the protein complex leading to the formation of RNAPII holoenzyme during the initiation step. The role of the main proteins allowing specific promoter recognition is detailed.

Key concepts:

  • The transcription is a regulated multistep process (initiation, elongation and termination) leading to RNA synthesis.

  • RNA polymerase synthesizes RNA in a DNA‐dependent manner.

  • Six RNA polymerases are known in eukaryote: RNAPI (synthesizing rRNAs), RNAPII (synthesizing mRNAs and snRNAs), RNAPIII (synthesizing tRNAs, 5S rRNA and some snRNAs), spRNAP‐IV (synthesizing mRNAs) and RNAP IV (synthesizing siRNA).

  • Transcription requires cis‐acting promoter elements (core and regulatory elements) and trans‐acting factors.

  • The core elements bind the transcription preinitiation complex (PIC) that include the GTFs (general transcription factor) and RNAPII.

  • Two main forms of RNAPII holoenzyme are identified, the SRB/MED‐containing and the PAF complex‐containing holoenzyme.

Keywords: transcription; initiation; RNA polymerase II; general transcription factor; core promoter; holoenzyme

Figure 1.

The RNA polymerase II (RNAPII) transcription initiation machinery. A typical RNAPII promoter includes core elements that define the start site of transcription and regulatory elements that affect transcription either positively or negatively. Core elements include the TATA box, which binds the TATA‐binding protein (TBP); the TFIIB‐responsive element (BRE); the initiation region (Inr), which encompasses the transcription start site; and downstream elements, which bind TBP‐associated factor (TAF) components of TFIID. Regulatory elements are typically located 50–1500 bp upstream of the core promoter and bind sequence‐specific factors that interact, either directly or indirectly, with the core machinery to stimulate (UAS) or repress (URS) transcription. The core machinery shown here includes RNAPII and the general transcription factors TFIID, composed of TBP and TAFs, TFIIB, TFIIE, TFIIF and TFIIH. TBP, presumably as a subunit of TFIID, binds the TATA box to nucleate assembly of the initiation complex, followed by association of the other factors, either stepwise or as components of an RNAPII holoenzyme complex. TFIIH catalyses open complex formation (promoter melting) and phosphorylation of the C‐terminal repeat domain (CTD) of RNAPII, followed by promoter clearance.

Figure 2.

Three‐dimensional structure of a human DNA–cTBP–cTFIIB ternary complex. The DNA template is shown as a stick figure displaying the template (blue) and coding (yellow) strands; the direction of transcription is indicated by the arrow. Core TATA‐binding protein (TBP) is shown as a ribbon drawing, depicting the N‐terminal (pink) and C‐terminal (red) domains. The N‐terminal (light green) and C‐terminal (dark green) repeat domains are shown. The C‐terminal domain of cTFIIB binds the TFIIB‐responsive element (BRE) upstream of TATA (Figure ). Figure courtesy of Francis Tsai and Paul Sigler, Yale University.

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Further Reading

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Nicolas, Moniaux, Jamila, Faivre, and Batra, Surinder K(Sep 2009) RNA Polymerase II Holoenzyme and Transcription Factors. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0003301.pub2]