RNA Polymerase II and Associated Transcription Factors

Abstract

Transcription of protein‐coding genes to messenger ribonucleic acid (mRNA) is a tightly regulated multistep process involving the spatial and temporal recruitment of numerous proteins and protein complexes to the genes. The three main steps of the process are transcription initiation with the formation of the transcription preinitiation complex, elongation, and termination. All these steps involve a protein complex known as RNA polymerase II that interacts with many factors during initiation, elongation and termination to regulate transcription, chromatin structure, mRNA processing and export, and associated deoxyribonucleic acid repair. This article focuses on RNA polymerase II and associated factors during transcriptional initiation and early stage of transcriptional elongation. RNA polymerase II C‐terminal domain phosphorylation and its functions in transcription cycle are also described. Further, a brief description of RNA polymerase II holoenzyme complexes is included here.

Key Concepts

  • Transcription is a multistep process consisting of initiation, elongation and termination for RNA (ribonucleic acid) synthesis.
  • RNA polymerase II (RNAPII) is a key enzyme/factor in transcription of the protein‐coding genes to messenger RNA (mRNA).
  • Transcriptional initiation of the protein‐coding genes occurs at the promoter via formation of the preinitiation complex (PIC), an assembly of general transcription factors (GTFs) and RNAPII.
  • The core elements of the promoter (or core promoter) are involved in formation of PIC for transcriptional initiation.
  • PIC formation at the core promoter is regulated by gene‐specific factors such as enhancers and repressors.
  • Shortly after transcriptional initiation, RNAPII pauses at the promoter‐proximal site, and subsequently, it is released following phosphorylation for productive transcriptional elongation.

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

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). Courtesy of Francis Tsai and Paul Sigler, Yale University.
Figure 3. RNA Polymerase II (RNAPII) C‐terminal domain (CTD) phosphorylation during active, paused and poised transcription cycles and its integration with chromatin modifications. (a) TFIIH phosphorylates Ser 5 residues of the hypo‐phosphorylated RNAPII at promoter region, which recruits HMT (Histone methyltransferase) to methylate H3K4. Transcription is usually aborted after 2–10 nucleotides (top cycle) as the initiating RNAPII is unstable. RNAPII then progresses to a pause site where it is halted by negative elongation factors. Pause release and productive elongation requires phosphorylation of Ser 2 residues by P‐TEFb. Ser 2 phosphorylation recruits HMT responsible for trimethylation of H3K36 and RNA processing factors. Subsequently, RNAPII terminates and dissociates from the full‐length transcript. RNAPII dissociation and recycling is mediated by phosphatases. (b) At many inactive genes, Ser 5 phosphorylated RNAPII remains paused in the promoter‐proximal regions in the absence of detectable expression, a phenomenon known as promoter‐proximal pausing. However, it is now known that all paused genes produce full‐length transcripts at low levels (light red arrow). Paused genes contain low levels of H3K4 trimethylation. The release of RNAP II from promoter‐proximal pausing is a universally important regulation checkpoint that primes genes for future activation. (c) Major cell‐identity genes contain poised RNAPII that becomes phosphorylated at Ser 5 but lacks Ser 7 or Ser 2 phosphorylation. Whether poised RNAPII undergoes abortive cycles of initiation (top cycle) or pausing is not clear. Elongation occurs even in the absence of Ser 2 phosphorylation and transcripts are generated at low levels. The CTD of poised RNAPII harbours a configuration (indicated by yellowtail) that is not recognized by an antibody that preferentially binds to nonphosphorylated Ser 2 residues (8WG16) and thus might contain undefined CTD modifications or conformation. ?, implies that some of the details of that portion of the transcription cycle are not known or incompletely understood.
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Further Reading

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Karmakar, Saswati, Ponnusamy, Moorthy P, Bhaumik, Sukesh R, and Batra, Surinder K(Oct 2018) RNA Polymerase II and Associated Transcription Factors. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0003301.pub3]