Eukaryotic Gene Transcription: Nuclear RNA polymerases

There are three distinct types of RNA pol in the nucleus of eukaryotic cells. All are large enzymes with multiple subunits. Each type of RNA pol recognizes particular genes. [Note: Mitochondria contain a single RNA pol that resembles the bacterial enzyme.]
1. RNA polymerase I: This enzyme synthesizes the precursor of the 28S, 18S, and 5.8S rRNA in the nucleolus.
2. RNA polymerase II: This enzyme synthesizes the nuclear precursors of mRNA that are processed and then translated to proteins. RNA pol II also synthesizes certain small ncRNA, such as snoRNA, snRNA, and miRNA.
a. Promoters for RNA polymerase II: In some genes transcribed by RNA pol II, a sequence of nucleotides (TATAAA) that is nearly identical to that of the Pribnow box  is found centered ~25 nucleotides upstream of the transcription start site. This core promoter consensus sequence is called the TATA, or Hogness, box. In the majority of genes, however, no TATA box is present. Instead, different core promoter elements such as Inr (initiator) or DPE (downstream promoter element) are present (Fig. 1). [Note: No one consensus sequence is found in all core promoters.] Because these sequences are on the same molecule of DNA as the gene being transcribed, they are cis-acting. The sequences serve as binding sites for proteins known as general transcription factors (GTF), which in turn interact with each other and with RNA pol II.

Figure 1: Eukaryotic gene cis-acting promoter and regulatory elements and their trans-acting general and specific transcription factors (GTF and STF, respectively). Inr = initiator; DPE = downstream promoter element.
b. General transcription factors: GTF are the minimal requirements for recognition of the promoter, recruitment of RNA pol II to the promoter, formation of the preinitiation complex, and initiation of transcription at a basal level (Fig. 2A). GTF are encoded by different genes, synthesized in the cytosol, and diffuse (transit) to their sites of action, and so are trans-acting. [Note: In contrast to the prokaryotic holoenzyme, eukaryotic RNA pol II does not itself recognize and bind the promoter. Instead, TFIID, a GTF containing TATA-binding protein and TATA-associated factors, recognizes and binds the TATA box (and other core promoter elements). TFIIF, another GTF, brings the polymerase to the promoter. The helicase activity of TFIIH melts the DNA, and its kinase activity phosphorylates polymerase, allowing it to clear the promoter.]

Figure 2: A. Association of the general transcription factors (TFII) and RNA polymerase II (RNA pol II) at the core promoter. [Note: The Roman numeral II denotes a TF for RNA pol II.] B. Enhancer stimulation of transcription. CTF = CAAT box transcription factor; Sp1 = specificity factor-1.
c. Regulatory elements and transcriptional activators: Additional consensus sequences lie upstream of the core promoter (see Fig. 2). Those close to the core promoter (within ~200 nucleotides) are the proximal regulatory elements, such as the CAAT and GC boxes. Those farther away are the distal regulatory elements such as enhancers . Proteins known as transcriptional activators or specific transcription factors (STF) bind these regulatory elements.
STF bind to promoter proximal elements to regulate the frequency of transcription initiation and to distal elements to mediate the response to signals such as hormones  and regulate which genes are expressed at a given point in time. A typical protein-coding eukaryotic gene has binding sites for many such factors. STF have two binding
domains. One is a DNA-binding domain, the other is a transcription activation domain that recruits the GTF to the core promoter as well as coactivator proteins such as the HAT enzymes involved in chromatin modification. [Note: Mediator, a multisubunit coactivator of RNA pol II–catalyzed transcription, binds the polymerase, the GTF, and the STF and regulates transcription initiation.]
Transcriptional activators bind DNA through a variety of motifs, such as the helix-loop-helix, zinc finger, and leucine zipper .

d. Role of enhancers: Enhancers are special DNA sequences that increase the rate of initiation of transcription by RNA pol II. Enhancers are typically on the same chromosome as the gene whose transcription they stimulate (Fig. 3B). However, they can 1) be located upstream (to the 5′-side) or downstream (to the 3′-side) of the transcription start site, 2) be close to or thousands of base pairs away from the promoter (Fig. 4), and 3) occur on either strand of the DNA. Enhancers contain DNA sequences called response elements that bind STF. By bending or looping the DNA, STF can interact with other TF bound to a promoter and with RNA pol II, thereby stimulating transcription (see Fig. 3B). Mediator also binds enhancers. [Note: Although silencers are similar to enhancers in that they also can act over long distances, they reduce gene expression.]

Figure 4: Some possible locations of enhancer sequences.
e. RNA polymerase II inhibitor: α-Amanitin, a potent toxin produced by the poisonous mushroom Amanita phalloides (sometimes called the “death cap”), binds RNA pol II tightly and slows its movement, thereby inhibiting mRNA synthesis.
3. RNA polymerase III: This enzyme synthesizes tRNA, 5S rRNA, and some snRNA and snoRNA.