RNA Polymerases

There are three distinct classes of RNA polymerase—RNA polymerase I, RNA polymerase II, and RNA polymerase III—in the nucleus of eukaryotic cells, and they are designed to carry out transcription. RNA polymerase I synthesizes large rRNA molecules. RNA polymerase II is mainly used to yield mRNA and, subsequently, proteins. RNA polymerase III produces snRNA, small rRNA, and tRNA molecules. Each class of RNA polymerase recognizes particular types of genes. However, RNA polymerases do not bind to DNA directly. Rather, they are recruited to DNA by other proteins that bind to promoters (Figure 2-2).

FIGURE 2-2. Transcription factors and RNA polymerase II complex.

FIGURE 2-2. Transcription factors and RNA polymerase II complex.

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Typical transcription factors contain DNA-binding domains, protein dimerization domains, and transcription activation domains. Some transcription factors (e.g., cAMP response element-binding protein [CREB]) may be modified by phosphorylation. The transcription activation domain interacts with an RNA polymerase II (Pol II) complex to induce transcription. TATA binding protein (TBP) binds to the TATA box element and associates with general transcription factors (TFII). This gene transcription apparatus recruits Pol II to the appropriate gene.

mRNA is transcribed from DNA by RNA polymerase II with heterogeneous nuclear RNA (hnRNA), an intermediate product. The core promoter recognized by RNA polymerase II is the TATA box (Hogness box), a sequence rich in nucleotides A and T, which is usually located 25-30 bases upstream of the transcription start site. The TATA box determines the start site of transcription and orients the basal transcription complex that binds to DNA and recruits RNA polymerase II to the TATA box; thus, it establishes the 5' to 3' direction in which RNA polymerase II synthesizes RNA. The formation of the basal transcription complex is promoted by a TATA binding protein (TBP) that binds to a core promoter, together with multiple TBP-associated factors and other general transcription factors. Enhancers are DNA sequences that increase the rate of initiation of transcription by RNA polymerase II through its interaction with transcription factors, which can be located "upstream" or "downstream" of the transcription start site. Enhancer elements are important to cell-specific and stimulus-dependent expression of hnRNA. Some RNA polymerase II species, including those for many genes that are expressed in neurons, lack a TATA box and possess instead an initiator, a poorly conserved genetic promoter element.

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