Chapter category: Gene Expression
Promoter Structure of Class III Genes
RNA Polymerase III Transcription
Second Edition
Edited by: Robert J. WhiteISBN: 1-57059-482-1
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Chapter authors:
Robert J. White
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The promoters of most class III genes include discontinuous intragenic structures, termed internal control regions (ICRs), that are composed of essential sequence blocks separated by nonessential nucleotides. The ICRs of 5S rRNA genes are sometimes referred to as type I. These comprise two functional domains: an A-block and a second domain consisting of an intermediate element and a C-block. Most class III genes, including tRNA, VA, Alu, EBER, 7SL, 4.5S, B1, and B2 genes, have type II ICRs: these again have two domains, an A-block and a B-block. The A-blocks of types I and II are homologous and can substitute for one another in Xenopus,1 although not in Neurospora.2 The A-block is located much further from the start site in type I than it is in type II promoters. As well as the ICR, extragenic sequences can also affect the strength of type I and II promoters. However, substitutions in the extragenic regions are generally well tolerated, unlike mutations in the ICR. In contrast, with type III promoters, such as those of the vertebrate U6 and 7SK genes, transcription is independent of intragenic elements and is dictated solely by 5' flanking regions.3–8 A schematic illustration of the three types of class III promoter is provided in Figure 1.
ICR sequences are highly conserved between different genes and different species. In contrast, the flanking sequences of type I and II promoters frequently show little or no conservation, although they can often have powerful modulatory effects. This suggests that the flanking sequences are more likely to be recognized by gene- or species-specific factors, or that their cognate factors have very flexible DNA-binding specificities.
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