Chapter category: Gene Expression
Chromatin 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 chromatin structure of a gene can be a major determinant of its transcrip-tional activity (reviewed in refs. 1–8). In chromatin, 146 bp of DNA is wrapped approximately twice around a nucleosome core comprising two molecules each of histones H2A, H2B, H3 and H4, arranged as two H2A/H2B dimers associated with a central (H3/H4)2 tetramer.9–12 Each of the core histones has a very similar C-terminal domain structure, containing three or four a-helices arranged in a "histone fold".12,13 Within this structure, a long central helix forms a dimerization interface and is flanked on each side by a loop and a shorter helix.12,13 Dimerization creates the DNA-binding surfaces, although the specific interfaces between the histone heterodimers are not extensive and have the potential for conformational flexibility.11–13 The C-terminal domains of the core histones make substantial protein-DNA contacts.11,12,14 Indeed, continuous contact of the histones with DNA is required for stable binding.11 The N-terminal tails of the core histones protrude outside the nucleosome.12,13
The flanking DNA is preferentially bound by a single molecule of a linker histone, most usually H1.11,15 Linker histones contain a DNA-binding domain called the "winged helix", which consists of a bundle of three a-helices attached to a three-stranded anti-parallel b-sheet.13 Linker histones also have basic N- and C-terminal domains that influence the path of the linker DNA between nucleosomes.13 H2A/H2B heterodimers need to be present to allow the stable association of linker histones with nucleosomal DNA.14,16 The linker histone interacts predominantly with one end of the nucleosomal DNA close to the surface of the octamer core and protects an additional 20 bp of DNA from micrococcal nuclease digestion, ~5 bp to one side of the core and ~15 bp to the other side.11,16,17 It may be able to adopt a variety of positions.11 Traditionally, the linker histone was thought to be located just outside the nucleosome, clamping the DNA as it enters and exits.18 However, the globular domain of H5 has been shown to interact in a more intimate manner with a nucleosome positioned on the X. borealis somatic 5S gene, making direct contacts with H2A and H2B, and binding DNA at a single location inside the superhelical gyres that wrap around the core particle.14,19 Association of the linker histone may cause allosteric changes in the histone octamer that could stabilize core histone contacts at the periphery of the nucleosome.11,14
Additional chapters from this book:
Perspective
Robert J. White
Our understanding of the details of pol III transcription has increased substan-tially in recent years. The characterization and cloning of many of the components of the system have been ac...
Regulation of RNA Polymerase III Transcription
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There are two families of active 5S genes in Xenopus laevis. One consists of the somatic 5S genes, of which there are 400 copies per haploid genome, organized in a single cluster.
Proteins that Modulate the Rate of RNA Polymerase III Transcription
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So far I have described the basal pol III transcription apparatus and how this functions to allow expression of class III genes. The level of transcription can be modulated in either a posi...
Chromatin Structure of Class III Genes
Robert J. White
The chromatin structure of a gene can be a major determinant of its transcrip-tional activity (reviewed in refs. 1–8). In chromatin, 146 bp of DNA is wrapped approximately twice around...
Transcription
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Once a preinitiation complex has formed on a yeast tRNA gene, RNA chain ini-tiation requires a further 5 min at 22°C (half-life ~2 min).1 During this period, three successiv...
Transcription Complex Formation on Class III Genes
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The formation of transcription complexes, composed of factors bound to DNA, was initially investigated by means of the template exclusion assay. This approach monitors the ability of a gene...
Transcription Factors Utilized by RNA Polymerase III
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Purified pol III initiates transcription randomly.1–4 Accurate and specific initia-tion requires the assistance of transcription factors in order to recruit the polymerase t...
RNA Polymerase III
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Pol III is the largest of the nuclear RNA polymerases, with an aggregate molecular weight of 600700 kD (reviewed by Thuriaux and Sentenac1–3). This is, perhaps, surprising s...
Promoter Structure of Class III Genes
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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 noness...
Class III Genes
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The genes transcribed by pol III encode a variety of small RNA molecules. (Table 1) Many of these have essential functions in cellular metabolism, such as tRNA and 5S rRNA, which are required ...
