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Review
. 2010 Feb;119(1):13-25.
doi: 10.1007/s00412-009-0236-2. Epub 2009 Aug 30.

Spatial organization of genes as a component of regulated expression

Dave A Pai  1 , David R Engelke
Affiliations
Review

Spatial organization of genes as a component of regulated expression

Dave A Pai et al. Chromosoma. 2010 Feb.

Abstract

The DNA of living cells is highly compacted. Inherent in this spatial constraint is the need for cells to organize individual genetic loci so as to facilitate orderly retrieval of information. Complex genetic regulatory mechanisms are crucial to all organisms, and it is becoming increasingly evident that spatial organization of genes is one very important mode of regulation for many groups of genes. In eukaryotic nuclei, it appears not only that DNA is organized in three-dimensional space but also that this organization is dynamic and interactive with the transcriptional state of the genes. Spatial organization occurs throughout evolution and with genes transcribed by all classes of RNA polymerases in all eukaryotic nuclei, from yeast to human. There is an increasing body of work examining the ways in which this organization and consequent regulation are accomplished. In this review, we discuss the diverse strategies that cells use to preferentially localize various classes of genes.

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Figures

Fig. 1
Fig. 1
Methods of linear gene organization. Eukaryotic cells have developed a variety of ways to arrange genetic information on the linear map to regulate gene expression. From top to bottom: Operons, which are transcribed as a single polycistronic transcript under control of an upstream operator; Linear clusters, such as the HOX genes, which are under control of a common regulator; Small RNAs, such as microRNAs, which are transcribed as a polycistronic unit and then processed into smaller RNAs; the Pol I-transcribed ribosomal repeats, transcribed in eukaryotes as a 35S transcript and then processed into 18S, 5.8S, and 28S rRNAs; and the small Pol III-transcribed 5S genes, which in most eukaryotes are present in tandemly repeated linear clusters
Fig. 2
Fig. 2
Comparison of yeast and metazoan nucleoli. The eukaryotic nucleolus is defined by the Pol I-transcribed ribosomal cluster. In yeast, the ribosomal cluster is located on the linear map in one group on chromosome XII; consequently, the yeast nucleolus can be visualized by FISH microscopy as a single crescent-shaped structure, typically localized to one side of the nucleus. In yeast, the tRNA genes can be visualized by FISH microscopy as a single cluster localized to the nucleolus. Metazoans generally have multiple clusters of ribosomal genes; thus, metazoan nuclei usually have several nucleoli spread throughout the nucleus. The metazoan nucleus is generally several times larger than the yeast nucleus
Fig. 3
Fig. 3
FISH microscopy showing distribution of mouse B2 SINE elements. Mouse embryonic fibroblasts were fixed in 1% paraformaldehyde and adhered to slides. Fluorescent oligonucleotides complementary to B2 SINEs hybridized to genomic DNA. There appears to be speckled signal of B2 elements throughout the nucleoplasm, suggesting clusters, but this signal appears not to be preferentially associated with either the nucleoli or the nuclear periphery. Red B2 SINE DNA, blue DAPI stain of AT-rich heterochromatin
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