The expression of genes is regulated at many levels. Perhaps the area in which least is known is how nuclear organization influences gene expression. Studies of higher-order chromatin arrangements and their dynamic interactions with other nuclear components have been boosted by recent technical advances. The emerging view is that chromosomes are compartmentalized into discrete territories. The location of a gene within a chromosome territory seems to influence its access to the machinery responsible for specific nuclear functions, such as transcription and splicing. This view is consistent with a topological model for gene regulation.

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Chromosome territories, nuclear architecture and gene regulation in mammalian cells.

tion of gene expression and other nuclear functions — namely the architecture of the nucleus as a whole. In particular, we describe evidence for a compartmentalized nuclear architecture in the mammalian cell nucleus based on chromosome territories (CTs) and an interchromatin compartment (IC) that contains macromolecular complexes that are required for replication, transcription, splicing and repair (summarized in FIG. 1). Other nuclear components, such as the nucleolus, nuclear lamina and pores, are not reviewed here (for reviews, see REFS 15,16), and although the focus of this review is the mammalian nucleus, the nuclear architecture of other organisms will be mentioned where appropriate. During the past two decades, various new methods have expanded the cell biologist’s ‘toolkit’ for the study of nuclear architecture and function (BOX 1). These methods have provided the basis for detailed studies of CTs, as well as for studies of the topology and dynamics of non-chromatin domains in the nucleus of fixed and, more recently, living cells. Computer simulations of CTs and nuclear architecture are also being used to make quantitative predictions that can be tested experimentally. On the basis of Despite all the celebrations associated with the sequencing of the human genome, and the genomes of other model organisms, our abilities to interpret genome sequences are quite limited. For example, we cannot understand the orchestrated activity — and the silencing — of many thousands of genes in any given cell just on the basis of DNA sequences, such as promoter and enhancer elements. How are the profound differences in gene activities established and maintained in a large number of cell types to ensure the development and functioning of a complex multicellular organism? To answer this question fully, we need to understand how genomes are organized in the nucleus, the basic principles of nuclear architecture and the changes in nuclear organization that occur during cellular differentiation. During recent years, EPIGENETIC mechanisms of gene regulation, such as DNA methylation and histone modification, have entered the centre stage of chromatin research. Modifications of DNA and nucleosomes, however, as well as boundaries and insulators, that affect gene regulation at the chromatin level are not the focus of this article. Instead, we review experimental data and models for a higher level of the regulaCHROMOSOME TERRITORIES, NUCLEAR ARCHITECTURE AND GENE REGULATION IN MAMMALIAN CELLS

Nuclear architecture and gene regulation in mammalian cells

The Determination of Nucleic Acids

Identification of a nuclear protein matrix.

DNA REPLICATION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 276 TRANSCRIPTION AND PRE-mRNA PROCESSING .... . . ) ....... ,.... 279 Localization of Transcriptionally Active Nuclear Regions by [ HJ-Uridine Incorporation or In Situ Nick Translation . . . . . . . . . . . . . . . . 279 Pre-mRNA Splicing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 280 An Arginine/Serine-Rich Domain Targets Proteins to Nuclear Speckles . . . . . . 284 Effect of RNA Polymerase II Transcription on the Localization of Splicing Factors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ,.... 285 Distribution of hnRNP Proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 287 Localization of Splicing Factors in the Amphibian Germinal Vesicle . . . . . . . . 289 Localization of Splicing Factors in Yeast 290 Distribution of Poly(A)'t RNA . . . . . . ... . . . . ..... . ..... . . . . .... 291 Distribution of Specific Cellular Transcripts . . . . . . . . . . . . . . . . . . . . . . . 291 NUCLEOLAR ORGANIZATION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 293

Macromolecular domains within the cell nucleus.

Effects of thioacetamide on the composition and biosynthesis of nucleolar and nuclear ribonucleic acid in rat liver.

One hour after the injection of 5 µc. of l-lysine-U-C14 into each of a group of normal rats bearing the Walker 256 carcinosarcoma, isolated nuclei were prepared from liver and tumor. The nuclei were fractionated by extraction with 0.14 m NaCl, 0.10 m Tris buffer, 2.0 m NaCl, and 0.05 n NaOH, in that order. The initial 2.0 m NaCl fraction was fractionated into histones, acid-insoluble proteins, and phenol-insoluble proteins. Most of the fractions were characterized by their amino acid composition, NH2-terminal amino acid composition, nucleic acid content, and specific activity.

Although the amino acid analyses of most of the fractions were remarkably similar in the higher concentrations of glutamic and aspartic acids than the basic amino acids, the glutamic acid content of a number of fractions of liver was higher than that of the tumor, and individual fractions differed in their content of glycine, leucine, lysine, serine, and valine. The major NH2-terminal amino acids were found to be serine, alanine, glycine, lysine, and aspartic acid in the nonhistone fractions. The over-all distribution of nuclear proteins was similar for isolated nuclei of liver and Walker tumor, with the exception of the Tris, alkali-soluble, and histone fractions, which were greater in amount in the tumor. In liver, the specific activities (counts/min/mg) of the acidic nuclear protein fractions, other than those of the nuclear sap, were highest, and the specific activity of the histone fraction was the lowest. In the Walker tumor, the specific activity of the histones was greater than that of the acidic proteins. In both the liver nuclei and those of the Walker tumor, 75 per cent of the total lysine incorporated into nuclear proteins was incorporated into deoxyribonucleoproteins. Of this, two-thirds was found in the acidic proteins in the liver and one-third was found in the histones; in the tumor, two-thirds of the lysine incorporated into the nuclear proteins was found in the histones, and only one-third was found in the acidic nuclear proteins.

William J. Steele

Papers

Effects of thioacetamide on the composition and biosynthesis of nucleolar and nuclear ribonucleic acid in rat liver.

Studies on acidic nuclear proteins of the walker tumor and liver.

A nuclear ribonucleoprotein network

Synthesis of 28-S RNA in the nucleolus

Isolation of nucleoli.