How Nuclear Structure and Organisation Influence Gene Expression

Mankind is defined by a genetic blue-print encoded in a haploid genome of roughly 3 x 10⁹ bp of DNA. Simplifying the locating of genes responsible for different genetic defects has been one of the justifications behind initiatives to sequence the human genome. Once the sequence and location of putative genes is established it is a relatively simple matter to identify cell types in which they are expressed. A better understanding of gene function in mammalian cells will be part of the solution in identifying how different diseases might be related to individual genetic defects.

DNA sequence provides the information required to activate gene expression. However, eukaryotic nuclei are so intricate that this information is not sufficient to predict either levels or patterns of gene expression in individual cells. A variety of epigenetic features must influence critical aspect of nuclear function in mammalian cells.

The aim of our research is to establish how nuclear structure and organisation influence gene expression in mammalian cells. We have shown that eukaryotic nuclei are highly structured and that the major nuclear processes all take place at specialised nuclear sites (Figure 1). Dedicated nuclear sites can be identified in cells growing in medium supplemented with the transcription precursor analogue Bromo-uridine. This is introduced into the nascent RNA chains and can be subsequently identified using specific antibodies. In this example, the sites of transcription (green) are distributed throughout the dispersed euchromatin (blue - a green fluorescent protein-histone shows the distribution of open and condensed chromatin) and excluded from the speckles (red - immunostained for Sm proteins) that define an important nuclear compartment involved in RNA processing. Interactions within these compartments generate chromatin domains that are intimately linked to gene expression and form part of an organisational hierarchy that must be fundamental to both the structure and function of eukaryotic chromatin. Understanding how chromosome structure and nuclear organisation influence gene expression is of fundamental importance. A detailed picture of the features that influence gene expression is vital if we are to be successful in developing gene therapy.

Publications

Iborra F, Cook PR and Jackson DA (2003) Applying microscopy to the analysis of nuclear structure and function. Methods. 29:131-41.

Jackson DA (2002) Location, location, location--the nuclear view. Chromosome Res. 10:615-20.

Jackson DA (2002) Chromosome structure and nuclear architecture: implications for gene therapy. Curr Opin Mol Ther. 4:290-8.

Iborra FJ, Jackson DA and Cook PR (2001) Coupled transcription and translation within nuclei of mammalian cells. Science. 293:1139-42.

Pombo A, Jones E, Iborra FJ, Kimura H, Sugaya K, Cook PR and Jackson DA (2000) Specialized transcription factories within mammalian nuclei. Crit Rev Eukaryot Gene Expr. 10:21-9.

Jackson DA, Pombo A and Iborra F. (2000) The balance sheet for transcription: an analysis of nuclear RNA metabolism in mammalian cells. FASEB J. 14:242-54.

Jackson DA (2000) Features of nuclear architecture that influence gene expression in higher eukaryotes: confronting the enigma of epigenetics. J Cell Biochem Suppl. 35:69-77.

Funding

The Leukaemia Research Fund, BBSRC