Nuclear genome organization: common themes and individual patterns

Abstract

Gene loci are non-randomly organized. This applies to their linear arrangements on chromosomes, as well as to their spatial organization in the nucleus. Recent chromosome-wide and genome-wide studies give insights into which loci interact at the nuclear periphery with the lamina or nuclear pores. The functional role of peripheral localization in gene silencing is still unclear. Recent studies suggest that it regulates the silencing of some but not all loci. Active loci are enriched in the nuclear interior, and here they frequently associate with splicing speckles. Juxtaposition of chromosomal loci at such nuclear domains can falsely imply functional interactions. True functional interactions between chromosomal loci do, however, appear to regulate gene activity in many ways. Further detailed analyses of single genes as well as genome-wide studies will be required in order to unravel the complex interplay between nuclear organization and other regulatory systems in the control of individual loci.