The nucleus is a highly compartmentalised organelle. Associations of genomic loci with nuclear structures are correlated with gene activity or silencing, and functional long-range interactions between loci in the same or different chromosomes have been described recently. Therefore, chromosome organisation confers potential for the spatial regulation of gene expression. . Chromosomes occupy distinct territories during interphase, and previous models of chromosome organisation had suggested that there is little or no intermingling between them. However, the frequency of chromosome translocations and the existence of interchromosomal associations seemed to indicate otherwise. I used a high-resolution approach to study chromosome organisation in human lymphocytes and showed that chromosomes intermingle significantly during interphase, with implications in translocations. Changes in transcription affect chromosome organisation and, in particular, transcription inhibition influences chromosome intermingling in a specific manner, suggesting that transcription-dependent long-range interactions help to establish preferential chromosomal neighbourhoods. To gain mechanistic insights into the formation of interchromosomal associations, I investigated a previously reported i6teraction between the TH2 locus and lfng in murine naIve T cells. I found no evidence for a close and direct interaction between the two loci, although they are indirectly non-randomly positioned in relation to each other, possibly by sharing associations with a large nuclear structure. Finally, I studied the role of nuclear organisation in the regulation of a gene-dense cluster in the mouse genome, before and after the insertion of a strong enhancer element. Nuclear organisation seems to benefit clustering of genes in the genome by promoting and maintaining active states across th~ loc'!ls, but expression of individual genes is further regulated by other mechanisms, such as longrange interactions via chromatin looping. My work brings new insights into the organisation of chromosomes in the mammalian nucleus, and its relationship with transcription and gene regulation.