Chromosome associations in budding yeast

The distribution of chromosomes within interphase nuclei is not random. First, in most species there exists a polarized arrangement of chromosome arms, the so-called Rabl orientation, where centromeres are assembled near one pole of the nucleus, while telomeres point towards the opposite pole [for examples from various organisms, see the following references (Foe and Alberts, 1985; Fussell, 1987; Dong and Jiang, 1998; Zickler and Kleckner, 1998; Jin et al., 2000; Goto et al., 2001)]. Second, there exist clear cases of somatic homologous pairing, especially in dipteran insects (Metz, 1916). Somatic pairing or transient homologous associations have been claimed to occur also in other organisms including budding yeast (Burgess and Kleckner, 1999; Burgess et al., 1999). Under certain circumstances, non-allelic chromosomal loci tend to co-localize within the nucleus (Nikiforova et al., 2000; Abranches et al., 2000). Moreover, specific chromosome regions often reside in subcompartments of the nucleus. Telomeres tend to be positioned near the nuclear periphery (Gotta et al., 1996). Tandem repeat regions often fuse into clusters described as ectopic heterochromatin pairing. These spatial relationships between specific chromosomal regions may underlie epigenetic phenomenons such as gene silencing or co-ordinated expression of genes or of the alleles of a gene (transvection) (Henikoff, 1997; Marshall et al., 1997a; Lamond and Earnshaw, 1998; Gasser, 2001). Since in most cell types it is impossible to trace individual chromosomes during interphase, fluorescence in situ hybridization has been used to label chromosomes or parts thereof to study their positions inside nuclei. As a means to investigate chromosome distribution and behaviour in living cells of various organisms, the lacO/LacI-GFP system was introduced (Straight et al., 1996; Belmont and Straight, 1998; Belmont, 2001). Also, the similar tetO/TetR-GFP system was used to study the segregation behaviour of chromosomes in live yeast cells (Michaelis et al., 1997). Both systems are based on the transgenic expression of a bacterial regulating protein fused to green fluorescent protein (GFP). The fusion protein then binds to a target DNA sequence, of which many copies are tandemly integrated into a specified chromosomal region, at which the GFP tags produce microscopically visible fluorescence. When we attempted to adapt the tetO/TetR-GFP system to study various aspects of chromosomal organization within S. cerevisiae interphase nuclei, we observed that integration of tetO repeats into chromosomes promotes the association of the target loci. Here, we describe the nature of these associations and their effect on the architecture of interphase nuclei. We also discuss whether mechanisms similar to those by which tetO repeats associate, could play a role in various nonrandom chromosomal interactions with putative functions in DNA repair and epigenetic regulation of gene expression.