SUMMARY Active genes in yeast can be targeted to the nuclear periphery through interaction of cis-acting “DNA zip codes” with the nuclear pore complex. We find that genes with identical zip codes cluster together. This clustering was specific; pairs of genes that were targeted to the nuclear periphery by different zip codes did not cluster together. Insertion of two different zip codes (GRS I or GRS III) at an ectopic site induced clustering with endogenous genes having that zip code. Targeting to the nuclear periphery and interaction with the nuclear pore is a pre-requisite for gene clustering, but clustering can be maintained in the nucleoplasm. Finally, we find that the Put3 transcription factor recognizes the GRS I zip code to mediate both targeting to the NPC and interchromosomal clustering. These results suggest that zip code-mediated clustering of genes at the nuclear periphery influences the three-dimensional arrangement of the yeast genome.

The nucleus is a spatially organized compartment. The most obvious way in which this is achieved is at the level of chromosomes. The positioning of chromosomes with respect to nuclear landmarks and with respect to each other is both non-random and cell-type specific. This suggests that cells possess molecular mechanisms to influence the folding and disposition of chromosomes within the nucleus. The localization of many proteins is also heterogeneous within the nucleus. Therefore, chromosome folding and the localization of proteins leads to a model in which individual genes are positioned in distinct protein environments that can impact their transcriptional state. Here, we focus on the spatial organization of the nucleus and how it impacts gene expression.