Interchromosomal clustering of active genes at the nuclear pore complex

Abstract

Genomes are spatially organized on many levels and the positioning of genes within the nucleus contributes to their proper expression. This positioning can also result in the clustering of genes with similar expression patterns, a phenomenon sometimes called “gene kissing.” We have found that yeast genes are targeted to the nuclear periphery through interaction of the nuclear pore complex with small, cis-acting “DNA zip codes” in their promoters. Our recent study demonstrated that genes with the same zip codes cluster together at the nuclear periphery. The zip codes were necessary and sufficient to induce interchromosomal clustering. Finally, we identified a transcription factor (Put3) that binds to the GRS I zip code. Put3 binds to GRS I and is required for both GRS I-dependent positioning at the nuclear periphery and interchromosomal clustering of GRS I-targeted genes. We speculate that our findings might provide insight into other types of gene kissing, some of which also require cis-acting DNA sequences and trans-acting proteins.

Keywords: :

• nuclear pore complex
• transcription
• nuclear organization
• gene kissing
• nuclear body

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Acknowledgments

The authors would like to thank the members of the Brickner Lab for stimulating scientific discussions about this manuscript. The work in Brickner et al. (2012) was supported by NIH grant GM080484 and a W.M. Keck Young Scholars in Biomedical Research Award (J.H.B).