Intergenic polyA/T tracts explain the propensity of yeast de novo genes to encode transmembrane domains

Abstract

New genes can emerge de novo from non-genic genomic regions. In budding yeast, computational predictions have shown that intergenic regions harbor a higher-than-expected propensity to encode transmembrane domains, and this propensity seems to be linked to the high prevalence of predicted transmembrane domains in evolutionarily young genes. However, what accounts for this enriched propensity is not known. Here we show that specific arrangements of polyA/T tracts, which are abundant and enriched in yeast intergenic regions explain this observation. We provide evidence that polyA/T tracts, which are known to act as Nucleosome Depleted Regions in a regulatory context, have been coopted through de novo gene emergence for the evolution of novel small genes encoding proteins with predicted transmembrane domains. Our findings contribute to our understanding of the process of de novo gene evolution and show how seemingly distinct but interacting levels of functionality can exist within the same genomic loci.