Work

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

Year: 2025

Type: article

Abstract: New genes can emerge de novo from non-genic genomic regions. In budding yeast, computational predictions have shown that intergenic regions harbour a higher-than-expected propensity to encode transmembrane domains, if theoretically translated into proteins. 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. These tracts are known to function as nucleosome-depleted regions, which prevent or reduce nucleosome formation to enable transcription of surrounding genes. We provide evidence that these polyA/T tracts have been repeatedly coopted through de novo gene emergence for the evolution of novel small genes encoding proteins with predicted transmembrane domains. These findings support a previously proposed "transmembrane-first" model of de novo gene birth and help explain why evolutionarily young yeast genes are rich in transmembrane domains. They contribute to our understanding of the process of de novo gene evolution and show how seemingly distinct but potentially interacting levels of functionality can exist within the same genomic loci.

Source: Journal of Evolutionary Biology

DOI: 10.1093/jeb/voaf089

Authors: Nikolaos Vakirlis, Timothy Fuqua

Institutions: Pasteur Hellenic Institute, SIB Swiss Institute of Bioinformatics, University of Zurich

Language: English

Topic: Chromosomal and Genetic Variations

Subfield: Plant Science

Field: Agricultural and Biological Sciences

Domain: Life Sciences

Open Access status: hybrid

Estimated APC paid: $3,123

Funders: Universität Zürich, Hellenic Foundation for Research and Innovation