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Intergenic Regions of Saccharomycotina Yeasts are Enriched in Potential to Encode Transmembrane Domains
Intergenic genomic regions have essential regulatory and structural roles that impose constraints on their sequences. But regions that do not currently encode proteins also carry the potential to do so in the future. De novo gene emergence, the evolution of novel genes out of previously noncoding se...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10063215/ https://www.ncbi.nlm.nih.gov/pubmed/36917489 http://dx.doi.org/10.1093/molbev/msad059 |
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author | Tassios, Emilios Nikolaou, Christoforos Vakirlis, Nikolaos |
author_facet | Tassios, Emilios Nikolaou, Christoforos Vakirlis, Nikolaos |
author_sort | Tassios, Emilios |
collection | PubMed |
description | Intergenic genomic regions have essential regulatory and structural roles that impose constraints on their sequences. But regions that do not currently encode proteins also carry the potential to do so in the future. De novo gene emergence, the evolution of novel genes out of previously noncoding sequences has now been established as a potent force for genomic novelty. Recently, it was shown that intergenic regions in the genome of Saccharomyces cerevisiae harbor pervasive cryptic potential to, if theoretically translated, form transmembrane domains (TM domains) more frequently than expected by chance given their nucleotide composition, a property that we refer to as TM-forming enrichment. The source and biological relevance of this property is unknown. Here, we expand the investigation into the TM-forming potential of intergenic regions to the entire Saccharomycotina budding yeast subphylum, in an effort to explain this property and understand its importance. We find pervasive but variable enrichment in TM-forming potential across the subphylum regardless of the composition and average size of intergenic regions. This cryptic property is evenly spread across the genome, cannot be explained by the hydrophobic content of the sequence, and does not appear to localize to regions containing regulatory motifs. This TM-forming enrichment specifically, and not the actual TM-forming potential, is associated, across genomes, with more TM domains in evolutionarily young genes. Our findings shed light on this newly discovered feature of yeast genomes and constitute a first step toward understanding its evolutionary importance. |
format | Online Article Text |
id | pubmed-10063215 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-100632152023-03-31 Intergenic Regions of Saccharomycotina Yeasts are Enriched in Potential to Encode Transmembrane Domains Tassios, Emilios Nikolaou, Christoforos Vakirlis, Nikolaos Mol Biol Evol Discoveries Intergenic genomic regions have essential regulatory and structural roles that impose constraints on their sequences. But regions that do not currently encode proteins also carry the potential to do so in the future. De novo gene emergence, the evolution of novel genes out of previously noncoding sequences has now been established as a potent force for genomic novelty. Recently, it was shown that intergenic regions in the genome of Saccharomyces cerevisiae harbor pervasive cryptic potential to, if theoretically translated, form transmembrane domains (TM domains) more frequently than expected by chance given their nucleotide composition, a property that we refer to as TM-forming enrichment. The source and biological relevance of this property is unknown. Here, we expand the investigation into the TM-forming potential of intergenic regions to the entire Saccharomycotina budding yeast subphylum, in an effort to explain this property and understand its importance. We find pervasive but variable enrichment in TM-forming potential across the subphylum regardless of the composition and average size of intergenic regions. This cryptic property is evenly spread across the genome, cannot be explained by the hydrophobic content of the sequence, and does not appear to localize to regions containing regulatory motifs. This TM-forming enrichment specifically, and not the actual TM-forming potential, is associated, across genomes, with more TM domains in evolutionarily young genes. Our findings shed light on this newly discovered feature of yeast genomes and constitute a first step toward understanding its evolutionary importance. Oxford University Press 2023-03-14 /pmc/articles/PMC10063215/ /pubmed/36917489 http://dx.doi.org/10.1093/molbev/msad059 Text en © The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Discoveries Tassios, Emilios Nikolaou, Christoforos Vakirlis, Nikolaos Intergenic Regions of Saccharomycotina Yeasts are Enriched in Potential to Encode Transmembrane Domains |
title | Intergenic Regions of Saccharomycotina Yeasts are Enriched in Potential to Encode Transmembrane Domains |
title_full | Intergenic Regions of Saccharomycotina Yeasts are Enriched in Potential to Encode Transmembrane Domains |
title_fullStr | Intergenic Regions of Saccharomycotina Yeasts are Enriched in Potential to Encode Transmembrane Domains |
title_full_unstemmed | Intergenic Regions of Saccharomycotina Yeasts are Enriched in Potential to Encode Transmembrane Domains |
title_short | Intergenic Regions of Saccharomycotina Yeasts are Enriched in Potential to Encode Transmembrane Domains |
title_sort | intergenic regions of saccharomycotina yeasts are enriched in potential to encode transmembrane domains |
topic | Discoveries |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10063215/ https://www.ncbi.nlm.nih.gov/pubmed/36917489 http://dx.doi.org/10.1093/molbev/msad059 |
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