Hearing loss genes reveal patterns of adaptive evolution at the coding and non-coding levels in mammals

Abstract Background Mammals possess unique hearing capacities that differ significantly from those of the rest of the amniotes. In order to gain insights into the evolution of the mammalian inner ear, we aim to identify the set of genetic changes and the evolutionary forces that underlie this proces...

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Autores principales:	Anabella P. Trigila, Francisco Pisciottano, Lucía F. Franchini
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Inner ear, Evolution, Hearing loss, Mammals, HARs, TSARs Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/f92c50289d434efcbe6399e53ffe25f7
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spelling	oai:doaj.org-article:f92c50289d434efcbe6399e53ffe25f72021-11-21T12:42:22ZHearing loss genes reveal patterns of adaptive evolution at the coding and non-coding levels in mammals10.1186/s12915-021-01170-61741-7007https://doaj.org/article/f92c50289d434efcbe6399e53ffe25f72021-11-01T00:00:00Zhttps://doi.org/10.1186/s12915-021-01170-6https://doaj.org/toc/1741-7007Abstract Background Mammals possess unique hearing capacities that differ significantly from those of the rest of the amniotes. In order to gain insights into the evolution of the mammalian inner ear, we aim to identify the set of genetic changes and the evolutionary forces that underlie this process. We hypothesize that genes that impair hearing when mutated in humans or in mice (hearing loss (HL) genes) must play important roles in the development and physiology of the inner ear and may have been targets of selective forces across the evolution of mammals. Additionally, we investigated if these HL genes underwent a human-specific evolutionary process that could underlie the evolution of phenotypic traits that characterize human hearing. Results We compiled a dataset of HL genes including non-syndromic deafness genes identified by genetic screenings in humans and mice. We found that many genes including those required for the normal function of the inner ear such as LOXHD1, TMC1, OTOF, CDH23, and PCDH15 show strong signatures of positive selection. We also found numerous noncoding accelerated regions in HL genes, and among them, we identified active transcriptional enhancers through functional enhancer assays in transgenic zebrafish. Conclusions Our results indicate that the key inner ear genes and regulatory regions underwent adaptive evolution in the basal branch of mammals and along the human-specific branch, suggesting that they could have played an important role in the functional remodeling of the cochlea. Altogether, our data suggest that morphological and functional evolution could be attained through molecular changes affecting both coding and noncoding regulatory regions.Anabella P. TrigilaFrancisco PisciottanoLucía F. FranchiniBMCarticleInner ear, Evolution, Hearing loss, Mammals, HARs, TSARsBiology (General)QH301-705.5ENBMC Biology, Vol 19, Iss 1, Pp 1-24 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Inner ear, Evolution, Hearing loss, Mammals, HARs, TSARs Biology (General) QH301-705.5
spellingShingle	Inner ear, Evolution, Hearing loss, Mammals, HARs, TSARs Biology (General) QH301-705.5 Anabella P. Trigila Francisco Pisciottano Lucía F. Franchini Hearing loss genes reveal patterns of adaptive evolution at the coding and non-coding levels in mammals
description	Abstract Background Mammals possess unique hearing capacities that differ significantly from those of the rest of the amniotes. In order to gain insights into the evolution of the mammalian inner ear, we aim to identify the set of genetic changes and the evolutionary forces that underlie this process. We hypothesize that genes that impair hearing when mutated in humans or in mice (hearing loss (HL) genes) must play important roles in the development and physiology of the inner ear and may have been targets of selective forces across the evolution of mammals. Additionally, we investigated if these HL genes underwent a human-specific evolutionary process that could underlie the evolution of phenotypic traits that characterize human hearing. Results We compiled a dataset of HL genes including non-syndromic deafness genes identified by genetic screenings in humans and mice. We found that many genes including those required for the normal function of the inner ear such as LOXHD1, TMC1, OTOF, CDH23, and PCDH15 show strong signatures of positive selection. We also found numerous noncoding accelerated regions in HL genes, and among them, we identified active transcriptional enhancers through functional enhancer assays in transgenic zebrafish. Conclusions Our results indicate that the key inner ear genes and regulatory regions underwent adaptive evolution in the basal branch of mammals and along the human-specific branch, suggesting that they could have played an important role in the functional remodeling of the cochlea. Altogether, our data suggest that morphological and functional evolution could be attained through molecular changes affecting both coding and noncoding regulatory regions.
format	article
author	Anabella P. Trigila Francisco Pisciottano Lucía F. Franchini
author_facet	Anabella P. Trigila Francisco Pisciottano Lucía F. Franchini
author_sort	Anabella P. Trigila
title	Hearing loss genes reveal patterns of adaptive evolution at the coding and non-coding levels in mammals
title_short	Hearing loss genes reveal patterns of adaptive evolution at the coding and non-coding levels in mammals
title_full	Hearing loss genes reveal patterns of adaptive evolution at the coding and non-coding levels in mammals
title_fullStr	Hearing loss genes reveal patterns of adaptive evolution at the coding and non-coding levels in mammals
title_full_unstemmed	Hearing loss genes reveal patterns of adaptive evolution at the coding and non-coding levels in mammals
title_sort	hearing loss genes reveal patterns of adaptive evolution at the coding and non-coding levels in mammals
publisher	BMC
publishDate	2021
url	https://doaj.org/article/f92c50289d434efcbe6399e53ffe25f7
work_keys_str_mv	AT anabellaptrigila hearinglossgenesrevealpatternsofadaptiveevolutionatthecodingandnoncodinglevelsinmammals AT franciscopisciottano hearinglossgenesrevealpatternsofadaptiveevolutionatthecodingandnoncodinglevelsinmammals AT luciaffranchini hearinglossgenesrevealpatternsofadaptiveevolutionatthecodingandnoncodinglevelsinmammals
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Hearing loss genes reveal patterns of adaptive evolution at the coding and non-coding levels in mammals

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