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Region-specific expression of young small-scale duplications in the human central nervous system

BACKGROUND: The duplication of genes is one of the main genetic mechanisms that led to the gain in complexity of biological tissue. Although the implication of duplicated gene expression in brain evolution was extensively studied through comparisons between organs, their role in the regional special...

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Autores principales: Brohard-Julien, Solène, Frouin, Vincent, Meyer, Vincent, Chalabi, Smahane, Deleuze, Jean-François, Le Floch, Edith, Battail, Christophe
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8059171/
https://www.ncbi.nlm.nih.gov/pubmed/33882820
http://dx.doi.org/10.1186/s12862-021-01794-w
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author Brohard-Julien, Solène
Frouin, Vincent
Meyer, Vincent
Chalabi, Smahane
Deleuze, Jean-François
Le Floch, Edith
Battail, Christophe
author_facet Brohard-Julien, Solène
Frouin, Vincent
Meyer, Vincent
Chalabi, Smahane
Deleuze, Jean-François
Le Floch, Edith
Battail, Christophe
author_sort Brohard-Julien, Solène
collection PubMed
description BACKGROUND: The duplication of genes is one of the main genetic mechanisms that led to the gain in complexity of biological tissue. Although the implication of duplicated gene expression in brain evolution was extensively studied through comparisons between organs, their role in the regional specialization of the adult human central nervous system has not yet been well described. RESULTS: Our work explored intra-organ expression properties of paralogs through multiple territories of the human central nervous system (CNS) using transcriptome data generated by the Genotype-Tissue Expression (GTEx) consortium. Interestingly, we found that paralogs were associated with region-specific expression in CNS, suggesting their involvement in the differentiation of these territories. Beside the influence of gene expression level on region-specificity, we observed the contribution of both duplication age and duplication type to the CNS region-specificity of paralogs. Indeed, we found that small scale duplicated genes (SSDs) and in particular ySSDs (SSDs younger than the 2 rounds of whole genome duplications) were more CNS region-specific than other paralogs. Next, by studying the two paralogs of ySSD pairs, we observed that when they were region-specific, they tend to be specific to the same region more often than for other paralogs, showing the high co-expression of ySSD pairs. The extension of this analysis to families of paralogs showed that the families with co-expressed gene members (i.e. homogeneous families) were enriched in ySSDs. Furthermore, these homogeneous families tended to be region-specific families, where the majority of their gene members were specifically expressed in the same region. CONCLUSIONS: Overall, our study suggests the involvement of ySSDs in the differentiation of human central nervous system territories. Therefore, we show the relevance of exploring region-specific expression of paralogs at the intra-organ level. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12862-021-01794-w.
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spelling pubmed-80591712021-04-22 Region-specific expression of young small-scale duplications in the human central nervous system Brohard-Julien, Solène Frouin, Vincent Meyer, Vincent Chalabi, Smahane Deleuze, Jean-François Le Floch, Edith Battail, Christophe BMC Ecol Evol Research Article BACKGROUND: The duplication of genes is one of the main genetic mechanisms that led to the gain in complexity of biological tissue. Although the implication of duplicated gene expression in brain evolution was extensively studied through comparisons between organs, their role in the regional specialization of the adult human central nervous system has not yet been well described. RESULTS: Our work explored intra-organ expression properties of paralogs through multiple territories of the human central nervous system (CNS) using transcriptome data generated by the Genotype-Tissue Expression (GTEx) consortium. Interestingly, we found that paralogs were associated with region-specific expression in CNS, suggesting their involvement in the differentiation of these territories. Beside the influence of gene expression level on region-specificity, we observed the contribution of both duplication age and duplication type to the CNS region-specificity of paralogs. Indeed, we found that small scale duplicated genes (SSDs) and in particular ySSDs (SSDs younger than the 2 rounds of whole genome duplications) were more CNS region-specific than other paralogs. Next, by studying the two paralogs of ySSD pairs, we observed that when they were region-specific, they tend to be specific to the same region more often than for other paralogs, showing the high co-expression of ySSD pairs. The extension of this analysis to families of paralogs showed that the families with co-expressed gene members (i.e. homogeneous families) were enriched in ySSDs. Furthermore, these homogeneous families tended to be region-specific families, where the majority of their gene members were specifically expressed in the same region. CONCLUSIONS: Overall, our study suggests the involvement of ySSDs in the differentiation of human central nervous system territories. Therefore, we show the relevance of exploring region-specific expression of paralogs at the intra-organ level. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12862-021-01794-w. BioMed Central 2021-04-21 /pmc/articles/PMC8059171/ /pubmed/33882820 http://dx.doi.org/10.1186/s12862-021-01794-w Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research Article
Brohard-Julien, Solène
Frouin, Vincent
Meyer, Vincent
Chalabi, Smahane
Deleuze, Jean-François
Le Floch, Edith
Battail, Christophe
Region-specific expression of young small-scale duplications in the human central nervous system
title Region-specific expression of young small-scale duplications in the human central nervous system
title_full Region-specific expression of young small-scale duplications in the human central nervous system
title_fullStr Region-specific expression of young small-scale duplications in the human central nervous system
title_full_unstemmed Region-specific expression of young small-scale duplications in the human central nervous system
title_short Region-specific expression of young small-scale duplications in the human central nervous system
title_sort region-specific expression of young small-scale duplications in the human central nervous system
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8059171/
https://www.ncbi.nlm.nih.gov/pubmed/33882820
http://dx.doi.org/10.1186/s12862-021-01794-w
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