Locus-specific analysis of Transposable Elements during the progression of ALS in the SOD1G93A mouse model.

Transposable Elements (TEs) are ubiquitous genetic elements with the ability to move within a genome. TEs contribute to a large fraction of the repetitive elements of a genome, and because of their nature, they are not routinely analyzed in RNA-Seq gene expression studies. Amyotrophic Lateral Sclero...

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Autores principales:	Braulio Valdebenito-Maturana, Esteban Arancibia, Gonzalo Riadi, Juan Carlos Tapia, Mónica Carrasco
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/98fedb6517924a538b22278207bbf30b
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spelling	oai:doaj.org-article:98fedb6517924a538b22278207bbf30b2021-12-02T20:17:16ZLocus-specific analysis of Transposable Elements during the progression of ALS in the SOD1G93A mouse model.1932-620310.1371/journal.pone.0258291https://doaj.org/article/98fedb6517924a538b22278207bbf30b2021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0258291https://doaj.org/toc/1932-6203Transposable Elements (TEs) are ubiquitous genetic elements with the ability to move within a genome. TEs contribute to a large fraction of the repetitive elements of a genome, and because of their nature, they are not routinely analyzed in RNA-Seq gene expression studies. Amyotrophic Lateral Sclerosis (ALS) is a lethal neurodegenerative disease, and a well-accepted model for its study is the mouse harboring the human SOD1G93A mutant. In this model, landmark stages of the disease can be recapitulated at specific time points, making possible to understand changes in gene expression across time. While there are several works reporting TE activity in ALS models, they have not explored their activity through the disease progression. Moreover, they have done it at the expense of losing their locus of expression. Depending on their genomic location, TEs can regulate genes in cis and in trans, making locus-specific analysis of TEs of importance in order to understand their role in modulating gene expression. Particularly, the locus-specific role of TEs in ALS has not been fully elucidated. In this work, we analyzed publicly available RNA-Seq datasets of the SOD1G93A mouse model, to understand the locus-specific role of TEs. We show that TEs become up-regulated at the early stages of the disease, and via statistical associations, we speculate that they can regulate several genes, which in turn might be contributing to the genetic dysfunction observed in ALS.Braulio Valdebenito-MaturanaEsteban ArancibiaGonzalo RiadiJuan Carlos TapiaMónica CarrascoPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 10, p e0258291 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Braulio Valdebenito-Maturana Esteban Arancibia Gonzalo Riadi Juan Carlos Tapia Mónica Carrasco Locus-specific analysis of Transposable Elements during the progression of ALS in the SOD1G93A mouse model.
description	Transposable Elements (TEs) are ubiquitous genetic elements with the ability to move within a genome. TEs contribute to a large fraction of the repetitive elements of a genome, and because of their nature, they are not routinely analyzed in RNA-Seq gene expression studies. Amyotrophic Lateral Sclerosis (ALS) is a lethal neurodegenerative disease, and a well-accepted model for its study is the mouse harboring the human SOD1G93A mutant. In this model, landmark stages of the disease can be recapitulated at specific time points, making possible to understand changes in gene expression across time. While there are several works reporting TE activity in ALS models, they have not explored their activity through the disease progression. Moreover, they have done it at the expense of losing their locus of expression. Depending on their genomic location, TEs can regulate genes in cis and in trans, making locus-specific analysis of TEs of importance in order to understand their role in modulating gene expression. Particularly, the locus-specific role of TEs in ALS has not been fully elucidated. In this work, we analyzed publicly available RNA-Seq datasets of the SOD1G93A mouse model, to understand the locus-specific role of TEs. We show that TEs become up-regulated at the early stages of the disease, and via statistical associations, we speculate that they can regulate several genes, which in turn might be contributing to the genetic dysfunction observed in ALS.
format	article
author	Braulio Valdebenito-Maturana Esteban Arancibia Gonzalo Riadi Juan Carlos Tapia Mónica Carrasco
author_facet	Braulio Valdebenito-Maturana Esteban Arancibia Gonzalo Riadi Juan Carlos Tapia Mónica Carrasco
author_sort	Braulio Valdebenito-Maturana
title	Locus-specific analysis of Transposable Elements during the progression of ALS in the SOD1G93A mouse model.
title_short	Locus-specific analysis of Transposable Elements during the progression of ALS in the SOD1G93A mouse model.
title_full	Locus-specific analysis of Transposable Elements during the progression of ALS in the SOD1G93A mouse model.
title_fullStr	Locus-specific analysis of Transposable Elements during the progression of ALS in the SOD1G93A mouse model.
title_full_unstemmed	Locus-specific analysis of Transposable Elements during the progression of ALS in the SOD1G93A mouse model.
title_sort	locus-specific analysis of transposable elements during the progression of als in the sod1g93a mouse model.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/98fedb6517924a538b22278207bbf30b
work_keys_str_mv	AT brauliovaldebenitomaturana locusspecificanalysisoftransposableelementsduringtheprogressionofalsinthesod1g93amousemodel AT estebanarancibia locusspecificanalysisoftransposableelementsduringtheprogressionofalsinthesod1g93amousemodel AT gonzaloriadi locusspecificanalysisoftransposableelementsduringtheprogressionofalsinthesod1g93amousemodel AT juancarlostapia locusspecificanalysisoftransposableelementsduringtheprogressionofalsinthesod1g93amousemodel AT monicacarrasco locusspecificanalysisoftransposableelementsduringtheprogressionofalsinthesod1g93amousemodel
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Locus-specific analysis of Transposable Elements during the progression of ALS in the SOD1G93A mouse model.

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