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Identification and Expression Analysis of Long Noncoding RNAs in Fat-Tail of Sheep Breeds

Emerging evidence suggests that long non-coding RNAs (lncRNAs) participate in the regulation of a diverse range of biological processes. However, most studies have been focused on a few established model organisms and little is known about lncRNAs in fat-tail development in sheep. Here, the first pr...

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Autores principales: Bakhtiarizadeh, Mohammad Reza, Salami, Seyed Alireza
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Genetics Society of America 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6469412/
https://www.ncbi.nlm.nih.gov/pubmed/30787031
http://dx.doi.org/10.1534/g3.118.201014
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author Bakhtiarizadeh, Mohammad Reza
Salami, Seyed Alireza
author_facet Bakhtiarizadeh, Mohammad Reza
Salami, Seyed Alireza
author_sort Bakhtiarizadeh, Mohammad Reza
collection PubMed
description Emerging evidence suggests that long non-coding RNAs (lncRNAs) participate in the regulation of a diverse range of biological processes. However, most studies have been focused on a few established model organisms and little is known about lncRNAs in fat-tail development in sheep. Here, the first profile of lncRNA in sheep fat-tail along with their possible roles in fat deposition were investigated, based on a comparative transcriptome analysis between fat-tailed (Lori-Bakhtiari) and thin-tailed (Zel) Iranian sheep breeds. Among all identified lncRNAs candidates, 358 and 66 transcripts were considered novel intergenic (lincRNAs) and novel intronic (ilncRNAs) corresponding to 302 and 58 gene loci, respectively. Our results indicated that a low percentage of the novel lncRNAs were conserved. Also, synteny analysis identified 168 novel lincRNAs with the same syntenic region in human, bovine and chicken. Only seven lncRNAs were identified as differentially expressed genes between fat and thin tailed breeds. Q-RT-PCR results were consistent with the RNA-Seq data and validated the findings. Target prediction analysis revealed that the novel lncRNAs may act in cis or trans and regulate the expression of genes that are involved in the lipid metabolism. A gene regulatory network including lncRNA-mRNA interactions were constructed and three significant modules were found, with genes relevant to lipid metabolism, insulin and calcium signaling pathway. Moreover, integrated analysis with AnimalQTLdb database further suggested six lincRNAs and one ilncRNAs as candidates of sheep fat-tail development. Our results highlighted the putative contributions of lncRNAs in regulating expression of genes associated with fat-tail development in sheep.
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spelling pubmed-64694122019-04-23 Identification and Expression Analysis of Long Noncoding RNAs in Fat-Tail of Sheep Breeds Bakhtiarizadeh, Mohammad Reza Salami, Seyed Alireza G3 (Bethesda) Investigations Emerging evidence suggests that long non-coding RNAs (lncRNAs) participate in the regulation of a diverse range of biological processes. However, most studies have been focused on a few established model organisms and little is known about lncRNAs in fat-tail development in sheep. Here, the first profile of lncRNA in sheep fat-tail along with their possible roles in fat deposition were investigated, based on a comparative transcriptome analysis between fat-tailed (Lori-Bakhtiari) and thin-tailed (Zel) Iranian sheep breeds. Among all identified lncRNAs candidates, 358 and 66 transcripts were considered novel intergenic (lincRNAs) and novel intronic (ilncRNAs) corresponding to 302 and 58 gene loci, respectively. Our results indicated that a low percentage of the novel lncRNAs were conserved. Also, synteny analysis identified 168 novel lincRNAs with the same syntenic region in human, bovine and chicken. Only seven lncRNAs were identified as differentially expressed genes between fat and thin tailed breeds. Q-RT-PCR results were consistent with the RNA-Seq data and validated the findings. Target prediction analysis revealed that the novel lncRNAs may act in cis or trans and regulate the expression of genes that are involved in the lipid metabolism. A gene regulatory network including lncRNA-mRNA interactions were constructed and three significant modules were found, with genes relevant to lipid metabolism, insulin and calcium signaling pathway. Moreover, integrated analysis with AnimalQTLdb database further suggested six lincRNAs and one ilncRNAs as candidates of sheep fat-tail development. Our results highlighted the putative contributions of lncRNAs in regulating expression of genes associated with fat-tail development in sheep. Genetics Society of America 2019-02-20 /pmc/articles/PMC6469412/ /pubmed/30787031 http://dx.doi.org/10.1534/g3.118.201014 Text en Copyright © 2019 Bakhtiarizadeh, Salami http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Investigations
Bakhtiarizadeh, Mohammad Reza
Salami, Seyed Alireza
Identification and Expression Analysis of Long Noncoding RNAs in Fat-Tail of Sheep Breeds
title Identification and Expression Analysis of Long Noncoding RNAs in Fat-Tail of Sheep Breeds
title_full Identification and Expression Analysis of Long Noncoding RNAs in Fat-Tail of Sheep Breeds
title_fullStr Identification and Expression Analysis of Long Noncoding RNAs in Fat-Tail of Sheep Breeds
title_full_unstemmed Identification and Expression Analysis of Long Noncoding RNAs in Fat-Tail of Sheep Breeds
title_short Identification and Expression Analysis of Long Noncoding RNAs in Fat-Tail of Sheep Breeds
title_sort identification and expression analysis of long noncoding rnas in fat-tail of sheep breeds
topic Investigations
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6469412/
https://www.ncbi.nlm.nih.gov/pubmed/30787031
http://dx.doi.org/10.1534/g3.118.201014
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