Transcriptomic meta-analysis reveals unannotated long non-coding RNAs related to the immune response in sheep
dc.contributor.author | Bilbao Arribas, Martín | |
dc.contributor.author | Jugo Orrantia, Begoña Marina ![]() | |
dc.date.accessioned | 2022-12-19T17:19:59Z | |
dc.date.available | 2022-12-19T17:19:59Z | |
dc.date.issued | 2022-11 | |
dc.identifier.citation | Frontiers in Genetics 13 : (2022) // Article ID 1067350 | es_ES |
dc.identifier.issn | 1664-8021 | |
dc.identifier.uri | http://hdl.handle.net/10810/58884 | |
dc.description.abstract | Long non-coding RNAs (lncRNAs) are involved in several biological processes, including the immune system response to pathogens and vaccines. The annotation and functional characterization of lncRNAs is more advanced in humans than in livestock species. Here, we take advantage of the increasing number of high-throughput functional experiments deposited in public databases in order to uniformly analyse, profile unannotated lncRNAs and integrate 422 ovine RNA-seq samples from the ovine immune system. We identified 12302 unannotated lncRNA genes with support from independent CAGE-seq and histone modification ChIP-seq assays. Unannotated lncRNAs showed low expression levels and sequence conservation across other mammal species. There were differences in expression levels depending on the genomic location-based lncRNA classification. Differential expression analyses between unstimulated and samples stimulated with pathogen infection or vaccination resulted in hundreds of lncRNAs with changed expression. Gene co-expression analyses revealed immune gene-enriched clusters associated with immune system activation and related to interferon signalling, antiviral response or endoplasmic reticulum stress. Besides, differential co-expression networks were constructed in order to find condition-specific relationships between coding genes and lncRNAs. Overall, using a diverse set of immune system samples and bioinformatic approaches we identify several ovine lncRNAs associated with the response to an external stimulus. These findings help in the improvement of the ovine lncRNA catalogue and provide sheep-specific evidence for the implication in the general immune response for several lncRNAs. | es_ES |
dc.description.sponsorship | This research was supported by the University of the Basque Country (UPV/EHU) by means of Research Groups General grant GIU20/071 to BMJ and a predoctoral fellowship to MB-A (PIF17/306), and by the Basque Government, Department of Education, through Consolidated Research Group funding IT1693-22. | es_ES |
dc.language.iso | eng | es_ES |
dc.publisher | Frontiers Media | es_ES |
dc.rights | info:eu-repo/semantics/openAccess | es_ES |
dc.rights.uri | http://creativecommons.org/licenses/by/3.0/es/ | * |
dc.subject | sheep | es_ES |
dc.subject | genomics | es_ES |
dc.subject | lncRNAs | es_ES |
dc.subject | RNA-seq | es_ES |
dc.subject | immune system | es_ES |
dc.subject | transcriptomics | es_ES |
dc.title | Transcriptomic meta-analysis reveals unannotated long non-coding RNAs related to the immune response in sheep | es_ES |
dc.type | info:eu-repo/semantics/article | es_ES |
dc.rights.holder | © 2022 Bilbao-Arribas and Jugo. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. | es_ES |
dc.rights.holder | Atribución 3.0 España | * |
dc.relation.publisherversion | https://www.frontiersin.org/articles/10.3389/fgene.2022.1067350/full | es_ES |
dc.identifier.doi | 10.3389/fgene.2022.1067350 | |
dc.departamentoes | Genética, antropología física y fisiología animal | es_ES |
dc.departamentoeu | Genetika,antropologia fisikoa eta animalien fisiologia | es_ES |
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