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Functional evaluation of LTR-derived lncRNAs in porcine oocytes and zygotes with RNA-seq and small RNA-seq

Long noncoding RNAs (lncRNAs) are increasingly being recognized as modulators of early embryonic development in mammals. However, they are seldom investigated in pigs. Here, to annotate full-length RNA transcripts, we performed annotation using a newly developed computational pipeline—an RNA-seq and...

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Autores principales: Yang, Xu, Ji, Jingzhang, Cui, Hongdi, Zhao, Qi, Ding, Chunming, Xu, Chang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9606649/
https://www.ncbi.nlm.nih.gov/pubmed/36313467
http://dx.doi.org/10.3389/fgene.2022.1023041
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author Yang, Xu
Ji, Jingzhang
Cui, Hongdi
Zhao, Qi
Ding, Chunming
Xu, Chang
author_facet Yang, Xu
Ji, Jingzhang
Cui, Hongdi
Zhao, Qi
Ding, Chunming
Xu, Chang
author_sort Yang, Xu
collection PubMed
description Long noncoding RNAs (lncRNAs) are increasingly being recognized as modulators of early embryonic development in mammals. However, they are seldom investigated in pigs. Here, to annotate full-length RNA transcripts, we performed annotation using a newly developed computational pipeline—an RNA-seq and small RNA-seq combined strategy—using our previously obtained RNA-seq and small RNA-seq data from porcine oocytes and zygotes. As evidenced by the length comparison, the frequency of the core promoter, and the polyadenylation signal motifs, the transcripts appear to be full-length. Furthermore, our strategy allowed the identification of a large number of endogenous retrovirus-associated lncRNAs (ERV-lncRNAs) and found that some of them were highly expressed in porcine zygotes, as compared to oocytes. Through the knockdown strategy, two ERV-lncRNAs (TCONS_00035465 and TCONS_00031520) were identified as playing potential roles in the early embryo development of pigs, laying a foundation for future research.
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spelling pubmed-96066492022-10-28 Functional evaluation of LTR-derived lncRNAs in porcine oocytes and zygotes with RNA-seq and small RNA-seq Yang, Xu Ji, Jingzhang Cui, Hongdi Zhao, Qi Ding, Chunming Xu, Chang Front Genet Genetics Long noncoding RNAs (lncRNAs) are increasingly being recognized as modulators of early embryonic development in mammals. However, they are seldom investigated in pigs. Here, to annotate full-length RNA transcripts, we performed annotation using a newly developed computational pipeline—an RNA-seq and small RNA-seq combined strategy—using our previously obtained RNA-seq and small RNA-seq data from porcine oocytes and zygotes. As evidenced by the length comparison, the frequency of the core promoter, and the polyadenylation signal motifs, the transcripts appear to be full-length. Furthermore, our strategy allowed the identification of a large number of endogenous retrovirus-associated lncRNAs (ERV-lncRNAs) and found that some of them were highly expressed in porcine zygotes, as compared to oocytes. Through the knockdown strategy, two ERV-lncRNAs (TCONS_00035465 and TCONS_00031520) were identified as playing potential roles in the early embryo development of pigs, laying a foundation for future research. Frontiers Media S.A. 2022-10-13 /pmc/articles/PMC9606649/ /pubmed/36313467 http://dx.doi.org/10.3389/fgene.2022.1023041 Text en Copyright © 2022 Yang, Ji, Cui, Zhao, Ding and Xu. https://creativecommons.org/licenses/by/4.0/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.
spellingShingle Genetics
Yang, Xu
Ji, Jingzhang
Cui, Hongdi
Zhao, Qi
Ding, Chunming
Xu, Chang
Functional evaluation of LTR-derived lncRNAs in porcine oocytes and zygotes with RNA-seq and small RNA-seq
title Functional evaluation of LTR-derived lncRNAs in porcine oocytes and zygotes with RNA-seq and small RNA-seq
title_full Functional evaluation of LTR-derived lncRNAs in porcine oocytes and zygotes with RNA-seq and small RNA-seq
title_fullStr Functional evaluation of LTR-derived lncRNAs in porcine oocytes and zygotes with RNA-seq and small RNA-seq
title_full_unstemmed Functional evaluation of LTR-derived lncRNAs in porcine oocytes and zygotes with RNA-seq and small RNA-seq
title_short Functional evaluation of LTR-derived lncRNAs in porcine oocytes and zygotes with RNA-seq and small RNA-seq
title_sort functional evaluation of ltr-derived lncrnas in porcine oocytes and zygotes with rna-seq and small rna-seq
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9606649/
https://www.ncbi.nlm.nih.gov/pubmed/36313467
http://dx.doi.org/10.3389/fgene.2022.1023041
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