Cargando…

Expression Profile Analysis to Identify Circular RNA Expression Signatures in Muscle Development of Wu'an Goat Longissimus Dorsi Tissues

The growth and development of skeletal muscle is a physiological process regulated by a variety of genes and signaling pathways. As a posttranscriptional regulatory factor, circRNA plays a certain regulatory role in the development of animal skeletal muscle in the form of a miRNA sponge. However, th...

Descripción completa

Detalles Bibliográficos
Autores principales: Zhou, Zuyang, Li, Kunyu, Liu, Jiannan, Zhang, Hui, Fan, Yekai, Chen, Yulin, Han, Haiyin, Yang, Junqi, Liu, Yufang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9062782/
https://www.ncbi.nlm.nih.gov/pubmed/35518637
http://dx.doi.org/10.3389/fvets.2022.833946
_version_ 1784699023686369280
author Zhou, Zuyang
Li, Kunyu
Liu, Jiannan
Zhang, Hui
Fan, Yekai
Chen, Yulin
Han, Haiyin
Yang, Junqi
Liu, Yufang
author_facet Zhou, Zuyang
Li, Kunyu
Liu, Jiannan
Zhang, Hui
Fan, Yekai
Chen, Yulin
Han, Haiyin
Yang, Junqi
Liu, Yufang
author_sort Zhou, Zuyang
collection PubMed
description The growth and development of skeletal muscle is a physiological process regulated by a variety of genes and signaling pathways. As a posttranscriptional regulatory factor, circRNA plays a certain regulatory role in the development of animal skeletal muscle in the form of a miRNA sponge. However, the role of circRNAs in muscle development and growth in goats is still unclear. In our study, apparent differences in muscle fibers in Wu'an goats of different ages was firstly detected by hematoxylin-eosin (HE) staining, the circRNA expression profiles of longissimus dorsi muscles from 1-month-old (mon1) and 9-month-old (mon9) goats were screened by RNA-seq and verified by RT–qPCR. The host genes of differentially expressed (DE) circRNAs were predicted, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes analyses (KEGG) of host genes with DE circRNAs were performed to explore the functions of circRNAs. The circRNA-miRNA-mRNA networks were then constructed using Cytoscape software. Ten significantly differentially expressed circRNAs were also verified in the mon1 and mon9 groups by RT–qPCR. Luciferase Reporter Assay was used to verify the binding site between circRNA and its targeted miRNA. The results showed that a total of 686 DE circRNAs were identified between the mon9 and mon1 groups, of which 357 were upregulated and 329 were downregulated. Subsequently, the 467 host genes of DE circRNAs were predicted using Find_circ and CIRI software. The circRNA-miRNA-mRNA network contained 201 circRNAs, 85 miRNAs, and 581 mRNAs; the host mRNAs were associated with “muscle fiber development” and “AMPK signaling pathway” and were enriched in the FoxO signaling pathway. Competing endogenous RNA (ceRNA) network analysis showed that novel_circ_0005314, novel_circ_0005319, novel_circ_0009256, novel_circ_0009845, novel_circ_0005934 and novel_circ_0000134 may play important roles in skeletal muscle growth and development between the mon9 and mon1 groups. Luciferase Reporter Assay confirmed the combination between novel_circ_0005319 and chi-miR-199a-5p, novel_circ_0005934 and chi-miR-450-3p and novel_circ_0000134 and chi-miR-655. Our results provide specific information related to goat muscle development and a reference for the goat circRNA profile.
format Online
Article
Text
id pubmed-9062782
institution National Center for Biotechnology Information
language English
publishDate 2022
publisher Frontiers Media S.A.
record_format MEDLINE/PubMed
spelling pubmed-90627822022-05-04 Expression Profile Analysis to Identify Circular RNA Expression Signatures in Muscle Development of Wu'an Goat Longissimus Dorsi Tissues Zhou, Zuyang Li, Kunyu Liu, Jiannan Zhang, Hui Fan, Yekai Chen, Yulin Han, Haiyin Yang, Junqi Liu, Yufang Front Vet Sci Veterinary Science The growth and development of skeletal muscle is a physiological process regulated by a variety of genes and signaling pathways. As a posttranscriptional regulatory factor, circRNA plays a certain regulatory role in the development of animal skeletal muscle in the form of a miRNA sponge. However, the role of circRNAs in muscle development and growth in goats is still unclear. In our study, apparent differences in muscle fibers in Wu'an goats of different ages was firstly detected by hematoxylin-eosin (HE) staining, the circRNA expression profiles of longissimus dorsi muscles from 1-month-old (mon1) and 9-month-old (mon9) goats were screened by RNA-seq and verified by RT–qPCR. The host genes of differentially expressed (DE) circRNAs were predicted, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes analyses (KEGG) of host genes with DE circRNAs were performed to explore the functions of circRNAs. The circRNA-miRNA-mRNA networks were then constructed using Cytoscape software. Ten significantly differentially expressed circRNAs were also verified in the mon1 and mon9 groups by RT–qPCR. Luciferase Reporter Assay was used to verify the binding site between circRNA and its targeted miRNA. The results showed that a total of 686 DE circRNAs were identified between the mon9 and mon1 groups, of which 357 were upregulated and 329 were downregulated. Subsequently, the 467 host genes of DE circRNAs were predicted using Find_circ and CIRI software. The circRNA-miRNA-mRNA network contained 201 circRNAs, 85 miRNAs, and 581 mRNAs; the host mRNAs were associated with “muscle fiber development” and “AMPK signaling pathway” and were enriched in the FoxO signaling pathway. Competing endogenous RNA (ceRNA) network analysis showed that novel_circ_0005314, novel_circ_0005319, novel_circ_0009256, novel_circ_0009845, novel_circ_0005934 and novel_circ_0000134 may play important roles in skeletal muscle growth and development between the mon9 and mon1 groups. Luciferase Reporter Assay confirmed the combination between novel_circ_0005319 and chi-miR-199a-5p, novel_circ_0005934 and chi-miR-450-3p and novel_circ_0000134 and chi-miR-655. Our results provide specific information related to goat muscle development and a reference for the goat circRNA profile. Frontiers Media S.A. 2022-04-18 /pmc/articles/PMC9062782/ /pubmed/35518637 http://dx.doi.org/10.3389/fvets.2022.833946 Text en Copyright © 2022 Zhou, Li, Liu, Zhang, Fan, Chen, Han, Yang and Liu. 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 Veterinary Science
Zhou, Zuyang
Li, Kunyu
Liu, Jiannan
Zhang, Hui
Fan, Yekai
Chen, Yulin
Han, Haiyin
Yang, Junqi
Liu, Yufang
Expression Profile Analysis to Identify Circular RNA Expression Signatures in Muscle Development of Wu'an Goat Longissimus Dorsi Tissues
title Expression Profile Analysis to Identify Circular RNA Expression Signatures in Muscle Development of Wu'an Goat Longissimus Dorsi Tissues
title_full Expression Profile Analysis to Identify Circular RNA Expression Signatures in Muscle Development of Wu'an Goat Longissimus Dorsi Tissues
title_fullStr Expression Profile Analysis to Identify Circular RNA Expression Signatures in Muscle Development of Wu'an Goat Longissimus Dorsi Tissues
title_full_unstemmed Expression Profile Analysis to Identify Circular RNA Expression Signatures in Muscle Development of Wu'an Goat Longissimus Dorsi Tissues
title_short Expression Profile Analysis to Identify Circular RNA Expression Signatures in Muscle Development of Wu'an Goat Longissimus Dorsi Tissues
title_sort expression profile analysis to identify circular rna expression signatures in muscle development of wu'an goat longissimus dorsi tissues
topic Veterinary Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9062782/
https://www.ncbi.nlm.nih.gov/pubmed/35518637
http://dx.doi.org/10.3389/fvets.2022.833946
work_keys_str_mv AT zhouzuyang expressionprofileanalysistoidentifycircularrnaexpressionsignaturesinmuscledevelopmentofwuangoatlongissimusdorsitissues
AT likunyu expressionprofileanalysistoidentifycircularrnaexpressionsignaturesinmuscledevelopmentofwuangoatlongissimusdorsitissues
AT liujiannan expressionprofileanalysistoidentifycircularrnaexpressionsignaturesinmuscledevelopmentofwuangoatlongissimusdorsitissues
AT zhanghui expressionprofileanalysistoidentifycircularrnaexpressionsignaturesinmuscledevelopmentofwuangoatlongissimusdorsitissues
AT fanyekai expressionprofileanalysistoidentifycircularrnaexpressionsignaturesinmuscledevelopmentofwuangoatlongissimusdorsitissues
AT chenyulin expressionprofileanalysistoidentifycircularrnaexpressionsignaturesinmuscledevelopmentofwuangoatlongissimusdorsitissues
AT hanhaiyin expressionprofileanalysistoidentifycircularrnaexpressionsignaturesinmuscledevelopmentofwuangoatlongissimusdorsitissues
AT yangjunqi expressionprofileanalysistoidentifycircularrnaexpressionsignaturesinmuscledevelopmentofwuangoatlongissimusdorsitissues
AT liuyufang expressionprofileanalysistoidentifycircularrnaexpressionsignaturesinmuscledevelopmentofwuangoatlongissimusdorsitissues