Cargando…

Whole-Transcriptome Analysis of Preadipocyte and Adipocyte and Construction of Regulatory Networks to Investigate Lipid Metabolism in Sheep

Many local sheep breeds in China have poor meat quality. Increasing intramuscular fat (IMF) content can significantly improve the quality of mutton. However, the molecular mechanisms of intramuscular adipocyte formation and differentiation remain unclear. This study compared differences between prea...

Descripción completa

Detalles Bibliográficos
Autores principales: Xiao, Cheng, Wei, Tian, Liu, Li Xiang, Liu, Jian Qiang, Wang, Chun Xin, Yuan, Zhi Yu, Ma, Hui Hai, Jin, Hai Guo, Zhang, Li Chun, Cao, Yang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8358208/
https://www.ncbi.nlm.nih.gov/pubmed/34394181
http://dx.doi.org/10.3389/fgene.2021.662143
_version_ 1783737289459892224
author Xiao, Cheng
Wei, Tian
Liu, Li Xiang
Liu, Jian Qiang
Wang, Chun Xin
Yuan, Zhi Yu
Ma, Hui Hai
Jin, Hai Guo
Zhang, Li Chun
Cao, Yang
author_facet Xiao, Cheng
Wei, Tian
Liu, Li Xiang
Liu, Jian Qiang
Wang, Chun Xin
Yuan, Zhi Yu
Ma, Hui Hai
Jin, Hai Guo
Zhang, Li Chun
Cao, Yang
author_sort Xiao, Cheng
collection PubMed
description Many local sheep breeds in China have poor meat quality. Increasing intramuscular fat (IMF) content can significantly improve the quality of mutton. However, the molecular mechanisms of intramuscular adipocyte formation and differentiation remain unclear. This study compared differences between preadipocytes and mature adipocytes by whole-transcriptome sequencing and constructed systematically regulatory networks according to the relationship predicted among the differentially expressed RNAs (DERs). Sequencing results showed that in this process, there were 1,196, 754, 100, and 17 differentially expressed messenger RNAs (mRNAs), long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and circular RNAs (circRNAs), respectively. Gene Ontology analysis showed that most DERs enriched in Cell Part, Cellular Process, Biological Regulation, and Binding terms. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis found that the DERs primarily focused on Focal adhesion, phosphoinositide 3-kinase (PI3K)-Akt, mitogen-activated protein kinase (MAPK), peroxisome proliferator-activated receptor (PPAR) signaling pathways. Forty (40) DERs were randomly selected from the core regulatory network to verify the accuracy of the sequence data. The results of qPCR showed that the DER expression trend was consistent with sequence data. Four novel promising candidate miRNAs (miR-336, miR-422, miR-578, and miR-722) played crucial roles in adipocyte differentiation, and they also participated in multiple and important regulatory networks. We verified the expression pattern of the miRNAs and related pathways’ members at five time points in the adipocyte differentiation process (0, 2, 4, 6, 8, 10 days) by qPCR, including miR-336/ACSL4/LncRNA-MSTRG71379/circRNA0002331, miR-422/FOXO4/LncRNA-MSTRG54995/circRNA0000520, miR-578/IGF1/LncRNA-MSTRG102235/circRNA0002971, and miR-722/PDK4/LncRNA-MSTRG107440/circ RNA0002909. In this study, our data provided plenty of valuable candidate DERs and regulatory networks for researching the molecular mechanisms of sheep adipocyte differentiation and will assist studies in improving the IMF.
format Online
Article
Text
id pubmed-8358208
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher Frontiers Media S.A.
record_format MEDLINE/PubMed
spelling pubmed-83582082021-08-13 Whole-Transcriptome Analysis of Preadipocyte and Adipocyte and Construction of Regulatory Networks to Investigate Lipid Metabolism in Sheep Xiao, Cheng Wei, Tian Liu, Li Xiang Liu, Jian Qiang Wang, Chun Xin Yuan, Zhi Yu Ma, Hui Hai Jin, Hai Guo Zhang, Li Chun Cao, Yang Front Genet Genetics Many local sheep breeds in China have poor meat quality. Increasing intramuscular fat (IMF) content can significantly improve the quality of mutton. However, the molecular mechanisms of intramuscular adipocyte formation and differentiation remain unclear. This study compared differences between preadipocytes and mature adipocytes by whole-transcriptome sequencing and constructed systematically regulatory networks according to the relationship predicted among the differentially expressed RNAs (DERs). Sequencing results showed that in this process, there were 1,196, 754, 100, and 17 differentially expressed messenger RNAs (mRNAs), long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and circular RNAs (circRNAs), respectively. Gene Ontology analysis showed that most DERs enriched in Cell Part, Cellular Process, Biological Regulation, and Binding terms. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis found that the DERs primarily focused on Focal adhesion, phosphoinositide 3-kinase (PI3K)-Akt, mitogen-activated protein kinase (MAPK), peroxisome proliferator-activated receptor (PPAR) signaling pathways. Forty (40) DERs were randomly selected from the core regulatory network to verify the accuracy of the sequence data. The results of qPCR showed that the DER expression trend was consistent with sequence data. Four novel promising candidate miRNAs (miR-336, miR-422, miR-578, and miR-722) played crucial roles in adipocyte differentiation, and they also participated in multiple and important regulatory networks. We verified the expression pattern of the miRNAs and related pathways’ members at five time points in the adipocyte differentiation process (0, 2, 4, 6, 8, 10 days) by qPCR, including miR-336/ACSL4/LncRNA-MSTRG71379/circRNA0002331, miR-422/FOXO4/LncRNA-MSTRG54995/circRNA0000520, miR-578/IGF1/LncRNA-MSTRG102235/circRNA0002971, and miR-722/PDK4/LncRNA-MSTRG107440/circ RNA0002909. In this study, our data provided plenty of valuable candidate DERs and regulatory networks for researching the molecular mechanisms of sheep adipocyte differentiation and will assist studies in improving the IMF. Frontiers Media S.A. 2021-07-29 /pmc/articles/PMC8358208/ /pubmed/34394181 http://dx.doi.org/10.3389/fgene.2021.662143 Text en Copyright © 2021 Xiao, Wei, Liu, Liu, Wang, Yuan, Ma, Jin, Zhang and Cao. 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
Xiao, Cheng
Wei, Tian
Liu, Li Xiang
Liu, Jian Qiang
Wang, Chun Xin
Yuan, Zhi Yu
Ma, Hui Hai
Jin, Hai Guo
Zhang, Li Chun
Cao, Yang
Whole-Transcriptome Analysis of Preadipocyte and Adipocyte and Construction of Regulatory Networks to Investigate Lipid Metabolism in Sheep
title Whole-Transcriptome Analysis of Preadipocyte and Adipocyte and Construction of Regulatory Networks to Investigate Lipid Metabolism in Sheep
title_full Whole-Transcriptome Analysis of Preadipocyte and Adipocyte and Construction of Regulatory Networks to Investigate Lipid Metabolism in Sheep
title_fullStr Whole-Transcriptome Analysis of Preadipocyte and Adipocyte and Construction of Regulatory Networks to Investigate Lipid Metabolism in Sheep
title_full_unstemmed Whole-Transcriptome Analysis of Preadipocyte and Adipocyte and Construction of Regulatory Networks to Investigate Lipid Metabolism in Sheep
title_short Whole-Transcriptome Analysis of Preadipocyte and Adipocyte and Construction of Regulatory Networks to Investigate Lipid Metabolism in Sheep
title_sort whole-transcriptome analysis of preadipocyte and adipocyte and construction of regulatory networks to investigate lipid metabolism in sheep
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8358208/
https://www.ncbi.nlm.nih.gov/pubmed/34394181
http://dx.doi.org/10.3389/fgene.2021.662143
work_keys_str_mv AT xiaocheng wholetranscriptomeanalysisofpreadipocyteandadipocyteandconstructionofregulatorynetworkstoinvestigatelipidmetabolisminsheep
AT weitian wholetranscriptomeanalysisofpreadipocyteandadipocyteandconstructionofregulatorynetworkstoinvestigatelipidmetabolisminsheep
AT liulixiang wholetranscriptomeanalysisofpreadipocyteandadipocyteandconstructionofregulatorynetworkstoinvestigatelipidmetabolisminsheep
AT liujianqiang wholetranscriptomeanalysisofpreadipocyteandadipocyteandconstructionofregulatorynetworkstoinvestigatelipidmetabolisminsheep
AT wangchunxin wholetranscriptomeanalysisofpreadipocyteandadipocyteandconstructionofregulatorynetworkstoinvestigatelipidmetabolisminsheep
AT yuanzhiyu wholetranscriptomeanalysisofpreadipocyteandadipocyteandconstructionofregulatorynetworkstoinvestigatelipidmetabolisminsheep
AT mahuihai wholetranscriptomeanalysisofpreadipocyteandadipocyteandconstructionofregulatorynetworkstoinvestigatelipidmetabolisminsheep
AT jinhaiguo wholetranscriptomeanalysisofpreadipocyteandadipocyteandconstructionofregulatorynetworkstoinvestigatelipidmetabolisminsheep
AT zhanglichun wholetranscriptomeanalysisofpreadipocyteandadipocyteandconstructionofregulatorynetworkstoinvestigatelipidmetabolisminsheep
AT caoyang wholetranscriptomeanalysisofpreadipocyteandadipocyteandconstructionofregulatorynetworkstoinvestigatelipidmetabolisminsheep