A genome-wide landscape of mRNAs, lncRNAs, circRNAs and miRNAs during intramuscular adipogenesis in cattle

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Abstract

Background

Intramuscular preadipocyte differentiation plays a critical role in bovine intramuscular fat (IMF) deposition. However, the roles of different RNAs, including mRNAs, circRNAs, lncRNAs and miRNAs, in regulating the adipogenic differentiation of intramuscular preadipocytes remain largely unclear.

Results

In the present study, a whole transcriptome sequencing and analysis, including the analysis of mRNAs, circRNAs, lncRNAs and miRNAs, during different differentiation stages (0, 3, 6, and 9 d) of intramuscular preadipocytes from Qinchuan cattle was performed. All samples were prepared with 3 biological replicates. Here, a total of 27,153 mRNAs, 14,070 circRNAs, 7035 lncRNAs, and 427 miRNAs were annotated. Among them, we identified 4848 differentially expressed mRNAs (DEMs), 181 DE circRNAs (DECs), 501 DE lncRNAs (DELs) and 77 DE miRNAs (DEmiRs) between 0 d and other differentiation days (3, 6, and 9 d). GO and KEGG functional enrichment analyses showed that these differentially expressed genes were mainly enriched in cell differentiation, fat metabolism and adipogenesis-related pathways. Furthermore, weighted gene coexpression network analysis (WGCNA) and co-expression network analysis screened out multiple important mRNAs, circRNAs and lncRNAs related to intramuscular adipogenesis. Based on the competing endogenous RNA (ceRNA) regulatory mechanism, we finally identified 24 potential ceRNA networks and 31 potential key genes, including FOXO1/miR-330/circRNA2018/MSTRG.20301, GPAM/miR-27b/ciRNA489 and SESN3/miR-433/circRNA2627MSTRG.20342.

Conclusions

This study provides new insights into the differential expression patterns of different transcript types (i.e., mRNAs, circRNAs, lncRNAs and miRNAs) in intramuscular preadipocyte differentiation. Our findings provide data support for studying the molecular mechanism of key mRNAs and noncoding RNAs in IMF deposition, and provide new candidate markers for the molecular breeding of beef cattle.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08911-z.

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Most cited references 67

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Author and article information

Contributors

Chugang Mei: meichugang@163.com

Linsen Zan: zanlinsen@163.com

Journal

Journal ID (nlm-ta): BMC Genomics

Journal ID (iso-abbrev): BMC Genomics

Title: BMC Genomics

Publisher: BioMed Central (London )

ISSN (Electronic): 1471-2164

Publication date (Electronic): 6 October 2022

Publication date PMC-release: 6 October 2022

Publication date Collection: 2022

Volume: 23

Electronic Location Identifier: 691

Affiliations

[1 ]GRID grid.144022.1, ISNI 0000 0004 1760 4150, College of Animal Science and Technology, , Northwest A&F University, ; Yangling, 712100 Shaanxi China

[2 ]GRID grid.144022.1, ISNI 0000 0004 1760 4150, College of Grassland Agriculture, , Northwest A&F University, ; Yangling, 712100 Shaanxi China

[3 ]GRID grid.144022.1, ISNI 0000 0004 1760 4150, National Beef Cattle Improvement Center, , Northwest A&F University, ; Yangling, 712100 Shaanxi China

Article

Publisher ID: 8911

DOI: 10.1186/s12864-022-08911-z

PMC ID: 9535873

SO-VID: 59755982-9d3b-4aa6-aa75-ac819f7e9ae9

License:

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

History

Date received : 11 June 2022

Date accepted : 26 September 2022

Custom metadata

ScienceOpen disciplines: Genetics

Keywords: cattle,imf,preadipocyte differentiation,circrna,lncrna,mirna,rna-seq,wgcna,cerna

Data availability:

ScienceOpen disciplines: Genetics

Keywords: cattle, imf, preadipocyte differentiation, circrna, lncrna, mirna, rna-seq, wgcna, cerna

A genome-wide landscape of mRNAs, lncRNAs, circRNAs and miRNAs during intramuscular adipogenesis in cattle

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Abstract

Background

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Supplementary Information

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Genome Integrity

Most cited references 67

Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.

Trimmomatic: a flexible trimmer for Illumina sequence data

Cytoscape: a software environment for integrated models of biomolecular interaction networks.

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