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. 2020 Feb 26:11:98.
doi: 10.3389/fgene.2020.00098. eCollection 2020.

Comparison of Long Non-Coding RNA Expression Profiles of Cattle and Buffalo Differing in Muscle Characteristics

Hui Li  1 , Kongwei Huang  1 , Pengcheng Wang  1 , Tong Feng  1   2 , Deshun Shi  1 , Kuiqing Cui  1 , Chan Luo  1 , Laiba Shafique  1 , Qian Qian  2 , Jue Ruan  2 , Qingyou Liu  1   2
Affiliations

Comparison of Long Non-Coding RNA Expression Profiles of Cattle and Buffalo Differing in Muscle Characteristics

Hui Li et al. Front Genet. .

Abstract

Buffalo meat consist good qualitative characteristics as it contains "thined tender" which is favorable for cardavascular system. However, the regulatory mechanisms of long non-coding RNA (lncRNA), differences in meat quality are not well known. The chemical-physical parameters revealed the muscle quality of buffalo that can be equivalent of cattle, but there are significant differences in shearing force and muscle fiber structure. Then, we examined lncRNA expression profiles of buffalo and cattle skeletal muscle that provide first insights into their potential roles in buffalo myogenesis. Here, we profiled the expression of lncRNA in cattle and buffalo skeletal muscle tissues, and 16,236 lncRNA candidates were detected with 865 up-regulated lncRNAs and 1,296 down-regulated lncRNAs when comparing buffalo to cattle muscle tissue. We constructed coexpression and ceRNA networks, and found lncRNA MSTRG.48330.7, MSTRG.30030.4, and MSTRG.203788.46 could be as competitive endogenous RNA (ceRNA) containing potential binding sites for miR-1/206 and miR-133a. Tissue expression analysis showed that MSTRG.48330.7, MSTRG.30030.4, and MSTRG.203788.46 were highly and specifically expressed in muscle tissue. Present study may be used as a reference tool for starting point investigations into the roles played by several of those lncRNAs during buffalo myogenesis.

Keywords: RNA-seq; buffalo; cattle; lncRNA; myogenesis.

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Figures

Figure 1
Figure 1
Histological analysis of longissimus dorsi muscles. The HE staining of muscle results showed that the muscle fiber area, isometric diameter, circumference and density of buffalo (A) were significantly smaller than those of cattle (B).
Figure 2
Figure 2
Identification of lncRNAs in buffalo and cattle skeletal muscle tissue. (A) Workflow for the preparation and analysis of lncRNA libraries. (B) Pie charts representing the percentage of reads mapping to indicated genomic regions. (C) Venn diagram depicting the overlap of lncRNAs discovered in lncRNAs identification. (D, E) Distribution of lncRNAs along each chromosome. (F) Classification of lncRNAs, as defined by their genomic location relative to neighboring or overlapping genes.
Figure 3
Figure 3
Differentially expressed lncRNAs in buffalo and cattle skeletal muscle. (A, B) The expression levels of lncRNAs, plotted as fragments per kilobase of exon per million fragments mapped (FPKM). (C) Weighted gene coexpression network analysis of lncRNAs in buffalo and cattle muscle sample. (D) Heatmap of differentially expressed lncRNAs in buffalo and cattle muscle tissue. (E, F) The top 30 enriched KEGG pathways by cis (E) and trans (F) regulation. (G–I) Scatter plot, MA interactive maps and volcano plot showing the correlation between abundances of individual lncRNAs in buffalo and cattle muscle sample.
Figure 4
Figure 4
Comparison and analysis of genomic features of mRNA and lncRNA in muscle tissue. (A) Distribution of transcript lengths of lncRNAs and mRNA. (B) Distribution of ORF lengths of lncRNAs and mRNA. (C) Distribution of exon number of lncRNAs and mRNA. (D) Distribution of expression levels of lncRNAs and mRNA. (E) Distribution of isoform number of lncRNAs and mRNA. (F, G) Volcano plot and MA interactive maps showing the correlation between abundances of differentially expressed lncRNAs and mRNA. (H) Distribution of differentially expressed lncRNAs along each chromosome.
Figure 5
Figure 5
Coexpression network and competing endogenous RNA network in cattle and buffalo muscle tissues. (A) LncRNAs and their potential cis regulated nearby genes are shown in the network. (B) The network includes lncRNA-miRNA and miRNA-mRNA interactions, whereby edges indicate sequence matching, and lncRNAs connect ties suggesting miRNA-mediated mRNA expression.
Figure 6
Figure 6
Validation of putative lncRNA. (A) 14 lncRNAs were selected and identified, as they exhibited significantly different expression patterns (assessed from our RNA-sequencing approach) when comparing longissimus dorsi muscles, using quantitative real-time PCR (qRT-PCR). (B) 14 lncRNAs were identified in fetus cattle and buffalo longissimus dorsi muscles using qRT-PCR. (C) 14 lncRNAs were identified in fetus cattle and buffalo leg muscles using qRT-PCR. (D) The expression of 14 lncRNAs in cattle and buffalo muscle tissue. *P < 0.05, **P < 0.01.
Figure 7
Figure 7
Expression levels of 14 candidate lncRNAs in different tissues of fetus buffalo.
Figure 8
Figure 8
Expression levels of 14 candidate lncRNAs in different tissues of fetus cattle.
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