Growth retardation-responsive analysis of mRNAs and long noncoding RNAs in the liver tissue of Leiqiong cattle

Abstract

As an important type of non-coding RNA molecule, long non-coding RNAs (lncRNAs) have varied roles in many biological processes, and have been studied extensively over the past few years. However, little is known about lncRNA-mediated regulation during cattle growth and development. Therefore, in the present study, RNA sequencing was used to determine the expression level of mRNAs and lncRNAs in the liver of adult Leiqiong cattle under the condition of growth retardation and normal growth. We totally detected 1,124 and 24 differentially expressed mRNAs and lncRNAs, respectively. The differentially expressed mRNAs were mainly associated with growth factor binding, protein K63-linked ubiquitination and cellular protein metabolic process; additionally, they were significantly enriched in the growth and development related pathways, including PPAR signaling pathway, vitamin B6 metabolism, glyoxylate and dicarboxylate metabolism. Combined analysis showed that the co-located differentially expressed lncRNA Lnc_002583 might positively influence the expression of the corresponding genes IFI44 and IFI44L, exerting co-regulative effects on Leiqiong cattle growth and development. Thus, we made the hypothesis that Lnc_002583, IFI44 and IFI44L might function synergistically to regulate the growth of Leiqiong cattle. This study provides a catalog of Leiqiong cattle liver mRNAs and lncRNAs, and will contribute to a better understanding of the molecular mechanism underlying growth regulataion.

Figure 1

Analyses of differentially expressed mRNAs in the RNA sequencing (RNA-seq) libraries. (A) Volcano plot showing the overall distribution of the differential transcript or gene, with the threshold set to q < 0.05. Red: relatively high expression; Green: relatively low expression. (B) Hierarchical clustering analysis of mRNA expression profiles from 11 libraries with 1,124 differentially expressed mRNAs. Data are expressed as fragments per kilo base of exon per million fragments mapped (FPKM). Red: relatively high expression; Blue: relatively low expression.

Figure 2

Analyses of differentially expressed lncRNAs in the RNA sequencing (RNA-seq) libraries. (A) Volcano plot showing the overall distribution of the differential transcripts or genes, with the threshold set to P = 0.05. Red: relatively high expression; Green: relatively low expression. (B) Hierarchical clustering analysis of lncRNA expression profiles from 11 libraries with 24 differentially expressed lncRNAs. Data are expressed as fragments per kilo base of exon per million fragments mapped (FPKM). Red: relatively high expression; Blue: relatively low expression.

Figure 3

Validation of six differentially expressed mRNAs and long non-coding RNAs (lncRNAs) using quantitative real-time reverse transcription PCR (qRT-PCR). (A) The qRT-PCR results of differentially expressed mRNAs were compared with the RNA sequencing (RNA-seq) data. Red: RNA-seq; Blue: qRT-PCR. (B) The qRT-PCR results of differentially expressed lncRNAs were compared with the RNA-seq data. Red: RNA-seq; Blue: qRT-PCR.