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Comparative Study
. 2020 Jan 16;10(1):516.
doi: 10.1038/s41598-019-57404-9.

Comprehensive analysis of circRNAs from cashmere goat skin by next generation RNA sequencing (RNA-seq)

Yuanyuan Zheng  1 , Taiyu Hui  1 , Chang Yue  1 , Jiaming Sun  1 , Dan Guo  2 , Suling Guo  3 , Suping Guo  1 , Bojiang Li  1 , Zeying Wang  4 , Wenlin Bai  5
Affiliations
Comparative Study

Comprehensive analysis of circRNAs from cashmere goat skin by next generation RNA sequencing (RNA-seq)

Yuanyuan Zheng et al. Sci Rep. .

Abstract

Circular RNA (circRNA) is endogenous non-coding RNA (ncRNA) with a covalently closed circular structure. It is mainly generated through RNA alternative splicing or back-splicing. CircRNA is known in the majority of eukaryotes and very stable. However, knowledge of the circRNA involved in regulating cashmere fineness is limited. Skin samples were collected from Liaoning cashmere goats (LCG) and Inner Mongolia cashmere goats (MCG) during the anagen period. For differentially expressed circRNAs, RNA sequencing was performed, and the analysis led to an identification of 17 up-regulated circRNAs and 15 down-regulated circRNAs in LCG compared with MCG skin samples. In order to find the differentially expressed circRNAs in LCG, we carried out qPCRs on 10 candidate circRNAs in coarse type skin of LCG (CT-LCG) and fine type skin of LCG (FT-LCG). Four circRNAs: ciRNA128, circRNA6854, circRNA4154 and circRNA3620 were confirmed to be significantly differential expression in LCG. Also, a regulatory network of circRNAs-miRNAs was bioinformatically deduced and may help to understand molecular mechanisms of potential circRNA involvement in regulating cashmere fineness.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
Information on circRNAs from RNA-seq in Liaoning cashmere goats (LCG) and Inner Mongolia cashmere goats (MCG) skin tissue. (a) The types of circRNAs. (b) Distribution of exons, introns, and intergenic circRNAs. (c) The number of exons in circRNAs. (d) The lengths of circRNAs.
Figure 2
Figure 2
Differentially expressed circRNAs in LCG and MCG. (a) Volcano map of differentially expressed circRNAs. Red dots indicate up-regulation and blue dots indicate down-regulation. (b) Cluster heatmap of differentially expressed circRNAs. The sample is represented by the abscissa and the log value of circRNA expression is regarded by the ordinate, which means that the heatmap is drawn from log10 of circRNA expression. The highly expressed circRNA is indicated by red, meanwhile, the lowly expressed circRNA is presented by blue.
Figure 3
Figure 3
Quantitative real-time PCR (qPCR) result of circRNAs expression. (a) Divergent primers used in the amplification of circular junctions. (b) Validation of putative circRNAs by qPCR. Blue: LCG; Red: MCG. Error bars indicate mean ± SE for three individuals, “*”p < 0.05, “**”p < 0.01.
Figure 4
Figure 4
(a) Numbers of circRNAs produced by the same gene. (b) Exon distribution of candidate circRNAs. Different colors represent different exons.
Figure 5
Figure 5
Gene ontology (GO) analysis of differentially expressed circRNAs. (a) Top 25 biological processes, top 15 cell components, and top 10 molecular functions. (b) The top 20 GO terms. The color of the dot corresponds to different p-value ranges, and the size of the dot indicates the number of genes in the pathway. Rich factor denotes the number of differentially expressed circRNAs in the GO/ the total number of circRNAs in the GO.
Figure 6
Figure 6
Top 20 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of host genes of differentially expressed circRNAs. The color of the dot corresponds to different p-value ranges, and the size of the dot indicates the number of genes in the pathway. Rich factor denotes the number of differentially expressed circRNAs in the KEGG/the total number of circRNAs in the KEGG.
Figure 7
Figure 7
The circRNAs-miRNAs network. (a) Network of 32 differentially expressed circRNAs. Red and green represent up- and down-regulation, and blue represents target-miRNA. (b) The circRNAs-miRNAs network of 10 candidate circRNAs.
Figure 8
Figure 8
Quantitative real-time PCR results of circRNAs expression. Blue: CT-LCG; Red: FT-LCG. Error bars represents standard deviations within the group, the “*”indicates the significant difference p < 0.05, “**”indicates p < 0.01.
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