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. 2022 Sep 3;23(1):633.
doi: 10.1186/s12864-022-08848-3.

Integrated analysis of the expression profiles of the lncRNA-miRNA-mRNA ceRNA network in granulosa and cumulus cells from yak ovaries

Ling Zhao  1 , Yangyang Pan  1 , Meng Wang  1 , Junqian Wang  1 , Yaying Wang  1 , Xiaohong Han  1 , Jinglei Wang  1 , Tongxiang Zhang  1 , Tian Zhao  1 , Honghong He  1 , Yan Cui  1 , Sijiu Yu  2   3
Affiliations

Integrated analysis of the expression profiles of the lncRNA-miRNA-mRNA ceRNA network in granulosa and cumulus cells from yak ovaries

Ling Zhao et al. BMC Genomics. .

Abstract

Background: Growing oocytes acquire the ability to mature through two-way communication between gametes and surrounding somatic cumulus cells (CCs). Granulosa cells (GCs) support oocyte growth, regulate meiosis progression, and modulate global oocyte transcription activity. However, the proliferation and differentiation of the yak ovary in GCs and CCs remain unclear. To characterize the important roles of long non-coding RNA, (lncRNA), microRNA (miRNA), and messenger RNA (mRNA), whole-transcriptome analysis was performed. Real-time quantitative fluorescence PCR was performed to verify the selected RNA sequences.

Results: Important gene ontology terms and Kyoto Encyclopedia of Genes and Genomes pathways related to differentiation and oocyte development were identified for the target genes of differentially expressed lncRNAs, miRNAs, and mRNAs. In total,6223 mRNAs (2197 upregulated, 4026 downregulated), 643 lncRNAs (204 upregulated, 479 downregulated), and 559 miRNAs (311 upregulated, 248 downregulated) were significantly altered between the two groups. Target genes involved in cell adhesion, cell differentiation, regulation of developmental processes, cell proliferation, embryo development, signal transduction, apoptosis, and aromatic compound biosynthetic processes were significantly enriched. These RNAs were involved in ECM-receptor interaction, MAPK signaling, Hippo signaling, PI3K-Akt signaling, cell cycle, cell adhesion, leukocyte trans-endothelial migration, and actin cytoskeleton regulation.

Conclusions: A comprehensive analysis of the co-expression network of competing endogenous RNAs (ceRNAs) will facilitate the understanding of the process of granulosa cell proliferation and differentiation and offer a theoretical basis for the development of oocytes.

Keywords: Cumulus cells; Granulosa cells; LncRNA; ceRNA network; miRNA.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1
Fig. 1
Workflow to identify the ceRNA-networks involved in granulosa and cumulus cells from yak ovaries
Fig. 2
Fig. 2
Primary culture of granulosa cells and cumulus cells (10× magnification). A Granulosa cells, B Cumulus cells
Fig. 3
Fig. 3
Different genes of upregulation and downregulation. A lncRNA, B mRNA, C miRNA
Fig. 4
Fig. 4
Each column represents a sample, and each row represents a lncRNA. The expression level of lncRNA in different samples is represented by different colors. The redder the color, the higher expression level, and the bluer the color, the lower the expression level. Gene expression number and profiling analyses of differentially expressed lncRNA and mRNA among CC and GC. (A) Heat map of the DE lncRNAs, (B) Heat map of the DE mRNAs, (C) Heat map of the DE miRNAs
Fig. 5
Fig. 5
GO functional annotation histogram of the candidate genes related to DE lncRNAs and DE mRNAs
Fig. 6
Fig. 6
KEGG pathway assessment of the source genes of differential top 20 lncRNAs and mRNAs
Fig. 7
Fig. 7
Radar map representations of the target genes of differential miRNAs. A GO functional annotation. B KEGG pathway assessment
Fig. 8
Fig. 8
(A) CeRNA regulatory network in cumulus cells and granulosa cells in yak ovary, (B) Subnetwork of MSTRG.13544.2-miR-221-x|miR-2357-x|miR-338-y|novel-m0707-5p-ncbi_102270546 (CCND1), (C)MSTRG.9576.6-miR-11,987-x|miR-2284-y|novel-m0070-3p|novel-m0191–3p-ncbi_102265941 (ITGA6), (D) MSTRG.5969.1-novel-m0122-5p|novel-m0468-3p-ncbi_102268672 (CDKN1A)
Fig. 9
Fig. 9
Comparison of the gene expression levels determined by RNA-seq and RT-qPCR. A DE lncRNAs, B DE mRNAs, C DE miRNAs
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