Identification of Ovarian Circular RNAs and Differential Expression Analysis between MeiShan and Large White Pigs

Liang, Guoming; Yan, Junyu; Guo, Jin; Tang, Zhonglin

doi:10.3390/ani10071114

Cited by 17 publications

(18 citation statements)

References 51 publications

(62 reference statements)

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“…Liang et al show that circSCIN can be sponged with miR-133 and miR-148a/b, and its regulation determines the reproductive performance of Meishan and large white pigs [50]. CirceGFR, being a competitive endogenous RNA of miR-125a-3p, regulates FYN expression in mouse ovarian granulocyte cells [51]. Here, based on miRNA target site prediction analysis, we found that oar-miR-27a could be a target of novel_circ_0005497.…”

Section: Discussionmentioning

confidence: 71%

Differential Expression and Functional Analysis of CircRNA in the Ovaries of Low and High Fecundity Hanper Sheep

Liu

Zhang

et al. 2021

Animals

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Litter size is a considerable quality that determines the production efficiency of mutton sheep. Therefore, revealing the molecular regulation of high and low fertility may aid the breeding process to develop new varieties of mutton sheep. CircRNAs are the important factors regulating follicular development, but their mechanism role in the regulation of litter size in Hanper sheep is not clear. In the present study, ovarian tissues from the follicular (F) or luteal phase (L) of Hanper sheep that were either consecutive monotocous (M) or polytocous were collected. Then, we performed transcriptome sequencing to screen for differentially expressed circRNAs (DE-circRNAs) and elucidate their function. In total, 4256 circRNA derived from 2184 host genes were identified in which 183 (146 were upregulated, while 37 were downregulated) were differentially expressed in monotocous sheep in the follicular phase versus polytocous sheep in the follicular phase (MF vs. PF). Moreover, 34 circRNAs (14 were upregulated, while 20 were downregulated) were differentially expressed in monotocous sheep in the luteal phase versus polytocous sheep in the luteal sheep (ML vs. PL). This was achieved through DE-circRNAs function enrichment annotation analysis by GESA, GO, and KEGG, which function through the EGF-EGFR-RAS-JNK, TGF-β and thyroid hormone signaling pathway to affect the litter size of Hanper sheep in MF vs. PF and ML vs. PL. STEM results showed that MAPK signaling pathways play a key role in MF vs. PF and ML vs. PL. Through WGCNA analysis, AKT3 was a core gene in MF vs. PF and ML vs. PL. Moreover, competitive endogenous RNA (ceRNA) network analysis revealed the target binding sites for miRNA such as oar-miR-27a, oar-miR-16b, oar-miR-200a/b/c, oar-miR-181a, oar-miR-10a/b, and oar-miR-432 in the identified DE-cirRNAs.

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Section: Discussionmentioning

confidence: 71%

Differential Expression and Functional Analysis of CircRNA in the Ovaries of Low and High Fecundity Hanper Sheep

Liu

Zhang

et al. 2021

Animals

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“…This finding uncovers litter size‐related circRNAs and provides potential candidate loci that may be informative for future pig breeding programs. As recent finding by Liang's research group, they identified 85 differentially expressed circRNAs in the ovarian tissues from MeiShan sows and Large White sows (Liang, Yan, Guo, & Tang, 2020). Furthermore, role investigation circRNAs showed that there is a circular RNA named circSCIN can target and sponge miR‐133 and miR‐148a/b affecting oestrogen secretion.…”

Section: Methodsmentioning

confidence: 88%

Biological functions of circRNAs and their progress in livestock and poultry

Huang

Wang

Zhang

et al. 2020

Reprod Domestic Animals

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CircRNAs are a class of newly discovered RNAs extensively expressed in eukaryotic cells (Jeck et al., 2013). Compared with conventional linear RNAs (containing 5′ and 3′ ends), circRNAs are covalently closed RNA molecules. It was recognized as a class of functional RNA that differs from miRNA, piRNA and lncRNA due to its character of circularity (Xu, Wu, Han, Zhao, & Song, 2017). CircRNAs were first found in RNA viruses as a viroid as early as in 1976 (Sanger, Klotz, Riesner, Gross, & Kleinschmidt, 1976). And then in 1986, it was also founded that the HDV, an animal virus, has a circRNA genome, which were considered to be a characteristic of viroids (Kos, Dijkema, Arnberg, van der Meide, & Schellekens, 1986). Due to limitation of technology at that time, circRNAs were less reported and were once considered as by-products of mis-splicing or regarded as a meaningless abnormally cut RNA, which never got any attention by some researchers because traditional molecular techniques employed in RNA analysis were not able to detect circRNAs because they did not have cap of 5′ end and tail of 3′ end (Jeck & Sharpless, 2014). It was not until 1991 that endogenous circRNAs were demonstrated in human cells, which originated from exons (Nigro et al., 1991). Since then, with advancement of bioinformatics analysis and RNA sequencing technologies, circRNA has attracted more and more attention of many scientists because it has been reported to be ubiquitously present in eukaryotic organisms and have longer half-lives than linear RNAs (Memczak et al., 2013;

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“…Its upregulated status in the uterus suggests that ATP2A3 helps in oviposition [ 34 ]. In addition, miR-133a-5p is a target of the circular RNA scinderin (circSCIN), which affects estrogen secretion [ 35 ]. These findings suggest that these miRNA-mRNA interaction networks may play key roles in the regulation of prolificacy in follicular phase ovaries in Yunshang black goats, thus providing new insights for further understanding the regulatory mechanisms of goat prolificacy.…”

Section: Discussionmentioning

confidence: 99%

Integrated analyses of miRNA-mRNA expression profiles of ovaries reveal the crucial interaction networks that regulate the prolificacy of goats in the follicular phase

Liu

Zhou

et al. 2021

BMC Genomics

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Background Litter size is an important index of mammalian prolificacy and is determined by the ovulation rate. The ovary is a crucial organ for mammalian reproduction and is associated with follicular development, maturation and ovulation. However, prolificacy is influenced by multiple factors, and its molecular regulation in the follicular phase remains unclear. Methods Ten female goats with no significant differences in age and weight were randomly selected and divided into either the high-yielding group (n = 5, HF) or the low-yielding group (n = 5, LF). Ovarian tissues were collected from goats in the follicular phase and used to construct mRNA and miRNA sequencing libraries to analyze transcriptomic variation between high- and low-yield Yunshang black goats. Furthermore, integrated analysis of the differentially expressed (DE) miRNA-mRNA pairs was performed based on their correlation. The STRING database was used to construct a PPI network of the DEGs. RT–qPCR was used to validate the results of the predicted miRNA-mRNA pairs. Luciferase analysis and CCK-8 assay were used to detect the function of the miRNA-mRNA pairs and the proliferation of goat granulosa cells (GCs). Results A total of 43,779 known transcripts, 23,067 novel transcripts, 424 known miRNAs and 656 novel miRNAs were identified by RNA-seq in the ovaries from both groups. Through correlation analysis of the miRNA and mRNA expression profiles, 263 negatively correlated miRNA-mRNA pairs were identified in the LF vs. HF comparison. Annotation analysis of the DE miRNA-mRNA pairs identified targets related to biological processes such as “estrogen receptor binding (GO:0030331)”, “oogenesis (GO:0048477)”, “ovulation cycle process (GO:0022602)” and “ovarian follicle development (GO:0001541)”. Subsequently, five KEGG pathways (oocyte meiosis, progesterone-mediated oocyte maturation, GnRH signaling pathway, Notch signaling pathway and TGF-β signaling pathway) were identified in the interaction network related to follicular development, and a PPI network was also constructed. In the network, we found that CDK12, FAM91A1, PGS1, SERTM1, SPAG5, SYNE1, TMEM14A, WNT4, and CAMK2G were the key nodes, all of which were targets of the DE miRNAs. The PPI analysis showed that there was a clear interaction among the CAMK2G, SERTM1, TMEM14A, CDK12, SYNE1 and WNT4 genes. In addition, dual luciferase reporter and CCK-8 assays confirmed that miR-1271-3p suppressed the proliferation of GCs by inhibiting the expression of TXLNA. Conclusions These results increase the understanding of the molecular mechanisms underlying goat prolificacy. These results also provide a basis for studying interactions between genes and miRNAs, as well as the functions of the pathways in ovarian tissues involved in goat prolificacy in the follicular phase.

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Identification of Ovarian Circular RNAs and Differential Expression Analysis between MeiShan and Large White Pigs

Cited by 17 publications

References 51 publications

Differential Expression and Functional Analysis of CircRNA in the Ovaries of Low and High Fecundity Hanper Sheep

Differential Expression and Functional Analysis of CircRNA in the Ovaries of Low and High Fecundity Hanper Sheep

Biological functions of circRNAs and their progress in livestock and poultry

Integrated analyses of miRNA-mRNA expression profiles of ovaries reveal the crucial interaction networks that regulate the prolificacy of goats in the follicular phase

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