Identification and characterization of a conservative W chromosome-linked circRNA in half-smooth tongue sole (Cynoglossus semilaevis) reveal its female-biased expression in immune organs

Lv, Yingjun; Liu, Rongrong; Yu, Yan; Shan, Chang-Min; Bian, Weihua; Jiang, Jing; Zhang, Daolai; Yang, Cheng; Sun, Yeying

doi:10.1016/j.fsi.2018.08.063

Cited by 13 publications

(7 citation statements)

References 28 publications

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“…Until recently, an increasing number of studies on circRNAs in fish have been carried out and reported. These studies confirmed the existence of circRNAs in several species, such as zebrafish ( Danio rerio ) [ 1 , 9 ], large yellow croaker ( Larimichthys crocea ) [ 10 ], tongue sole ( Cynoglossus semilaevis ) [ 11 ], olive flounder ( Paralichthys olivaceus ) [ 12 ], grass carp ( Ctenopharyngodon idella ) [ 13 ], Nile tilapia ( Oreochromis niloticus ) [ 14 ], European Sea Bass ( Dicentrarchus labrax L.) [ 15 ] and medaka ( Oryzias latipes ) [ 16 ]. These findings suggest that circRNAs perform certain biological functions in fish.…”

Section: Introductionmentioning

confidence: 64%

Comprehensive CircRNA Profiling and Selection of Key CircRNAs Reveal the Potential Regulatory Roles of CircRNAs throughout Ovarian Development and Maturation in Cynoglossus semilaevis

Bao

Wang

et al. 2021

Biology

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CircRNAs are novel endogenous non-coding small RNAs involved in the regulation of multiple biological processes. However, little is known regarding circRNAs in ovarian development and maturation of fish. Our study, for the first time, provides the genome-wide overview of the types and relative abundances of circRNAs in tongue sole tissues during three ovarian developmental stages. We detected 6790 circRNAs in the brain, 5712 in the pituitary gland, 4937 in the ovary and 4160 in the liver. Some circRNAs exhibit tissue-specific expression, and qRT-PCR largely confirmed 6 differentially expressed (DE) circRNAs. Gene Ontology and KEGG pathway analyses of DE mRNAs were performed. Some DE circRNA parental genes were closely associated with biological processes in key signalling pathways and may play essential roles in ovarian development and maturation. We found that the selected circRNAs were involved in 10 pathways. RNase R digestion experiment and Sanger sequencing verified that the circRNA had a ring structure and was RNase R resistant. qRT-PCR results largely confirmed differential circRNA expression patterns from the RNA-seq data. These findings indicate that circRNAs are widespread in terms of present in production-related tissues of tongue sole with potentially important regulatory roles in ovarian development and maturation.

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Section: Introductionmentioning

confidence: 64%

Comprehensive CircRNA Profiling and Selection of Key CircRNAs Reveal the Potential Regulatory Roles of CircRNAs throughout Ovarian Development and Maturation in Cynoglossus semilaevis

Bao

Wang

et al. 2021

Biology

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“…However, there has been no report about the important roles of circRNAs during the immune process of P. olivaceus . In fish, few circRNA researches have been published on teleosts, including half-smooth tongue sole ( Cynoglossus semilaevis ) (Li et al, 2018a), large yellow croaker ( Larimichthys crocea ) (Xu et al, 2017), zebrafish ( Danio rerio ) (Shen et al, 2017), coelacanth (Anne et al, 2014) and grass carp ( Ctenopharyngodon idella ) (He et al, 2017). Interestingly, the most recent progresses reveal that circRNAs also take part in immune regulation and viral infection (Wang et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

Identification of Potential Immune-Related circRNA–miRNA–mRNA Regulatory Network in Intestine of Paralichthys olivaceus During Edwardsiella tarda Infection

et al. 2019

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Olive flounder ( Paralichthys olivaceus ) is an important economical flatfish in Japan, Korea, and China, but its production has been greatly threatened by disease outbreaks. In this research, we aimed to explore the immune responsive mechanism of P. olivaceus against Edwardsiella tarda infection by profiling the expression of circRNA, miRNA, and mRNA by RNA-seq and constructing a regulatory circular circRNA–miRNA–mRNA network. Illumina sequencing of samples from normal control (H0), 2 h (H2), 8 h (H8), and 12 h (H12) post-challenge was conducted. Differentially expressed (DE) circRNA (DE–circRNAs), miRNAs (DE–miRNAs), and mRNAs [differential expression genes (DEGs)] between challenge and control groups were identified, resulting in a total of 62 DE–circRNAs, 39 DE–miRNAs, and 3,011 DEGs. Based on the differentially expressed gene results, miRNA target interactions (circRNA–miRNA pairs and miRNA–mRNA pairs) were predicted by MiRanda software. Once these paired were combined, a preliminary circRNA–miRNA–mRNA network was generated with 198 circRNA–miRNA edges and 3,873 miRNA–mRNA edges, including 44 DE–circRNAs, 32 DE–miRNAs, and 1,774 DEGs. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis was performed to evaluate the function of the DEGs in this network, and we focused and identified two important intestinal immune pathways (herpes simplex infection and intestinal immune network for IgA production) that showed statistical significance between the challenge and control groups. Furthermore, three critical DEGs (nectin2, MHC II α-chain, and MHC II β-chain) were identified, mapped into the preliminary circRNA–miRNA–mRNA network, and new circRNA–miRNA–mRNA regulatory networks were constructed. In conclusion, we, for the first time, identified circRNA–miRNA–mRNA network from P. olivaceus in the pathogenesis of E. tarda and provided valuable resources for further analyses of the molecular mechanisms and signaling networks.

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“…CircRNAs were differentially expressed during sex reversal of ricefield eel. In other fish, 5052, 3762, 3868, 975 and 2727 circRNAs were identified in grass carp [ 58 ], half-smooth tongue sole [ 59 ], zebrafish [ 5 ], large yellow croaker [ 60 ] and medaka [ 22 ], respectively. In our study, the expression pattern of circRNAs in sex reversal of ricefield eel has been analyzed.…”

Section: Discussionmentioning

confidence: 99%

Circular RNA expression profiles and CircSnd1-miR-135b/c-foxl2 axis analysis in gonadal differentiation of protogynous hermaphroditic ricefield eel Monopterus albus

Yang

Chen

et al. 2022

BMC Genomics

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Background The expression and biological functions of circular RNAs (circRNAs) in reproductive organs have been extensively reported. However, it is still unclear whether circRNAs are involved in sex change. To this end, RNA sequencing (RNA-seq) was performed in gonads at 5 sexual stages (ovary, early intersexual stage gonad, middle intersexual stage gonad, late intersexual stage gonad, and testis) of ricefield eel, and the expression profiles and potential functions of circRNAs were studied. Results Seven hundred twenty-one circRNAs were identified, and the expression levels of 10 circRNAs were verified by quantitative real-time PCR (qRT–PCR) and found to be in accordance with the RNA-seq data, suggesting that the RNA-seq data were reliable. Then, the sequence length, category, sequence composition and the relationship between the parent genes of the circRNAs were explored. A total of 147 circRNAs were differentially expressed in the sex change process, and GO and KEGG analyses revealed that some differentially expressed (such as novel_circ_0000659, novel_circ_0004005 and novel_circ_0005865) circRNAs were closely involved in sex change. Furthermore, expression pattern analysis demonstrated that both circSnd1 and foxl2 were downregulated in the process of sex change, which was contrary to mal-miR-135b. Finally, dual-luciferase reporter assay and RNA immunoprecipitation showed that circSnd1 and foxl2 can combine with mal-miR-135b and mal-miR-135c. These data revealed that circSnd1 regulates foxl2 expression in the sex change of ricefield eel by acting as a sponge of mal-miR-135b/c. Conclusion Our results are the first to demonstrate that circRNAs have potential effects on sex change in ricefield eel; and circSnd1 could regulate foxl2 expression in the sex change of ricefield eel by acting as a sponge of mal-miR-135b/c. These data will be useful for enhancing our understanding of sequential hermaphroditism and sex change in ricefield eel or other teleosts.

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Identification and characterization of a conservative W chromosome-linked circRNA in half-smooth tongue sole (Cynoglossus semilaevis) reveal its female-biased expression in immune organs

Cited by 13 publications

References 28 publications

Comprehensive CircRNA Profiling and Selection of Key CircRNAs Reveal the Potential Regulatory Roles of CircRNAs throughout Ovarian Development and Maturation in Cynoglossus semilaevis

Comprehensive CircRNA Profiling and Selection of Key CircRNAs Reveal the Potential Regulatory Roles of CircRNAs throughout Ovarian Development and Maturation in Cynoglossus semilaevis

Identification of Potential Immune-Related circRNA–miRNA–mRNA Regulatory Network in Intestine of Paralichthys olivaceus During Edwardsiella tarda Infection

Circular RNA expression profiles and CircSnd1-miR-135b/c-foxl2 axis analysis in gonadal differentiation of protogynous hermaphroditic ricefield eel Monopterus albus

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