Integrated Analysis of circRNA-miRNA-mRNA Regulatory Networks in the Intestine of Sebastes schlegelii Following Edwardsiella tarda Challenge

Cao, Min; Xu, Yan; Su, Baofeng; Fu, Qiang; Xue, Ting; Song, Lin; Li, Qi; Li, Chao

doi:10.3389/fimmu.2020.618687

Cited by 22 publications

(18 citation statements)

References 76 publications

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“…CircRNAs are a large category of ncRNAs without 5' cap and a 3' poly (A) tail, generating from precursor mRNA alternative back-splicing with covalently closed continuous loop structures ( 29 , 36 ). It has been demonstrated that the events of alternative circularization phenomenon (circRNAs) were found to exist widely in various species and were involved in diverse biological processes ( 22 , 37 , 38 ). Herein, our results suggest that significant changes occurred in the chicken transcriptome (circRNAs) upon APEC infection, which first performed the genome-wide identification and investigated the potential function of circRNAs in response to APEC infection in chicken macrophages.…”

Section: Discussionmentioning

confidence: 99%

Analysis of circRNA expression in chicken HD11 cells in response to avian pathogenic E.coli

Sun

Yang

et al. 2022

Front. Vet. Sci.

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Avian pathogenic E. coli (APEC), one of the widespread zoonotic-pathogen, can cause a series of diseases collectively known as colibacillosis. This disease can cause thousands of million dollars economic loss each year in poultry industry and threaten to human health via meat or egg contamination. However, the detailed molecular mechanism underlying APEC infection is still not fully understood. Circular RNAs, a new type of endogenous noncoding RNA, have been demonstrated to involve in various biological processes. However, it is still not clear whether the circRNAs participate in host response against APEC infection. Herein, we utilized the high-throughput sequence technology to identify the circRNA expression profiles in APEC infected HD cells. A total of di erentially expressed (DE) circRNAs were detected in the comparison of APEC infected HD cells vs. wild type HD cells, which were involved in MAPK signaling pathway, Endocytosis, Focal adhesion, mTOR signaling pathway, and VEGF signaling pathway. Specifically, the source genes (BRAF, PPP CB, BCL L , RAB A, and TSC ) and their corresponding DE circRNAs may play a significant role in APEC infection. Moreover, based on ceRNA regulation, we constructed the circRNA-miRNA network and identified a couple of important regulatory relationship pairs related to APEC infection, including circRAB A-gga-miR-b-p, circRAB A-gga-miR-, and circTSC -gga-miR--p. Results indicate that the aforementioned specific circRNAs and circRNA-miRNA network might have important role in regulating host immune response against APEC infection. This study is the first time to investigate the circRNAs expression profile and the biological function of the source genes of the identified DE circRNAs after APEC infection of chicken HD cells. These results would contribute to a better understanding of the molecular mechanisms in host response against APEC infection.

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Section: Discussionmentioning

confidence: 99%

Analysis of circRNA expression in chicken HD11 cells in response to avian pathogenic E.coli

Sun

Yang

et al. 2022

Front. Vet. Sci.

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“…Similarly, 87 DE-circRNAs were identified by expression profile analysis in the intestine of Sebastes schlegelii after pathogen infection. The circRNA-miRNA-mRNA regulation network was found involved in the regulation of the NF-kB signaling pathway and the expression of interleukin 1 receptor [32]. Novel_circ_0004195, serving as ceRNA of novel_530, could activate the downstream NF-kB signaling pathway.…”

Section: Discussionmentioning

confidence: 99%

Revealing New Landscape of Turbot (Scophthalmus maximus) Spleen Infected with Aeromonas salmonicida through Immune Related circRNA-miRNA-mRNA Axis

Xue

Liu

Cao

et al. 2021

Biology

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Increasing evidence suggests that non-coding RNAs (ncRNA) play an important role in a variety of biological life processes by regulating gene expression at the transcriptional and post-transcriptional levels. Turbot (Scophthalmus maximus) has been threatened by various pathogens. In this study, the expression of circular RNAs (circRNAs), microRNAs (miRNAs), and mRNA in the immune organs spleen of turbot infected with Aeromonas salmonicida was analyzed by high-throughput sequencing, and a circRNA-miRNA-mRNA network was constructed, so as to explore the function of non-coding RNA in the immune system of teleost. Illumina sequencing was performed on the uninfected group and infected group. A total of 119 differential expressed circRNAs (DE-circRNAs), 140 DE-miRNAs, and 510 DE-mRNAs were identified in the four infected groups compared with the uninfected group. Most DE-mRNAs and the target genes of DE-ncRNAs were involved in immune-related pathways. The quantitative real-time PCR (qRT-PCR) results verified the reliability and accuracy of the high-throughput sequencing data. Ninety-six differentially expressed circRNA-miRNA-mRNA regulatory networks were finally constructed. Among them, 15 circRNA-miRNA-mRNA were presented in the form of “up (circRNA)-down (miRNA)-up (mRNA)” or “down-up-down”. Immune-related genes gap junction CX32.2, cell adhesion molecule 3, and CC chemokine were also found in these networks. These results indicate that ncRNA may regulate the expression of immune-related genes through the circRNA-miRNA-mRNA regulatory network and thus participate in the immune response of turbot spleen after pathogen infection.

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“…For example, it is reported that teleost miRNAs can promote the antibacterial resistance by regulating several immune-related pathways, including FoxO signaling pathway (19), Complement and coagulation cascades (20), and Intestinal immune network for IgA production (21). Nevertheless, there are a few studies on the mechanism of interactions between noncoding RNAs and coding RNAs in bony fishes (21)(22)(23)(24)(25). Compared with the analysis of single miRNAs or mRNAs, integrated analysis of mRNA-seq and miRNA-seq would more accurately determine the key genes regulating immunity and the miRNAs targeting these genes, which has become a trend and method to study the mechanism of anti-pathogen immune response.…”

Section: Introductionmentioning

confidence: 99%

Integrative analyses of mRNA and microRNA expression profiles reveal the innate immune mechanism for the resistance to Vibrio parahaemolyticus infection in Epinephelus coioides

Qiao

et al. 2022

Front. Immunol.

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Vibrio parahaemolyticus, as one of the main pathogens of marine vibriosis, has brought huge losses to aquaculture. However, the interaction mechanism between V. parahaemolyticus and Epinephelus coioides remains unclear. Moreover, there is a lack of comprehensive multi-omics analysis of the immune response of grouper spleen to V. parahaemolyticus. Herein, E. coioides was artificially injected with V. parahaemolyticus, and it was found that the mortality was 16.7% in the early stage of infection, and accompanied by obvious histopathological lesions in the spleen. Furthermore, 1586 differentially expressed genes were screened by mRNA-seq. KEGG analysis showed that genes were significantly enriched in immune-related pathways, Acute-phase immune response, Apoptosis, Complement system and Cytokine-cytokine receptor interaction. As for miRNA-seq analysis, a total of 55 significantly different miRNAs were identified. Further functional annotation analysis indicated that the target genes of differentially expressed miRNAs were enriched in three important pathways (Phosphatidylinositol signaling system, Lysosome and Focal adhesions). Through mRNA-miRNA integrated analysis, 1427 significant miRNA–mRNA pairs were obtained and “p53 signaling pathway”, “Intestinal immune network for IgA production” were considered as two crucial pathways. Finally, miR-144-y, miR-497-x, novel-m0459-5p, miR-7133-y, miR-378-y, novel-m0440-5p and novel-m0084-3p may be as key miRNAs to regulate immune signaling pathways via the miRNA-mRNA interaction network. The above results suggest that the mRNA-miRNA integrated analysis not only sheds new light on the molecular mechanisms underlying the interaction between host and V. parahaemolyticus but also provides valuable and new insights into resistance to vibrio infection.

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Integrated Analysis of circRNA-miRNA-mRNA Regulatory Networks in the Intestine of Sebastes schlegelii Following Edwardsiella tarda Challenge

Cited by 22 publications

References 76 publications

Analysis of circRNA expression in chicken HD11 cells in response to avian pathogenic E.coli

Analysis of circRNA expression in chicken HD11 cells in response to avian pathogenic E.coli

Revealing New Landscape of Turbot (Scophthalmus maximus) Spleen Infected with Aeromonas salmonicida through Immune Related circRNA-miRNA-mRNA Axis

Integrative analyses of mRNA and microRNA expression profiles reveal the innate immune mechanism for the resistance to Vibrio parahaemolyticus infection in Epinephelus coioides

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