Identification of Potential Immune-Related circRNA–miRNA–mRNA Regulatory Network in Intestine of Paralichthys olivaceus During Edwardsiella tarda Infection
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 p...
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2019-08-01
|
| Series: | Frontiers in Genetics |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/article/10.3389/fgene.2019.00731/full |
| _version_ | 1818293387574378496 |
|---|---|
| author | Yunji Xiu Yunji Xiu Guangpeng Jiang Shun Zhou Jing Diao Hongjun Liu Baofeng Su Chao Li |
| author_facet | Yunji Xiu Yunji Xiu Guangpeng Jiang Shun Zhou Jing Diao Hongjun Liu Baofeng Su Chao Li |
| author_sort | Yunji Xiu |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-13T03:15:03Z |
| format | Article |
| id | doaj.art-7e16bf6cc85d4e44a9cf33f9bf163c07 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-13T03:15:03Z |
| publishDate | 2019-08-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-7e16bf6cc85d4e44a9cf33f9bf163c072022-12-22T00:01:30ZengFrontiers Media S.A.Frontiers in Genetics1664-80212019-08-011010.3389/fgene.2019.00731441798Identification of Potential Immune-Related circRNA–miRNA–mRNA Regulatory Network in Intestine of Paralichthys olivaceus During Edwardsiella tarda InfectionYunji Xiu0Yunji Xiu1Guangpeng Jiang2Shun Zhou3Jing Diao4Hongjun Liu5Baofeng Su6Chao Li7School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, ChinaShandong Key Laboratory of Disease Control in Mariculture, Marine Biology Institute of Shandong Province, Qingdao, ChinaSchool of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, ChinaSchool of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, ChinaShandong Key Laboratory of Disease Control in Mariculture, Marine Biology Institute of Shandong Province, Qingdao, ChinaShandong Key Laboratory of Disease Control in Mariculture, Marine Biology Institute of Shandong Province, Qingdao, ChinaSchool of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, United StatessSchool of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, ChinaOlive 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.https://www.frontiersin.org/article/10.3389/fgene.2019.00731/fullcircRNAmiRNAmRNAcircRNA–miRNA–mRNA networkimmune responseParalichthys olivaceus |
| spellingShingle | Yunji Xiu Yunji Xiu Guangpeng Jiang Shun Zhou Jing Diao Hongjun Liu Baofeng Su Chao Li Identification of Potential Immune-Related circRNA–miRNA–mRNA Regulatory Network in Intestine of Paralichthys olivaceus During Edwardsiella tarda Infection Frontiers in Genetics circRNA miRNA mRNA circRNA–miRNA–mRNA network immune response Paralichthys olivaceus |
| title | Identification of Potential Immune-Related circRNA–miRNA–mRNA Regulatory Network in Intestine of Paralichthys olivaceus During Edwardsiella tarda Infection |
| title_full | Identification of Potential Immune-Related circRNA–miRNA–mRNA Regulatory Network in Intestine of Paralichthys olivaceus During Edwardsiella tarda Infection |
| title_fullStr | Identification of Potential Immune-Related circRNA–miRNA–mRNA Regulatory Network in Intestine of Paralichthys olivaceus During Edwardsiella tarda Infection |
| title_full_unstemmed | Identification of Potential Immune-Related circRNA–miRNA–mRNA Regulatory Network in Intestine of Paralichthys olivaceus During Edwardsiella tarda Infection |
| title_short | Identification of Potential Immune-Related circRNA–miRNA–mRNA Regulatory Network in Intestine of Paralichthys olivaceus During Edwardsiella tarda Infection |
| title_sort | identification of potential immune related circrna mirna mrna regulatory network in intestine of paralichthys olivaceus during edwardsiella tarda infection |
| topic | circRNA miRNA mRNA circRNA–miRNA–mRNA network immune response Paralichthys olivaceus |
| url | https://www.frontiersin.org/article/10.3389/fgene.2019.00731/full |
| work_keys_str_mv | AT yunjixiu identificationofpotentialimmunerelatedcircrnamirnamrnaregulatorynetworkinintestineofparalichthysolivaceusduringedwardsiellatardainfection AT yunjixiu identificationofpotentialimmunerelatedcircrnamirnamrnaregulatorynetworkinintestineofparalichthysolivaceusduringedwardsiellatardainfection AT guangpengjiang identificationofpotentialimmunerelatedcircrnamirnamrnaregulatorynetworkinintestineofparalichthysolivaceusduringedwardsiellatardainfection AT shunzhou identificationofpotentialimmunerelatedcircrnamirnamrnaregulatorynetworkinintestineofparalichthysolivaceusduringedwardsiellatardainfection AT jingdiao identificationofpotentialimmunerelatedcircrnamirnamrnaregulatorynetworkinintestineofparalichthysolivaceusduringedwardsiellatardainfection AT hongjunliu identificationofpotentialimmunerelatedcircrnamirnamrnaregulatorynetworkinintestineofparalichthysolivaceusduringedwardsiellatardainfection AT baofengsu identificationofpotentialimmunerelatedcircrnamirnamrnaregulatorynetworkinintestineofparalichthysolivaceusduringedwardsiellatardainfection AT chaoli identificationofpotentialimmunerelatedcircrnamirnamrnaregulatorynetworkinintestineofparalichthysolivaceusduringedwardsiellatardainfection |