Identification and integrated analysis of lncRNAs and miRNAs in IPEC-J2 cells provide novel insight into the regulation of the innate immune response by PDCoV infection
Abstract Background Noncoding RNAs (ncRNAs), including microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), are pivotal regulators involved in the pathogenic mechanism of multiple coronaviruses. Porcine deltacoronavirus (PDCoV) has evolved multiple strategies to escape the innate immune response of...
| Main Authors: | , , , , , , , , , , , , , , |
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| Format: | Article |
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BMC
2022-07-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-022-08722-2 |
| _version_ | 1811219220030029824 |
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| author | Shan Jiang Jianfei Chen Xiuli Li Weike Ren Fengxiang Li Ting Wang Cheng Li Zhimin Dong Xiangxue Tian Li Zhang Lili Wang Chao lu Jingjing Chi Li Feng Minghua Yan |
| author_facet | Shan Jiang Jianfei Chen Xiuli Li Weike Ren Fengxiang Li Ting Wang Cheng Li Zhimin Dong Xiangxue Tian Li Zhang Lili Wang Chao lu Jingjing Chi Li Feng Minghua Yan |
| author_sort | Shan Jiang |
| collection | DOAJ |
| description | Abstract Background Noncoding RNAs (ncRNAs), including microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), are pivotal regulators involved in the pathogenic mechanism of multiple coronaviruses. Porcine deltacoronavirus (PDCoV) has evolved multiple strategies to escape the innate immune response of host cells, but whether ncRNAs are involved in this process during PDCoV infection is still unknown. Results In this study, the expression profiles of miRNAs, lncRNAs and mRNAs in IPEC-J2 cells infected with PDCoV at 0, 12 and 24 hours postinfection (hpi) were identified through small RNA and RNA sequencing. The differentially expressed miRNAs (DEmiRNAs), lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) were screened from the comparison group of IPEC-J2 cells at 0 and 12 hpi as well as the comparison group of IPEC-J2 cells at 12 and 24 hpi. The target genes of these DEncRNAs were predicted. The bioinformatics analysis of the target genes revealed multiple significantly enriched functions and pathways. Among them, the genes that were associated with innate immunity were specifically screened. The expression of innate immunity-related ncRNAs and mRNAs was validated by RT–qPCR. Competing endogenous RNA (ceRNA) regulatory networks among innate immunity-related ncRNAs and their target mRNAs were established. Moreover, we found that the replication of PDCoV was significantly inhibited by two innate immunity-related miRNAs, ssc-miR-30c-3p and ssc-miR-374b-3p, in IPEC-J2 cells. Conclusions This study provides a data platform to conduct studies of the pathogenic mechanism of PDCoV from a new perspective and will be helpful for further elucidation of the functional role of ncRNAs involved in PDCoV escaping the innate immune response. |
| first_indexed | 2024-04-12T07:22:23Z |
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| id | doaj.art-213c80ee8886491a991d987cee34641b |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-12T07:22:23Z |
| publishDate | 2022-07-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-213c80ee8886491a991d987cee34641b2022-12-22T03:42:16ZengBMCBMC Genomics1471-21642022-07-0123111710.1186/s12864-022-08722-2Identification and integrated analysis of lncRNAs and miRNAs in IPEC-J2 cells provide novel insight into the regulation of the innate immune response by PDCoV infectionShan Jiang0Jianfei Chen1Xiuli Li2Weike Ren3Fengxiang Li4Ting Wang5Cheng Li6Zhimin Dong7Xiangxue Tian8Li Zhang9Lili Wang10Chao lu11Jingjing Chi12Li Feng13Minghua Yan14Tianjin Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural SciencesState Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural SciencesTianjin Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural SciencesTianjin Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural SciencesMinistry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai UniversityInstitute of Pathogenic Microorganism and College of Bioscience and Engineering, Jiangxi Agricultural UniversityTianjin Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural SciencesTianjin Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural SciencesTianjin Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural SciencesTianjin Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural SciencesTianjin Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural SciencesTianjin Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural SciencesTianjin Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural SciencesState Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural SciencesTianjin Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural SciencesAbstract Background Noncoding RNAs (ncRNAs), including microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), are pivotal regulators involved in the pathogenic mechanism of multiple coronaviruses. Porcine deltacoronavirus (PDCoV) has evolved multiple strategies to escape the innate immune response of host cells, but whether ncRNAs are involved in this process during PDCoV infection is still unknown. Results In this study, the expression profiles of miRNAs, lncRNAs and mRNAs in IPEC-J2 cells infected with PDCoV at 0, 12 and 24 hours postinfection (hpi) were identified through small RNA and RNA sequencing. The differentially expressed miRNAs (DEmiRNAs), lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) were screened from the comparison group of IPEC-J2 cells at 0 and 12 hpi as well as the comparison group of IPEC-J2 cells at 12 and 24 hpi. The target genes of these DEncRNAs were predicted. The bioinformatics analysis of the target genes revealed multiple significantly enriched functions and pathways. Among them, the genes that were associated with innate immunity were specifically screened. The expression of innate immunity-related ncRNAs and mRNAs was validated by RT–qPCR. Competing endogenous RNA (ceRNA) regulatory networks among innate immunity-related ncRNAs and their target mRNAs were established. Moreover, we found that the replication of PDCoV was significantly inhibited by two innate immunity-related miRNAs, ssc-miR-30c-3p and ssc-miR-374b-3p, in IPEC-J2 cells. Conclusions This study provides a data platform to conduct studies of the pathogenic mechanism of PDCoV from a new perspective and will be helpful for further elucidation of the functional role of ncRNAs involved in PDCoV escaping the innate immune response.https://doi.org/10.1186/s12864-022-08722-2PDCoVmiRNAlncRNAPathogenesisHost defense responseIntestinal porcine epithelial cells |
| spellingShingle | Shan Jiang Jianfei Chen Xiuli Li Weike Ren Fengxiang Li Ting Wang Cheng Li Zhimin Dong Xiangxue Tian Li Zhang Lili Wang Chao lu Jingjing Chi Li Feng Minghua Yan Identification and integrated analysis of lncRNAs and miRNAs in IPEC-J2 cells provide novel insight into the regulation of the innate immune response by PDCoV infection BMC Genomics PDCoV miRNA lncRNA Pathogenesis Host defense response Intestinal porcine epithelial cells |
| title | Identification and integrated analysis of lncRNAs and miRNAs in IPEC-J2 cells provide novel insight into the regulation of the innate immune response by PDCoV infection |
| title_full | Identification and integrated analysis of lncRNAs and miRNAs in IPEC-J2 cells provide novel insight into the regulation of the innate immune response by PDCoV infection |
| title_fullStr | Identification and integrated analysis of lncRNAs and miRNAs in IPEC-J2 cells provide novel insight into the regulation of the innate immune response by PDCoV infection |
| title_full_unstemmed | Identification and integrated analysis of lncRNAs and miRNAs in IPEC-J2 cells provide novel insight into the regulation of the innate immune response by PDCoV infection |
| title_short | Identification and integrated analysis of lncRNAs and miRNAs in IPEC-J2 cells provide novel insight into the regulation of the innate immune response by PDCoV infection |
| title_sort | identification and integrated analysis of lncrnas and mirnas in ipec j2 cells provide novel insight into the regulation of the innate immune response by pdcov infection |
| topic | PDCoV miRNA lncRNA Pathogenesis Host defense response Intestinal porcine epithelial cells |
| url | https://doi.org/10.1186/s12864-022-08722-2 |
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