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N6-Methyladenosine Methylation Analysis of Long Noncoding RNAs and mRNAs in IPEC-J2 Cells Treated With Clostridium perfringens beta2 Toxin

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Title: N6-Methyladenosine Methylation Analysis of Long Noncoding RNAs and mRNAs in IPEC-J2 Cells Treated With Clostridium perfringens beta2 Toxin
Authors: Jiaojiao Yang, Qiaoli Yang, Juanli Zhang, Xiaoli Gao, Ruirui Luo, Kaihui Xie, Wei Wang, Jie Li, Xiaoyu Huang, Zunqiang Yan, Pengfei Wang, Shuangbao Gun
Source: Frontiers in Immunology, Vol 12 (2021)
Publisher Information: Frontiers Media S.A., 2021.
Publication Year: 2021
Collection: LCC:Immunologic diseases. Allergy
Subject Terms: M6A methylation, MeRIP-seq, RNA-seq, IPEC-J2, CPB2, Immunologic diseases. Allergy, RC581-607
More Details: BackgroundThe n6-methyladenosine (m6A) modification is present widely in mRNAs and long non-coding RNAs (lncRNAs), and is related to the occurrence and development of certain diseases. However, the role of m6A methylation in Clostridium perfringens type C infectious diarrhea remains unclear.MethodsHere, we treated intestinal porcine jejunum epithelial cells (IPEC-J2 cells) with Clostridium perfringens beta2 (CPB2) toxin to construct an in vitro model of Clostridium perfringens type C (C. perfringens type C) infectious diarrhea, and then used methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA sequencing (RNA-seq) to identify the methylation profiles of mRNAs and lncRNAs in IPEC-J2 cells.ResultsWe identified 6,413 peaks, representing 5,825 m6A-modified mRNAs and 433 modified lncRNAs, of which 4,356 m6A modified mRNAs and 221 m6A modified lncRNAs were significantly differential expressed between the control group and CPB2 group. The motif GGACU was enriched significantly in both the control group and the CPB2 group. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation analysis showed that the differentially methylated modified mRNAs were mainly enriched in Hippo signaling pathway and Wnt signaling pathway. In addition, the target genes of the differentially m6A modified lncRNAs were related to defense response to virus and immune response. For example, ENSSSCG00000042575, ENSSSCG00000048701 and ENSSSCG00000048785 might regulate the defense response to virus, immune and inflammatory response to resist the harmful effects of viruses on cells.ConclusionIn summary, this study established the m6A transcription profile of mRNAs and lncRNAs in IPEC-J2 cells treated by CPB2 toxin. Further analysis showed that m6A-modified RNAs were related to defense against viruses and immune response after CPB2 toxin treatment of the cells. Threem6A-modified lncRNAs, ENSSSCG00000042575, ENSSSCG00000048785 and ENSSSCG00000048701, were most likely to play a key role in CPB2 toxin-treated IPEC-J2 cells. The results provide a theoretical basis for further research on the role of m6A modification in piglet diarrhea.
Document Type: article
File Description: electronic resource
Language: English
ISSN: 1664-3224
Relation: https://www.frontiersin.org/articles/10.3389/fimmu.2021.769204/full; https://doaj.org/toc/1664-3224
DOI: 10.3389/fimmu.2021.769204
Access URL: https://doaj.org/article/7435b4d5c1b24b05a4452cd1b3aff6e4
Accession Number: edsdoj.7435b4d5c1b24b05a4452cd1b3aff6e4
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  Data: N6-Methyladenosine Methylation Analysis of Long Noncoding RNAs and mRNAs in IPEC-J2 Cells Treated With Clostridium perfringens beta2 Toxin
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  Data: <searchLink fieldCode="AR" term="%22Jiaojiao+Yang%22">Jiaojiao Yang</searchLink><br /><searchLink fieldCode="AR" term="%22Qiaoli+Yang%22">Qiaoli Yang</searchLink><br /><searchLink fieldCode="AR" term="%22Juanli+Zhang%22">Juanli Zhang</searchLink><br /><searchLink fieldCode="AR" term="%22Xiaoli+Gao%22">Xiaoli Gao</searchLink><br /><searchLink fieldCode="AR" term="%22Ruirui+Luo%22">Ruirui Luo</searchLink><br /><searchLink fieldCode="AR" term="%22Kaihui+Xie%22">Kaihui Xie</searchLink><br /><searchLink fieldCode="AR" term="%22Wei+Wang%22">Wei Wang</searchLink><br /><searchLink fieldCode="AR" term="%22Jie+Li%22">Jie Li</searchLink><br /><searchLink fieldCode="AR" term="%22Xiaoyu+Huang%22">Xiaoyu Huang</searchLink><br /><searchLink fieldCode="AR" term="%22Zunqiang+Yan%22">Zunqiang Yan</searchLink><br /><searchLink fieldCode="AR" term="%22Pengfei+Wang%22">Pengfei Wang</searchLink><br /><searchLink fieldCode="AR" term="%22Shuangbao+Gun%22">Shuangbao Gun</searchLink>
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  Data: Frontiers in Immunology, Vol 12 (2021)
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  Data: Frontiers Media S.A., 2021.
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  Data: 2021
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  Data: LCC:Immunologic diseases. Allergy
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  Data: <searchLink fieldCode="DE" term="%22M6A+methylation%22">M6A methylation</searchLink><br /><searchLink fieldCode="DE" term="%22MeRIP-seq%22">MeRIP-seq</searchLink><br /><searchLink fieldCode="DE" term="%22RNA-seq%22">RNA-seq</searchLink><br /><searchLink fieldCode="DE" term="%22IPEC-J2%22">IPEC-J2</searchLink><br /><searchLink fieldCode="DE" term="%22CPB2%22">CPB2</searchLink><br /><searchLink fieldCode="DE" term="%22Immunologic+diseases%2E+Allergy%22">Immunologic diseases. Allergy</searchLink><br /><searchLink fieldCode="DE" term="%22RC581-607%22">RC581-607</searchLink>
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  Data: BackgroundThe n6-methyladenosine (m6A) modification is present widely in mRNAs and long non-coding RNAs (lncRNAs), and is related to the occurrence and development of certain diseases. However, the role of m6A methylation in Clostridium perfringens type C infectious diarrhea remains unclear.MethodsHere, we treated intestinal porcine jejunum epithelial cells (IPEC-J2 cells) with Clostridium perfringens beta2 (CPB2) toxin to construct an in vitro model of Clostridium perfringens type C (C. perfringens type C) infectious diarrhea, and then used methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA sequencing (RNA-seq) to identify the methylation profiles of mRNAs and lncRNAs in IPEC-J2 cells.ResultsWe identified 6,413 peaks, representing 5,825 m6A-modified mRNAs and 433 modified lncRNAs, of which 4,356 m6A modified mRNAs and 221 m6A modified lncRNAs were significantly differential expressed between the control group and CPB2 group. The motif GGACU was enriched significantly in both the control group and the CPB2 group. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation analysis showed that the differentially methylated modified mRNAs were mainly enriched in Hippo signaling pathway and Wnt signaling pathway. In addition, the target genes of the differentially m6A modified lncRNAs were related to defense response to virus and immune response. For example, ENSSSCG00000042575, ENSSSCG00000048701 and ENSSSCG00000048785 might regulate the defense response to virus, immune and inflammatory response to resist the harmful effects of viruses on cells.ConclusionIn summary, this study established the m6A transcription profile of mRNAs and lncRNAs in IPEC-J2 cells treated by CPB2 toxin. Further analysis showed that m6A-modified RNAs were related to defense against viruses and immune response after CPB2 toxin treatment of the cells. Threem6A-modified lncRNAs, ENSSSCG00000042575, ENSSSCG00000048785 and ENSSSCG00000048701, were most likely to play a key role in CPB2 toxin-treated IPEC-J2 cells. The results provide a theoretical basis for further research on the role of m6A modification in piglet diarrhea.
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