N6-Methyladenosine Methylation Analysis of Long Noncoding RNAs and mRNAs in IPEC-J2 Cells Treated With Clostridium perfringens beta2 Toxin
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.MethodsH...
| Main Authors: | , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2021-11-01
|
| Series: | Frontiers in Immunology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fimmu.2021.769204/full |
| _version_ | 1831677144464359424 |
|---|---|
| author | Jiaojiao Yang Qiaoli Yang Juanli Zhang Xiaoli Gao Ruirui Luo Kaihui Xie Wei Wang Jie Li Xiaoyu Huang Zunqiang Yan Pengfei Wang Shuangbao Gun Shuangbao Gun |
| author_facet | Jiaojiao Yang Qiaoli Yang Juanli Zhang Xiaoli Gao Ruirui Luo Kaihui Xie Wei Wang Jie Li Xiaoyu Huang Zunqiang Yan Pengfei Wang Shuangbao Gun Shuangbao Gun |
| author_sort | Jiaojiao Yang |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-20T04:36:29Z |
| format | Article |
| id | doaj.art-7435b4d5c1b24b05a4452cd1b3aff6e4 |
| institution | Directory Open Access Journal |
| issn | 1664-3224 |
| language | English |
| last_indexed | 2024-12-20T04:36:29Z |
| publishDate | 2021-11-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Immunology |
| spelling | doaj.art-7435b4d5c1b24b05a4452cd1b3aff6e42022-12-21T19:53:14ZengFrontiers Media S.A.Frontiers in Immunology1664-32242021-11-011210.3389/fimmu.2021.769204769204N6-Methyladenosine Methylation Analysis of Long Noncoding RNAs and mRNAs in IPEC-J2 Cells Treated With Clostridium perfringens beta2 ToxinJiaojiao Yang0Qiaoli Yang1Juanli Zhang2Xiaoli Gao3Ruirui Luo4Kaihui Xie5Wei Wang6Jie Li7Xiaoyu Huang8Zunqiang Yan9Pengfei Wang10Shuangbao Gun11Shuangbao Gun12College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, ChinaCollege of Animal Science and Technology, Gansu Agricultural University, Lanzhou, ChinaCollege of Animal Science and Technology, Gansu Agricultural University, Lanzhou, ChinaCollege of Animal Science and Technology, Gansu Agricultural University, Lanzhou, ChinaCollege of Animal Science and Technology, Gansu Agricultural University, Lanzhou, ChinaCollege of Animal Science and Technology, Gansu Agricultural University, Lanzhou, ChinaCollege of Animal Science and Technology, Northwest A&F University, Xian, ChinaCollege of Animal Science and Technology, Gansu Agricultural University, Lanzhou, ChinaCollege of Animal Science and Technology, Gansu Agricultural University, Lanzhou, ChinaCollege of Animal Science and Technology, Gansu Agricultural University, Lanzhou, ChinaCollege of Animal Science and Technology, Gansu Agricultural University, Lanzhou, ChinaCollege of Animal Science and Technology, Gansu Agricultural University, Lanzhou, ChinaGansu Research Center for Swine Production Engineering and Technology, Lanzhou, ChinaBackgroundThe 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.https://www.frontiersin.org/articles/10.3389/fimmu.2021.769204/fullM6A methylationMeRIP-seqRNA-seqIPEC-J2CPB2 |
| spellingShingle | Jiaojiao Yang Qiaoli Yang Juanli Zhang Xiaoli Gao Ruirui Luo Kaihui Xie Wei Wang Jie Li Xiaoyu Huang Zunqiang Yan Pengfei Wang Shuangbao Gun Shuangbao Gun N6-Methyladenosine Methylation Analysis of Long Noncoding RNAs and mRNAs in IPEC-J2 Cells Treated With Clostridium perfringens beta2 Toxin Frontiers in Immunology M6A methylation MeRIP-seq RNA-seq IPEC-J2 CPB2 |
| title | N6-Methyladenosine Methylation Analysis of Long Noncoding RNAs and mRNAs in IPEC-J2 Cells Treated With Clostridium perfringens beta2 Toxin |
| title_full | N6-Methyladenosine Methylation Analysis of Long Noncoding RNAs and mRNAs in IPEC-J2 Cells Treated With Clostridium perfringens beta2 Toxin |
| title_fullStr | N6-Methyladenosine Methylation Analysis of Long Noncoding RNAs and mRNAs in IPEC-J2 Cells Treated With Clostridium perfringens beta2 Toxin |
| title_full_unstemmed | N6-Methyladenosine Methylation Analysis of Long Noncoding RNAs and mRNAs in IPEC-J2 Cells Treated With Clostridium perfringens beta2 Toxin |
| title_short | N6-Methyladenosine Methylation Analysis of Long Noncoding RNAs and mRNAs in IPEC-J2 Cells Treated With Clostridium perfringens beta2 Toxin |
| title_sort | n6 methyladenosine methylation analysis of long noncoding rnas and mrnas in ipec j2 cells treated with clostridium perfringens beta2 toxin |
| topic | M6A methylation MeRIP-seq RNA-seq IPEC-J2 CPB2 |
| url | https://www.frontiersin.org/articles/10.3389/fimmu.2021.769204/full |
| work_keys_str_mv | AT jiaojiaoyang n6methyladenosinemethylationanalysisoflongnoncodingrnasandmrnasinipecj2cellstreatedwithclostridiumperfringensbeta2toxin AT qiaoliyang n6methyladenosinemethylationanalysisoflongnoncodingrnasandmrnasinipecj2cellstreatedwithclostridiumperfringensbeta2toxin AT juanlizhang n6methyladenosinemethylationanalysisoflongnoncodingrnasandmrnasinipecj2cellstreatedwithclostridiumperfringensbeta2toxin AT xiaoligao n6methyladenosinemethylationanalysisoflongnoncodingrnasandmrnasinipecj2cellstreatedwithclostridiumperfringensbeta2toxin AT ruiruiluo n6methyladenosinemethylationanalysisoflongnoncodingrnasandmrnasinipecj2cellstreatedwithclostridiumperfringensbeta2toxin AT kaihuixie n6methyladenosinemethylationanalysisoflongnoncodingrnasandmrnasinipecj2cellstreatedwithclostridiumperfringensbeta2toxin AT weiwang n6methyladenosinemethylationanalysisoflongnoncodingrnasandmrnasinipecj2cellstreatedwithclostridiumperfringensbeta2toxin AT jieli n6methyladenosinemethylationanalysisoflongnoncodingrnasandmrnasinipecj2cellstreatedwithclostridiumperfringensbeta2toxin AT xiaoyuhuang n6methyladenosinemethylationanalysisoflongnoncodingrnasandmrnasinipecj2cellstreatedwithclostridiumperfringensbeta2toxin AT zunqiangyan n6methyladenosinemethylationanalysisoflongnoncodingrnasandmrnasinipecj2cellstreatedwithclostridiumperfringensbeta2toxin AT pengfeiwang n6methyladenosinemethylationanalysisoflongnoncodingrnasandmrnasinipecj2cellstreatedwithclostridiumperfringensbeta2toxin AT shuangbaogun n6methyladenosinemethylationanalysisoflongnoncodingrnasandmrnasinipecj2cellstreatedwithclostridiumperfringensbeta2toxin AT shuangbaogun n6methyladenosinemethylationanalysisoflongnoncodingrnasandmrnasinipecj2cellstreatedwithclostridiumperfringensbeta2toxin |