{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,3]],"date-time":"2025-09-03T10:11:06Z","timestamp":1756894266562,"version":"3.41.2"},"reference-count":48,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2021,10,19]],"date-time":"2021-10-19T00:00:00Z","timestamp":1634601600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100019492","name":"National Natural Science Foundation of China-China Academy of General Technology Joint Fund for Basic Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100019492","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Genet."],"abstract":"<jats:p>Piglet diarrhea is a swine disease responsible for serious economic impacts in the pig industry. <jats:italic>Clostridium perfringens<\/jats:italic> beta2 toxin (CPB2), which is a major toxin of <jats:italic>C. perfringens<\/jats:italic> type C, may cause intestinal diseases in many domestic animals. N<jats:sup>6<\/jats:sup>-methyladenosine (m<jats:sup>6<\/jats:sup>A) RNA methylation plays critical roles in many immune and inflammatory diseases in livestock and other animals. However, the role of m<jats:sup>6<\/jats:sup>A methylation in porcine intestinal epithelial (IPEC-J2) cells exposed to CPB2 has not been studied. To address this issue, we treated IPEC-J2 cells with CPB2 toxin and then quantified methylation-related enzyme expression by RT-qPCR and assessed the m<jats:sup>6<\/jats:sup>A methylation status of the samples by colorimetric N<jats:sup>6<\/jats:sup>-methyladenosine quantification. The results showed that the methylation enzymes changed to varying degrees while the m<jats:sup>6<\/jats:sup>A methylation level increased (<jats:italic>p<\/jats:italic> &amp;lt; 0.01). On this basis, we performed N<jats:sup>6<\/jats:sup>-methyladenosine sequencing (m<jats:sup>6<\/jats:sup>A-seq) and RNA sequencing (RNA-seq) to examine the detailed m<jats:sup>6<\/jats:sup>A modifications and gene expression of the IPEC-J2 cells following CPB2 toxin exposure. Our results indicated that 1,448 m<jats:sup>6<\/jats:sup>A modification sites, including 437 up-regulated and 1,011 down-regulated, differed significantly between CPB2 toxin exposed cells and non-exposed cells (<jats:italic>p<\/jats:italic> &amp;lt; 0.05). KEGG pathway analysis results showed that m<jats:sup>6<\/jats:sup>A peaks up-regulated genes (<jats:italic>n<\/jats:italic> = 394) were mainly enriched in cancer, Cushing syndrome and Wnt signaling pathways, while m<jats:sup>6<\/jats:sup>A peaks down-regulated genes (<jats:italic>n<\/jats:italic> = 920) were mainly associated with apoptosis, small cell lung cancer, and the herpes simplex virus 1 infection signaling pathway. Furthermore, gene expression (RNA-seq data) analysis identified 1,636 differentially expressed genes (DEGs), of which 1,094 were up-regulated and 542 were down-regulated in the toxin exposed group compared with the control group. In addition, the down-regulated genes were involved in the Hippo and Wnt signaling pathways. Interestingly, the combined results of m<jats:sup>6<\/jats:sup>A-seq and RNA-seq identified genes with up-regulated m<jats:sup>6<\/jats:sup>A peaks but with down-regulated expression, here referred to as \u201chyper-down\u201d genes (<jats:italic>n<\/jats:italic> = 18), which were mainly enriched in the Wnt signaling pathway. Therefore, we speculate that the genes in the Wnt signaling pathway may be modified by m<jats:sup>6<\/jats:sup>A methylation in CPB2-induced IPEC-J2 cells. These findings provide new insights enabling further exploration of the mechanisms underlying piglet diarrhea caused by CPB2 toxin.<\/jats:p>","DOI":"10.3389\/fgene.2021.689748","type":"journal-article","created":{"date-parts":[[2021,10,20]],"date-time":"2021-10-20T20:37:03Z","timestamp":1634762223000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":9,"title":["Comprehensive Analysis of Transcriptome-wide m6A Methylome Upon Clostridium perfringens Beta2 Toxin Exposure in Porcine Intestinal Epithelial Cells by m6A Sequencing"],"prefix":"10.3389","volume":"12","author":[{"given":"Juanli","family":"Zhang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qiaoli","family":"Yang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiaojiao","family":"Yang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaoli","family":"Gao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ruirui","family":"Luo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaoyu","family":"Huang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zunqiang","family":"Yan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pengfei","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wei","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kaihui","family":"Xie","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bo","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shuangbao","family":"Gun","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2021,10,19]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"756","DOI":"10.1080\/15476286.2016.1201628","article-title":"m6A: Signaling for mRNA Splicing","volume":"13","author":"Adhikari","year":"2016","journal-title":"RNA Biol."},{"key":"B2","doi-asserted-by":"publisher","first-page":"1299","DOI":"10.1016\/j.cell.2015.08.011","article-title":"HNRNPA2B1 Is a Mediator of m6A-dependent Nuclear RNA Processing Events","volume":"162","author":"Alarc\u00f3n","year":"2015","journal-title":"Cell"},{"key":"B3","doi-asserted-by":"publisher","first-page":"495","DOI":"10.3390\/ijms17040495","article-title":"WNT9A Induction Linked to Suppression of Human Colorectal Cancer Cell Proliferation","volume":"17","author":"Ali","year":"2016","journal-title":"Ijms"},{"key":"B4","doi-asserted-by":"publisher","first-page":"W202","DOI":"10.1093\/nar\/gkp335","article-title":"MEME SUITE: Tools for Motif Discovery and Searching","volume":"37","author":"Bailey","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"B5","doi-asserted-by":"publisher","first-page":"100511","DOI":"10.1016\/j.biteb.2020.100511","article-title":"Occurrence and Distribution of Antibiotic Resistance Genes in the Coastal Sediments of Effluent-Receiving Areas of WWTPs, China","volume":"11","author":"Chen","year":"2020","journal-title":"Bioresour. 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