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

Abstract

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.

Comprehensive analysis of LncRNAs modified by m6A methylation in sheep skin

“…M 6 A methylation of lncRNAs in skeletal muscles of pig and Cattle-Yak has been excavated to find new candidate lncRNAs of muscle-fiber-type conversion and muscle development [32,33]. The change of m 6 A methylation of lncRNAs in IPEC-J2 cells induced by Clostridium perfringens beta2 toxin has been described [34]. However, the role of m 6 A methylation in lncRNAs in pigmentation remains unclear.…”

METTL3-Mediated LncRNA EN_42575 m6A Modification Alleviates CPB2 Toxin-Induced Damage in IPEC-J2 Cells

“…In addition, it impacts cellular antiviral capacity by modulating the protein level of MX1 [ 28 ]. Previous MeRIP-sequencing studies revealed that m6A-modified lncRNA EN_42575 was significantly altered in CPB2-group cells [ 13 ]. Here, we reported a significantly reduced expression of m6A-modified lncRNA EN_42575 in IPEC-J2 cells following treatment with the CPB2 toxin.…”

“…Similarly, m6A modifications could affect the functions of lncRNAs in diseases through multiple regulatory mechanisms [ 12 ]. The m6A-modified lncRNAs, namely, ENSSSCG00000048701 and ENSSSCG00000048785 , have been speculated to be involved in the immune and inflammatory responses of IPEC-J2 cells by regulating their target genes to resist bacteria-induced diarrhea in piglets [ 13 ]. However, studies on the mechanisms underlying disease regulation by m6A-modified lncRNAs are limited.…”

“…We previously constructed an in vitro cell model of C. perfringens type C piglet diarrhea and performed RNA immunoprecipitation sequencing (MeRIP-seq). The methylation and expression of lncRNA EN_42575 were significantly reduced after the treatment of cells with CPB2 toxins [ 13 ]. However, the function of lncRNA EN_42575 in C. perfringens type C-induced diarrhea in piglets and its potential mechanisms warrant further investigation.…”

Comprehensive Analysis Revealed the Potential Roles of N6-Methyladenosine (m6A) Mediating E. coli F18 Susceptibility in IPEC-J2 Cells

“…Functionally, m 6 A modification control numerous biological processes, such as metabolism, differentiation, and disease pathology [ 30 ]. Prior investigations demonstrated m 6 A as a critical contributor to host resistance of multiple pathogen/microbial infections [ 31 , 32 , 33 , 34 ]. METTL3 is a methyltransferase that accelerates m 6 A synthesis, which regulates viral replication and E. coli infection.…”