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Integrated analysis of lncRNAs and mRNAs reveals key trans-target genes associated with ETEC-F4ac adhesion phenotype in porcine small intestine epithelial cells.

ABSTRACT: BACKGROUND:Long non-coding RNAs (lncRNAs) play crucial roles in gene regulation at the transcriptional and post-transcriptional levels. LncRNAs are belonging to a large class of transcripts with ?200?nt in length which do not code for proteins, have been widely investigated in various physiological and pathological contexts by high-throughput sequencing techniques and bioinformatics analysis. However, little is known about the regulatory mechanisms by which lncRNAs regulate genes that are associated with Enterotoxigenic Escherichia coli F4 fimbriae (ETEC-F4ac) adhesion phenotype in small intestine epithelial cells of Large White piglets. To address this, we used RNA sequencing to profile lncRNAs and mRNAs of small intestine epithelial cells in Large White piglets differing in their ETEC-F4 adhesion phenotypes and ITGB5 genotypes. Eight male piglets were used in this study and were divided into two groups on the basis of their adhesion phenotype and ITGB5 genotypes, a candidate gene for F4ac receptor. Non-adhesive group (n?=?4) with CC genotype and adhesive group (n?=?4) with TT genotype. RESULTS:In total, 78 differentially expressed lncRNAs (DE-lncRNA) and 223 differentially expressed mRNAs (log2 |FC|?>?1, P?

SUBMITTER: Augustino SMA

PROVIDER: S-EPMC7653856 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature

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Integrated analysis of lncRNAs and mRNAs reveals key trans-target genes associated with ETEC-F4ac adhesion phenotype in porcine small intestine epithelial cells.

Augustino Serafino M A SMA Xu Qinglei Q Liu Xueqin X Mi Siyuan S Shi Liangyu L Liu Yibing Y Wen Hui H Wang Di D Liu Lei L Zhang Qin Q Yu Ying Y

BMC genomics 20201110 1

<h4>Background</h4>Long non-coding RNAs (lncRNAs) play crucial roles in gene regulation at the transcriptional and post-transcriptional levels. LncRNAs are belonging to a large class of transcripts with ≥200 nt in length which do not code for proteins, have been widely investigated in various physiological and pathological contexts by high-throughput sequencing techniques and bioinformatics analysis. However, little is known about the regulatory mechanisms by which lncRNAs regulate genes that ar ...[more]

PMID: 33172394

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Project description:Background:Diarrhea represents one of the most frequent major problems during piglets' neonatal and post-weaning periods leading to tremendous economic losses in the swine industry. Enterotoxigenic Escherichia coli (ETEC) F4 is regarded as the most important cause of diarrhea in piglets. However, some pigs are naturally resistant to those diarrheas caused by ETEC-F4, because they have no F4 receptors (F4R) on their small intestine epithelial cells that allow F4 fimbriae attachment. Thus, our study characterized a complete transcriptome of small intestine epithelial cells of Large White piglets using RNA-Seq. The aim of the study was to identify DEGs with regard to differences in the F4R phenotypes and SNP (C/T) genotypes at ITGB5 and important pathways associated with ETEC-F4ac susceptibility in small intestine epithelial cells of Large White piglets and derive molecular markers as a result of loss of F4acR in swine. Methods:A total of eight samples of small intestine epithelial cells obtained from Large White piglets (35 days old) used in this study were selected on the basis of two criteria. One was the adhesion phenotype to ETEC-F4ac fimbriae, and the other was the comparison of ITGB5 SNP (C > T) genotype sequences across all the samples. The samples were then divided into two groups, non-adhesive with CC genotype (n = 4), and adhesive with TT genotype (n = 4). Results:More down-regulated DEGs (p < 0.05, |log2FC| > 2) were detected in the comparison of non-adhesive vs. adhesive small intestine epithelial cells in the present study. Six genes, of which two (CNGA4, SLC25A31) exclusively expressed and four (HCN4, MYLK, KCNMA1, and KCNMB1) DEGs with up-regulation pattern in adhesive (F4R positive) pigs were involved in two pathways associated with diarrhea. The DEGs with up-regulation pattern in non-adhesive (F4R negative) pigs were mostly engaged in multiple immune response-related pathways. Conclusion:The results provide insights on the biology of the phenotypes of F4R positive and negative pigs. One gene (MYLK) located on SSC13 locus for F4acR strongly support that it might have played a role in the adhesion phenotype which was obviously detected by adhesion assay in adhesive (F4R positive) group.

Dataset Information

Integrated analysis of lncRNAs and mRNAs reveals key trans-target genes associated with ETEC-F4ac adhesion phenotype in porcine small intestine epithelial cells.

Publications

Integrated analysis of lncRNAs and mRNAs reveals key trans-target genes associated with ETEC-F4ac adhesion phenotype in porcine small intestine epithelial cells.

Similar Datasets

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