Abstract
BackgroundLong 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.ResultsIn total, 78 differentially expressed lncRNAs (DE-lncRNA) and 223 differentially expressed mRNAs (log2 |FC| > 1, P < 0.05) were identified in the comparison of non-adhesive vs. adhesive small intestine epithelial cells. Furthermore, cis- and trans-regulatory target genes of DE-lncRNAs were identified, then interaction networks of lncRNAs and their cis- and trans-target differentially expressed genes (DEGs) were constructed separately. A total of 194 cis-targets were involved in the lncRNAs-cis genes interaction network and 61 trans-targets, were involved in lncRNA-trans gene interaction network that we constructed. We determined that cis-target genes were involved in alcoholism, systemic lupus erythematosus, viral carcinogenesis and malaria. Whereas trans-target DEGs were engaged in three important pathways related to the ETEC-F4 adhesion phenotype namely cGMP-PKG signaling pathway, focal adhesion, and adherens junction. The trans-target DEGs which directly involved in these pathways are KCNMB1 in cGMP-PKG signaling pathway, GRB2 in focal adhesion pathway and ACTN4 in focal adhesion and adherens junction pathways.ConclusionThe findings of the current study provides an insight into biological functions and epigenetic regulatory mechanism of lncRNAs on porcine small intestine epithelial cells adhesion to ETEC-F4-ac and piglets’ diarrhea susceptibility/resistance.
Highlights
Long non-coding RNAs play crucial roles in gene regulation at the transcriptional and posttranscriptional levels
Whereas trans-target differentially expressed genes (DEGs) were engaged in three important pathways related to the Eterotoxigenic Escherichia coli (ETEC)-F4 adhesion phenotype namely cyclic guanosine monophosphate (cGMP)-PKG signaling pathway, focal adhesion, and adherens junction
The findings of the current study provides an insight into biological functions and epigenetic regulatory mechanism of Long non-coding RNAs (lncRNAs) on porcine small intestine epithelial cells adhesion to ETEC-F4-ac and piglets’ diarrhea susceptibility/resistance
Summary
Long non-coding RNAs (lncRNAs) play crucial roles in gene regulation at the transcriptional and posttranscriptional levels. Many pathogens are implicated but, Enterotoxigenic Escherichia coli ETEC-F4ac strain is considered the most important enteric pathogens with the highest prevalence rate It accounts for 56.2 and 24.7% of the cases of diarrhea and death of piglets respectively [1] and inflicting huge economic burdens on swine farms [2]. Data available from high-throughput sequencing studies have revealed that only a very small percentage (1–2%) of the mammalian genome encode proteins, but tens of thousands of intergenic sites are transcribed to non-coding RNA [3]. This transcription plays a critical role in the regulation of gene expression during several biological processes [4]
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