Distribution and differential expression of microRNAs in the intestinal mucosal layer of necrotic enteritis induced Fayoumi chickens

Abstract

ObjectiveDespite an increasing number of investigations into the pathophysiology of necrotic enteritis (NE) disease, etiology of NE-associated diseases, and gene expression profiling of NE-affected tissues, the microRNA (miRNA) profiles of NE-affected poultry have been poorly studied. The aim of this study was to induce NE disease in the genetically disparate Fayoumi chicken lines, and to perform non-coding RNA sequencing in the intestinal mucosal layer.MethodsNE disease was induced in the Fayoumi chicken lines (M5.1 and M15.2), and non-coding RNA sequencing was performed in the intestinal mucosal layer of both NE-affected and uninfected chickens to examine the differential expression of miRNAs. Next, quantitative real-time polymerase chain reaction (real-time qPCR) was performed to further examine four miRNAs that showed the highest fold differences. Finally, bioinformatics analyses were performed to examine the four miRNAs target genes involvement in the signaling pathways, and to examine their interaction.ResultsAccording to non-coding RNA sequencing, total 50 upregulated miRNAs and 26 downregulated miRNAs were detected in the NE-induced M5.1 chickens. While 32 upregulated miRNAs and 11 downregulated miRNAs were detected in the NE-induced M15.2 chickens. Results of real-time qPCR analysis on the four miRNAs (gga-miR-9-5p, gga-miR-20b-5p, gga-miR-196-5p, and gga-let-7d) were mostly correlated with the results of RNAseq. Overall, gga-miR-20b-5p was significantly downregulated in the NE-induced M5.1 chickens and this was associated with the upregulation of its top-ranking target gene, mitogen-activated protein kinase, kinase 2. Further bioinformatics analyses revealed that 45 of the gene targets of gga-miR-20b-5p were involved in signal transduction and immune system-related pathways, and 35 of these targets were predicted to interact with each other.ConclusionOur study is a novel report of miRNA expression in Fayoumi chickens, and could be very useful in understanding the role of differentially expressed miRNAs in a NE disease model.

Expression and regulation of avian beta-defensin 8 protein in immune tissues and cell lines of chickens

“…Several earlier studies have reported that the chicken AvBDs are highly conserved due to the presence of beta-defensin functional domain that spans 32 to 36 amino acids and are evolutionarily related to other vertebrate defensins [ 4 , 5 , 8 , 23 , 24 ]. Analysis of protein–protein interactions mainly helps in determining co-expressed and co-functional proteins that trigger or inhibit some cellular functions [ 25 ]. Interactions of AvBD8 with other AvBD family members and other antimicrobial proteins were examined using the STRING program ( Figure 5 ).…”

MicroRNA expression profiling in the lungs of genetically different Ri chicken lines against the highly pathogenic avian influenza H5N1 virus

“…5 ). According to previous study, gga-miR-9-5p was involved in various signal transduction and immune-related pathways by regulating target genes in the intestinal mucosal layer (IML) of necrotic enteritis (NE)-induced Fayoumi chicken lines [ 46 ]. The immune-related target genes of gga-miR-9-5p, LSM14A and NFATC3 , were verified via RT-PCR.…”

Epigenetic Regulation by Non-Coding RNAs in the Avian Immune System

“…Necrotic enteritis is usually caused by Clostridium perfringens with symptoms of weight depression, appetite loss, and even cause death to chickens [153]. Small RNA-seq showed many miRNAs were differently expressed after challenged by NE [154][155][156]. miR-215, miR-194, miR-217, miR-200a, miR-216a, miR-200b, miR-216b, miR-34b, miR-429, miR-1684, miR-9-5p, miR-196-5p, miR-20b-5p and let-7d were confirmed by qRT-PCR [154,156].…”

“…Small RNA-seq showed many miRNAs were differently expressed after challenged by NE [154][155][156]. miR-215, miR-194, miR-217, miR-200a, miR-216a, miR-200b, miR-216b, miR-34b, miR-429, miR-1684, miR-9-5p, miR-196-5p, miR-20b-5p and let-7d were confirmed by qRT-PCR [154,156]. Some miRNAs were correlated with immune-related mRNA expression levels, such as miR-216 and TGFβR2 (transforming growth factor beta receptor 2), miR-30b/miR-30c/miR-455-5p and SOCS3, miR-181a/b and CXCL14 (C-X-C motif chemokine ligand 14), miR-429 and TNFSF11β (TNF superfamily member 11 beta), miR-223 and HSP90β1 (heat shock protein 90 beta family member 1), miR-1329 and NFKBIZ (NFKB inhibitor zeta), miR-1674 and ARHGEF (FERM, ARH/RhoGEF and pleckstrin domain protein 1), miR-30e/ miR-32 and SERPINF1 (serpin family F member 1) [155].…”