Expression analysis of genes related to lipid metabolism in peripheral blood lymphocytes of chickens challenged with reticuloendotheliosis virus

The underlying molecular mechanism of lipid metabolism in peripheral blood lymphocytes from chicken infected with reticuloendotheliosis virus (REV) remains poorly understood. Therefore, this scientific question was explored in vitro and in vivo. The results indicated that triglyceride content was significantly reduced, but the free fatty acid content and carnitine palmitoyltransferase-1 activity were significantly increased in blood lymphocytes after REV infection. By RNA sequencing, 97 known differentially expressed genes (DEG) related to lipid metabolism or glycometabolism were screened via Gene Ontology term analysis. On the basis of these 97 DEG, enriched pathways, including the peroxisome proliferators-activated receptor (PPAR) signaling pathway, were identified. Among these 97 DEG, some representative genes were related to lipolysis and fatty acid utilization (PPARG, LPL, PLIN2, ACOX1, ACSL1, FABP3, and FABP4). However, other genes related to lipid biosynthesis (ACSL3, ACSL6, DGAT2, LPIN1, and LPIN2) were downregulated. The quantitative polymerase chain reaction results confirmed the accuracy of the RNA sequencing data, and the in vivo outcome supports theses in vitro results. Our findings revealed that REV regulates fatty acid and lipid metabolism in peripheral blood lymphocytes from chicken. After the lymphocytes were infected with REV, the exogenous fatty acids were preferentially used; genes involved in fatty acid utilization were upregulated via the PPAR pathway, whereas genes involved in lipid and fatty acid biosynthesis were downregulated.

Chicken cecal DNA methylome alteration in the response to Salmonella enterica serovar Enteritidis inoculation

BACKGROUND

Salmonella enterica serovar Enteritidis (SE) is one of the pathogenic bacteria, which affects poultry production and poses a severe threat to public health. Chicken meat and eggs are the main sources of human salmonellosis. DNA methylation is involved in regulatory processes including gene expression, chromatin structure and genomic imprinting. To understand the methylation regulation in the response to SE inoculation in chicken, the genome-wide DNA methylation profile following SE inoculation was analyzed through whole-genome bisulfite sequencing in the current study.

RESULTS

There were 185,362,463 clean reads and 126,098,724 unique reads in the control group, and 180,530,750 clean reads and 126,782,896 unique reads in the inoculated group. The methylation density in the gene body was higher than that in the upstream and downstream regions of the gene. There were 8946 differentially methylated genes (3639 hypo-methylated genes, 5307 hyper-methylated genes) obtained between inoculated and control groups. Methylated genes were mainly enriched in immune-related Gene Ontology (GO) terms and metabolic process terms. Cytokine-cytokine receptor interaction, TGF-beta signaling pathway, FoxO signaling pathway, Wnt signaling pathway and several metabolism-related pathways were significantly enriched. The density of differentially methylated cytosines in miRNAs was the highest. HOX genes were widely methylated.

CONCLUSIONS

The genome-wide DNA methylation profile in the response to SE inoculation in chicken was analyzed. SE inoculation promoted the DNA methylation in the chicken cecum and caused methylation alteration in immune- and metabolic- related genes. Wnt signal pathway, miRNAs and HOX gene family may play crucial roles in the methylation regulation of SE inoculation in chicken. The findings herein will deepen the understanding of epigenetic regulation in the response to SE inoculation in chicken.

Cecal CircRNAs Are Associated With the Response to Salmonella Enterica Serovar Enteritidis Inoculation in the Chicken

Circular RNAs (circRNAs) are a class of endogenous noncoding RNA, which is different from linear RNA. CircRNA is an RNA molecule with a closed loop structure formed by reverse splicing. CircRNAs have been studied in several organisms, however, the circRNAs associated with the response to Salmonella enterica serovar Enteritidis (SE) inoculation in chickens are still unclear. In the current study, Jining Bairi chickens were inoculated with SE. CircRNAs involved in the response to SE inoculation were identified through next-generation sequencing. Our results showed that there were 5,118 circRNAs identified in the control and treated groups. There were 62 circRNAs significantly differentially expressed following SE inoculation. Functional classification revealed that those significantly differentially expressed circRNAs were associated with immune system process, rhythmic process and signaling following SE inoculation. CircRNAs NC_006091.4: 65510578|65515090, NC_006099.4: 16132825|16236906, and NC_006099.4: 15993284|16006290 play important roles in the response to SE inoculation. The findings in the current study provide evidence that circRNA alterations are involved in the response to SE inoculation in the chicken.

Chicken cecal microRNAs in the response to Campylobacter jejuni inoculation by Solexa sequencing

Campylobacter jejuni (C. jejuni) is one of major foodborne pathogen that cause human diarrhea by consuming C. jejuni contaminated chicken products. MicroRNAs play an integral role in many different biological processes including bacteria and virus inoculation in chickens. In this study, we identified chicken miRNAs responding to C. jejuni inoculation through Solexa sequencing in the cecum. As a result, four miRNAs were significantly differentially expressed between inoculated and non-inoculated groups. There were 1,114 putative target genes regulated by those differentially expressed miRNAs predicted by miRanda, TargetScan, and miRTarget softwares. Functional analysis of those target genes showed that 113 gene ontology biological process terms and 14 pathways were significantly enriched. Hedgehog signaling pathway may contribute to chicken C. jejuni inoculation. MiR-155 played vital role in the C. jejuni inoculation. The result herein will lay the foundation for the further study of regulatory mechanism of chicken miRNAs in the response to C. jejuni inoculation.