In Silico Study Maps Regulatory Genes Behind Chicken Resistance to Necrotic Enteritis

Necrotic enteritis, a gut disease driven by the bacterium Clostridium perfringens, is among the most economically damaging conditions facing poultry production worldwide. A new in silico study has taken aim at the regulatory machinery that may underlie resistance to this disease, analyzing the promoters, transcription factor binding motifs and microRNAs associated with genes that become upregulated in resistant chickens co-infected with the parasite Eimeria maxima and C. perfringens. The work, published as an open access research article in BMC Genomic Data on 17 October 2026, is currently available as an early version that is citable and carries a permanent DOI, subject to further edits before the final Version of Record.

The research team, led by Reza Tohidi with contributors including Mohammadreza Nassiri, Olena Babenko and Mohammadreza Mohammadabadi, focused on White Leghorn chickens that are resistant to Marek’s disease. Rather than running new laboratory experiments, the investigators used bioinformatics tools to mine existing gene expression data from the spleens of these birds after co-infection with the two pathogens. Their goal was to characterize the regulatory elements, promoter motifs, transcription factors and miRNAs, that coordinate the immune response in resistant animals.

To define the gene set for network analysis, the researchers applied strict statistical thresholds. Only genes showing a p-value below 0.01 and a fold change greater than two relative to the control group were included, yielding 216 upregulated genes. From this set, the team constructed gene interaction networks, performed gene ontology and biological pathway analyses, identified hub genes, and examined promoter interactions as well as predicted interactions between microRNAs and those hub genes.

The results indicated that a substantial proportion of the analyzed upregulated genes participate in immune-related processes. Network analysis identified several hub genes, including molecules classified as CD markers and cytokines, and revealed that the interactions among these hub genes organized into three functional clusters. Across all three clusters, the same KEGG pathways appeared repeatedly: cell adhesion molecules, the intestinal immune network for IgA production, and cytokine-cytokine receptor interactions. The authors interpret this recurrence as a sign of the pathways’ importance within the co-expression network that accompanies resistance.

Promoter motif analysis added another layer to the picture. The team identified six effective motif binding sites for the upregulated genes, and at all six loci they found the transcription factors MIX-A, PHOX2B, ZNF384, KLF15, ZNF610 and PATZ1. The top five gene ontology terms predicted for these motifs were protein transport, translation, regulation of transcription, and DNA dependent processes, which the authors describe as common biological processes. These findings suggest that a shared set of transcriptional regulators may act on multiple resistance-associated genes simultaneously.

Post-transcriptional regulation was examined through microRNA prediction. The researchers used the miRDB database to predict miRNA targets of the hub genes, considering only high-confidence interactions with scores above 80. The integrated analysis, spanning immune-related pathways, hub genes, transcription factor binding motifs and miRNA-gene interactions, led the authors to conclude that both transcriptional and post-transcriptional mechanisms contribute to the host response against necrotic enteritis in resistant birds.

The authors suggest these may represent promising candidates for future functional validation and biomarker development. They emphasize that such validation remains a task for future work; the present study is computational and identifies candidates rather than demonstrating functional roles experimentally.

The authors frame their findings as insights into the molecular mechanisms underlying the immune response to necrotic enteritis in poultry, which could contribute to new strategies for disease control. Because the analysis was performed entirely in silico on spleen tissue from a single resistant chicken line, the conclusions are hypotheses about regulation rather than demonstrated causal mechanisms, and any practical application in breeding or disease management would depend on the proposed functional validation. Still, by linking expression data to promoter architecture and microRNA regulation in one integrated network, the study offers a roadmap for the next round of experiments aimed at understanding why some chickens withstand co-infection while others do not.

Subject of Research: Computational analysis of promoter motifs, transcription factors and microRNAs regulating upregulated immune genes in necrotic enteritis-resistant chickens co-infected with Eimeria maxima and Clostridium perfringens.

Article Title: Analysing the promoters and miRNAs of key upregulated genes in resistant chicken lines co-infected with Eimeria maxima/Clostridium perfringens: an in silico approach

Article References: Tohidi, R., Nassiri, M., Babenko, O., Stavetska, R., Ievstafiieva, I., Buchkovska, V., Kalashnyk, O., Afanasenko, V., & Mohammadabadi, M. (2026). Analysing the promoters and miRNAs of key upregulated genes in resistant chicken lines co-infected with Eimeria maxima/Clostridium perfringens: an in silico approach. BMC Genomic Data. https://doi.org/10.1186/s12863-026-01496-6

Image Credits: AI Generated

DOI: 10.1186/s12863-026-01496-6

Keywords: necrotic enteritis, chickens, Eimeria maxima, Clostridium perfringens, microRNAs, promoter motifs, transcription factors, hub genes, gene networks, bioinformatics, poultry immunity, TNFSF13B