Integrated Network Based Analysis of miRNA–Gene Regulation and Transcription Factors in Hub Genes Associated with Subfertility in Cattle

Document Type : Research Paper

Authors

1 Department of Animal Science, Faculty of Agriculture, University of Jiroft, Jiroft, Iran.

2 PhD in Animal Breeding, Department of Animal Science, Faculty of Agriculture, University of Zabol, Zabol, Iran.

Abstract

Objective
Subfertility in cattle, arising from complex interactions among genetic, metabolic, immune, and developmental factors, represents a major bio economic challenge for the livestock industry and threatens the sustainability of production systems. This study aimed to identify hub genes associated with subfertility in cattle and to clarify their underlying molecular mechanisms within multilayer miRNA-gene-transcription factor regulatory networks using a network based systems biology framework.
Materials and methods
In the present study, gene expression data from six fertile and five subfertility samples were obtained from the GEO database (accession number GSE107741). After normalization, differential gene expression analysis was performed. Fertility related genes were selected using functional enrichment analysis, and a protein–protein interaction network was constructed. Hub genes were identified based on centrality indices, and regulatory networks including miRNAs and their promoter motifs were extracted and integratively combined.
Results
Network analysis led to the identification of hub genes IGF1, CD4, SPP1, ACAN, and TGFB3, which play key roles in regulating immune pathways, follicular growth, corpus luteum function, extracellular matrix remodeling, metabolism, and embryonic development. Post transcriptional regulatory analysis showed that the expression of these genes is simultaneously controlled by several fertility related miRNAs, and the strength of regulation depends on the cumulative effect of these miRNAs, enabling gradual and precise modulation of gene expression. Furthermore, the identification of key transcription factors including PATZ1, PBX3, ZNF454, CTCF, and FEZF2 indicates the presence of an upstream regulatory layer that ensures coordinated expression of hub genes through transcriptional control and chromatin architecture organization.
Conclusions
Overall, the findings of the present study indicate that subfertility in cattle results from disruptions in multilayer and interconnected miRNA-gene-transcription factor regulatory networks. The proposed network framework may provide a valuable basis for identifying molecular biomarkers and for developing targeted breeding and management strategies aimed at improving reproductive efficiency in cattle.

Keywords

References

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Agricultural Biotechnology Journal
Volume 18, Issue 4
August 2026
Pages 161-186

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