Genomic, Transcriptome Analysis in Animals

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: 20 May 2026 | Viewed by 178

Special Issue Editors

College of Animal Science and Technology, Shihezi University, Shihezi 832061, China
Interests: bioinformatics; animal genetics and reproduction; genetic and epigenetic regulation; hair follicle cycle

E-Mail Website
Guest Editor
College of Animal Science and Technology, Shihezi University, Shihezi 832061, China
Interests: gene function; non-coding RNAs; genetic and epigenetic regulation; muscle development

Special Issue Information

Dear Colleagues,

The integration of genomic, transcriptomic, and metabolomic analysis has emerged as a transformative approach to unraveling the complex biological networks that govern animal physiology, adaptation, and disease. As we enter an era of precision biology, multi-omics methodologies are not only enhancing our understanding of molecular mechanisms but also bridging gaps between genetic potential and phenotypic expression. This Special Issue invites cutting-edge research that leverages these technologies to address critical questions in animal science, from evolutionary biology and environmental adaptation to livestock productivity and veterinary medicine. Recent advancements in high-throughput sequencing, mass spectrometry, and bioinformatics tools have empowered researchers to decode intricate interactions between genes, transcripts, and metabolites with unprecedented resolution. However, challenges remain in data integration, functional annotation, and translating omics findings into actionable insights for improving animal health and sustainability. This collection aims to highlight innovative strategies for overcoming these barriers while fostering interdisciplinary collaboration among geneticists, bioinformaticians, and translational scientists. We are particularly interested in studies that demonstrate the translational. Potential of multi-omics approaches, whether in identifying biomarkers for disease resistance, optimizing breeding programs, or elucidating responses to environmental stressors. By curating this Special Issue, we aspire to catalyze breakthroughs that redefine the boundaries of animal systems biology.

Dr. Min Yang
Dr. Mengxun Li
Guest Editors

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Keywords

  • multi-omics methodologies
  • genetic and epigenetic regulation
  • mechanisms of the elucidation of domesticated animal physiological characteristics and economic traits

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Published Papers (1 paper)

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Research

13 pages, 1359 KB  
Article
Study on the Regulatory Mechanism of oar-miR-29b in Lamb Encephalitis Caused by Enterococcus faecalis Infection
by Ming Zhou, Borui Qi, Pengfei Zhao, Longling Jiao, Shuzhu Cao, You Wu, Jingjing Ren, Runze Zhang, Yongjian Li and Yayin Qi
Genes 2026, 17(1), 29; https://doi.org/10.3390/genes17010029 (registering DOI) - 29 Dec 2025
Abstract
Background: Enterococcus faecalis is an opportunistic pathogen that is capable of causing bacterial encephalitis under specific pathological conditions. MicroRNAs (miRNAs) are a class of small, single-stranded non-coding RNAs, typically approximately 21 nucleotides in length. As master regulators of gene expression, they orchestrate critical [...] Read more.
Background: Enterococcus faecalis is an opportunistic pathogen that is capable of causing bacterial encephalitis under specific pathological conditions. MicroRNAs (miRNAs) are a class of small, single-stranded non-coding RNAs, typically approximately 21 nucleotides in length. As master regulators of gene expression, they orchestrate critical pathways across diverse organisms and a broad spectrum of diseases; however, their role during E. faecalis neuro-invasion remains unexplored. Methods: A lamb model of E. faecalis-induced encephalitis was established. Integrated analysis of high-throughput sequencing data identified oar-miR-29b as a key differentially expressed miRNA during infection. To first verify its association with inflammation, primary SBMECs were stimulated with lipoteichoic acid (LTA), confirming that oar-miR-29b expression was significantly upregulated under inflammatory conditions. Subsequently, independent gain- and loss-of-function experiments in SBMECs were performed, with inflammatory cytokine expression assessed by qPCR and tight-junction protein levels evaluated by Western blotting. Results: Functional studies demonstrated that oar-miR-29b acts as a pro-inflammatory mediator, significantly upregulating IL-1β, IL-6, and TNF-α while degrading tight-junction proteins (ZO-1, occludin, and claudin-5), thereby compromising endothelial barrier integrity. Mechanistically, bioinformatic prediction and dual-luciferase reporter assays confirmed C1QTNF6 as a direct target of oar-miR-29b. The oar-miR-29b/C1QTNF6 axis is thus defined as a novel regulatory pathway contributing to neuro-inflammation and blood-brain barrier disruption. Conclusions: Collectively, our findings identify the oar-miR-29b/C1QTNF6 axis as a novel pathogenic mechanism that exacerbates E. faecalis-induced neuroinflammation and blood-brain barrier disruption. Full article
(This article belongs to the Special Issue Genomic, Transcriptome Analysis in Animals)
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