Non-Coding Negative Regulatory Features in Livestock Genomes: Functional Annotation and Causal Validation

Non-coding negative regulation is an important but incompletely resolved component of gene-expression control in livestock. We conducted a narrative review using PubMed, Web of Science Core Collection, and Scopus, prioritizing primary studies in pigs, cattle, sheep, goats, and poultry and using model-organism studies only for directly relevant mechanistic or methodological evidence. We distinguish sequence-defined silencers, context-dependent enhancer-silencer elements, functional microRNA-binding sites, long non-coding RNA-associated regulation, and candidate repressive chromatin regions, and evaluate representative livestock studies using a four-tier framework comprising candidate annotation, molecular functional evidence, endogenous causal evidence, and animal-level validation. Current evidence is strongest for a small number of loci, whereas many of the livestock candidates reviewed here are supported primarily by association, chromatin state, or in vitro assays. We further assess how multi-omics data can prioritize candidates and assign target genes, while emphasizing that reporter activity, repressive chromatin marks, and population association do not establish endogenous causality. Progress will depend on locus-specific perturbation, rescue experiments, relevant animal phenotyping, and inheritance testing. This evidence-centered framework provides a focused basis for interpreting negative regulatory variation in livestock and identifying robust targets for future genetic improvement.