Viral MicroRNA Interactions in Host Gene Regulation

Viral microRNAs (v-miRNAs) represent a class of small non-coding RNAs encoded by diverse DNA and RNA viruses that modulate both host and viral gene expression. By engaging host RNA-silencing machinery, v-miRNAs can suppress antiviral responses, manipulate cell-cycle regulators and reprogramme chromatin states to favour viral persistence. Conversely, host-derived miRNAs may target viral transcripts or key host factors to restrict infection. Together, these interactions form a complex regulatory network that influences the balance between lytic replication and latency, shapes immune evasion strategies and impacts pathogenesis. Advances in deep sequencing and functional genomics have revealed mechanistic insights into v-miRNA biogenesis, target specificity and their roles in chronic infection, oncogenesis and neurological disease. This field underscores the potential of miRNA-based diagnostics and therapeutics to interrupt virus–host dialogues at the post-transcriptional level.

Research from Nature Portfolio

Recent studies have demonstrated that neuron-specific host miR-9 can be harnessed to promote epigenetic silencing of herpes simplex virus type 1. Through a functional screen, miR-9 was shown to target key transcription factors (including Oct-1 and Onecut family members), thereby reducing viral lytic gene expression in neuronal cultures and in vivo trigeminal ganglia models. Integrative analyses using ChIP-seq, ATAC-seq and RNA-seq revealed that miR-9 activity leads to enhanced heterochromatin formation at viral promoters and sustained latency. This work highlights how endogenous miRNAs can shape the chromatin landscape of latent viruses and offers a blueprint for miRNA-mediated epigenetic control of persistent infections.

Viral MicroRNA Interactions in Host Gene Regulation publication trend

The graph below shows the total number of articles in viral microrna interactions in host gene regulation across all publications each year (not limited to Nature Index journals).

Technical terms

microRNA (miRNA): Short (~22 nt) non-coding RNAs that guide RNA-induced silencing complexes to complementary mRNAs, leading to translational repression or degradation.

Viral microRNA (v-miRNA): miRNAs encoded by viral genomes that target host or viral transcripts to facilitate infection, latency or immune evasion.

Latency: A reversible, non-productive infection phase during which viral genomes persist in host cells with minimal gene expression.

Epigenetic silencing: Inhibition of gene transcription via chromatin modifications (e.g. histone methylation) or DNA methylation without altering DNA sequence.

Enhancer: A cis-acting DNA element that increases transcription of target genes by recruiting transcription factors and chromatin remodellers, often over long genomic distances.

References

1. Neuronal miR-9 promotes HSV-1 epigenetic silencing and latency by repressing Oct-1 and Onecut family genes. Nature Communications (2024).
2. Virus-Derived Small RNAs and microRNAs in Health and Disease. Annual Review of Biomedical Data Science (2023).
3. HPV16-miRNAs exert oncogenic effects through enhancers in human cervical cancer. Cancer Cell International (2024).
4. Identification of a SARS-CoV-2 virus-derived vmiRNA in COVID-19 patients holding potential as a diagnostic biomarker. Frontiers in Cellular and Infection Microbiology (2023).