In the relentless arms race between viruses and their hosts, the ability of pathogens to subvert innate immune defenses is critical for successful infection and replication. Among these defenses, pattern recognition receptors (PRRs) such as cyclic GMP–AMP synthase (cGAS) detect aberrant cytosolic DNA and trigger antiviral signaling cascades. However, many viruses have evolved sophisticated strategies to evade or suppress these sensing pathways. Recent research published in Nature Microbiology sheds new light on an unconventional viral immune evasion mechanism orchestrated by human cytomegalovirus (HCMV), which hijacks a long non-coding RNA (lncRNA) to directly antagonize nuclear cGAS activity, thereby dampening the interferon response and promoting viral propagation.
Human cytomegalovirus, a widespread beta-herpesvirus known for establishing lifelong latent infections in humans, utilizes a repertoire of immune modulators to persist despite robust host defenses. The study identifies a previously underappreciated viral lncRNA, termed RNA4.9, which accumulates during HCMV infection in human foreskin fibroblasts. This lncRNA is distinguished by a 75-nucleotide segment predicted to form distinct RNA secondary structures, including hairpin loops. Intriguingly, RNA4.9 localizes in close proximity to HCMV genomic DNA within the nucleus, positioning it strategically to engage nuclear immune sensors.
The researchers employed a combination of molecular interaction assays to demonstrate that RNA4.9 physically associates with cGAS, a DNA sensor predominantly characterized for its cytosolic activity but increasingly recognized to have functional nuclear roles as well. This binding was mapped specifically to the 75-nucleotide hairpin-rich region of RNA4.9, indicating a structural basis for interaction. Functionally, the RNA4.9-cGAS complex exhibited marked inhibition of cGAS enzymatic activity, disrupting the synthesis of the secondary messenger cyclic GMP–AMP (cGAMP), which ordinarily activates the adaptor protein STING to initiate type I interferon signaling.
By attenuating the enzymatic function of nuclear cGAS, RNA4.9 effectively suppresses the subsequent interferon responses that would otherwise restrict viral replication. The study further demonstrated that the presence of RNA4.9 contributes directly to enhanced viral DNA replication and productive infection in human fibroblasts. Conversely, targeted interference with the folding of the RNA4.9 75-nucleotide region using antisense oligonucleotides (ASOs) effectively prevented its interaction with cGAS. This steric hindrance restored cGAS enzymatic activity, reactivated downstream immune signaling, and substantially impaired HCMV replication.
These findings highlight a novel strategy whereby a viral non-coding RNA acts as a molecular decoy, binding to and functionally incapacitating a critical DNA sensor within the host cell nucleus. The spatial correlation of RNA4.9’s nuclear localization near viral replication compartments suggests the virus maximizes immune suppression precisely where and when viral genomes are exposed to host detection. Notably, this represents one of the first reports implicating viral lncRNAs in direct modulation of host innate immunity at the nuclear level, expanding our understanding of viral immune evasion beyond protein-centric mechanisms.
The discovery that HCMV exploits RNA4.9 to neutralize nuclear cGAS enzymatic activity also underscores the nuanced role of cGAS in antiviral immunity. While cGAS is classically studied as a cytosolic DNA sensor, accumulating evidence suggests its nuclear presence is functionally significant. The study provides compelling data that nuclear cGAS is not simply dormant but actively involved in sensing viral DNA. Consequently, subversion of nuclear cGAS by RNA4.9 facilitates an immune-privileged environment within the nucleus, allowing HCMV to replicate its large genome with reduced susceptibility to host restriction.
Therapeutically, the ability to restore cGAS function by disrupting the RNA4.9 structure through antisense oligonucleotides offers an appealing antiviral avenue. Existing antiviral therapies often target viral proteins or replication machinery, but viral non-coding RNAs represent an untapped class of targets. Designing molecules that can selectively bind and perturb viral lncRNA structures could reinstate innate immune surveillance and repress viral propagation. The study opens a new paradigm for antiviral drug development, especially for DNA viruses employing nuclear immune evasion.
In a broader context, this work also raises questions about the potential roles of non-coding RNAs encoded by other viruses. The identification of viral lncRNAs as modulators of host sensors expands the molecular toolkit viruses can deploy to manipulate host cell biology. It is conceivable that viruses from diverse families might use analogous RNA-mediated mechanisms to dampen immune activation or co-opt cellular pathways. Future investigations into viral transcriptomes and host interactions may reveal a wealth of functional viral RNAs critical to pathogenesis.
Moreover, the study exemplifies the intricate biochemical interplay between nucleic acid structure and immune recognition. The specific hairpin conformation within RNA4.9 appears essential for cGAS binding and inhibition. This highlights how viruses can evolve highly specialized RNA secondary structures to precisely target host effectors. It also prompts reconsideration of how host RNA-binding proteins discriminate self from non-self nucleic acids based on structural motifs, underscoring the complexity of innate immune regulation.
The implications of this research extend to understanding the immunopathogenesis of cytomegalovirus infections. HCMV is a leading cause of congenital infections and serious complications in immunocompromised individuals. Immune evasion strategies like those mediated by RNA4.9 contribute to viral persistence and pathogenesis. Targeting such viral RNAs could refine therapeutic interventions and improve patient outcomes by enhancing innate immunity where it often fails during persistent infections.
Methodologically, the study utilized advanced techniques encompassing RNA immunoprecipitation, enzymatic activity assays, live-cell RNA imaging, and antisense oligonucleotide design. This multifaceted approach allowed precise dissection of RNA4.9’s functional domains and real-time assessment of its interaction with nuclear cGAS. The integrative methodology exemplifies modern molecular virology strategies essential to unraveling complex host–pathogen dynamics.
In conclusion, the identification of HCMV RNA4.9 as a long non-coding RNA antagonist of nuclear cGAS not only broadens our understanding of viral immune evasion but also opens new avenues for antiviral strategies targeting non-coding RNA regulators. This viral RNA-mediated suppression of innate immunity represents an elegant adaptation that enables cytomegalovirus to persist within host cells by stealthily counteracting nuclear DNA sensing mechanisms. As exploration of viral non-coding RNAs continues, these insights will undoubtedly reshape paradigms of virus-host interactions and therapeutic design.
Subject of Research: Viral immune evasion mechanisms involving non-coding RNAs and host innate immune DNA sensor cGAS.
Article Title: Human cytomegalovirus long non-coding RNA counteracts nuclear cGAS to facilitate immune evasion.
Article References:
Lee, S., Kim, S., Kim, H. et al. Human cytomegalovirus long non-coding RNA counteracts nuclear cGAS to facilitate immune evasion.
Nat Microbiol (2025). https://doi.org/10.1038/s41564-025-02078-5
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