Long Noncoding RNAs Emerge as a Shared Language Between Hosts and Pathogens

For decades, the molecules that captured the attention of infection biologists were the obvious ones: proteins on the surfaces of pathogens that latch onto host receptors, antibodies that neutralize invaders, enzymes that copy viral genomes. RNA was largely cast in a supporting role, valued as a messenger that carries genetic information from DNA to the protein-building machinery of the cell. That picture has been steadily rewritten. A growing body of evidence now places long noncoding RNAs, the thousands of transcript species that do not encode proteins, at the very center of the conversations that take place between hosts and the pathogens that seek to colonize them. A recent commentary published in Cell Research argues that these RNAs do not merely operate within a single organism; in effect, they cross kingdoms, allowing bacteria, fungi, plants, animals, and viruses to influence one another’s gene expression in ways that were previously difficult to imagine.

Long noncoding RNAs, typically defined as transcripts longer than two hundred nucleotides that are not translated into proteins, were once dismissed by many researchers as transcriptional noise. Early genome sequencing projects revealed that while only a small fraction of the human genome encodes proteins, the vast majority of it is transcribed into RNA. Skeptics argued that most of these transcripts were accidental byproducts of a cellular machinery that transcribes promiscuously. Over the past two decades, however, careful functional studies have dismantled that view. Individual long noncoding RNAs have been shown to sculpt chromatin, modulate the stability and translation of messenger RNAs, serve as scaffolds for multi-protein complexes, and act as molecular decoys that sequester transcription factors or microRNAs. Their regulatory reach extends across nearly every layer of gene expression, and their expression patterns are often exquisitely specific to particular cell types, developmental stages, and physiological conditions, including infection.

What makes the cross-kingdom framing particularly compelling is that long noncoding RNAs are not a peculiarity of animals. Plants produce them in abundance, and plant pathologists have documented RNA molecules that move from fungal pathogens into plant cells and vice versa. Small RNAs were the first cross-kingdom RNA travelers to be described in detail, with fungal pathogens such as Botrytis cinerea shown to deliver small RNAs into plant cells where they hijack the host’s own RNA interference machinery to suppress immune genes. Long noncoding RNAs now appear to participate in comparable exchanges, functioning both as sources of regulatory small RNAs and as independent effectors in their own right. In agricultural contexts, this discovery has opened an entirely new frontier: if pathogen RNAs silence crop immune genes, then engineered host RNAs might be deployed to silence essential pathogen genes, a strategy sometimes described as host-induced gene silencing.

In mammalian systems, the interplay between long noncoding RNAs and pathogens is equally rich. Upon infection, host cells reprogram their long noncoding RNA landscape on a massive scale. Interferon signaling, the centerpiece of antiviral immunity, induces a constellation of noncoding transcripts whose functions are only beginning to be mapped. Some of these RNAs amplify antiviral responses, acting as positive regulators that stabilize interferon-stimulated messenger RNAs or promote the signaling cascades triggered by pattern-recognition receptors. Others do the opposite, serving as brakes on inflammation that prevent immune damage to host tissues. Pathogens, in turn, have learned to manipulate this layer of regulation. Viruses encode their own noncoding RNAs and also reshape the abundance of host long noncoding RNAs, co-opting regulatory molecules to create a cellular environment favorable to viral replication, persistence, and escape from immune surveillance.

Bacterial pathogens add yet another dimension to the dialogue. Although bacteria do not possess the same RNA processing machinery as eukaryotes, they are masters of RNA regulation, using small RNAs and structured RNA elements to fine-tune gene expression in response to environmental cues. Emerging work suggests that bacterial RNAs can be released into host cells, whether through outer membrane vesicles, secretion systems, or the controlled lysis of bacterial cells, and that these molecules can modulate host signaling pathways. Conversely, host long noncoding RNAs influence the outcome of bacterial infection by regulating the expression of genes involved in innate immunity, inflammasome activation, autophagy, and cell death. Each of these pathways is a battleground, and RNA regulation sits at the heart of the fight.

The mechanistic versatility of long noncoding RNAs helps explain why they are such effective mediators of this dialogue. Unlike proteins, which must be synthesized, folded, and often trafficked through elaborate pathways, RNAs can be produced rapidly and can act through base-pairing interactions that are comparatively simple to predict and, at least in principle, to engineer. A single long noncoding RNA can interact with DNA, other RNAs, and proteins simultaneously, functioning as a hub that integrates multiple regulatory inputs. This multifunctionality means that a pathogen that targets one host long noncoding RNA can, in a single move, perturb an entire regulatory network. It also means that experimental perturbation of these RNAs, through antisense oligonucleotides, small interfering RNAs, or CRISPR-based approaches, can reveal network-level effects that single-gene knockout studies of proteins might miss.

Technological advances have driven much of the recent progress. Long-read sequencing technologies now allow full-length characterization of transcript isoforms, revealing complexity that short-read approaches obscured. Strand-specific and single-cell RNA sequencing methods have made it possible to profile the noncoding transcriptome of individual infected cells, exposing the heterogeneity of host responses within a tissue. Cross-kingdom RNA detection has benefited from computational pipelines designed to distinguish pathogen-derived reads from host transcripts, a nontrivial challenge given the low abundance of microbial RNAs within a sea of host RNA. Functional validation remains the rate-limiting step: assigning a concrete mechanism to a differentially expressed long noncoding RNA requires loss-of-function and gain-of-function experiments, mapping of interaction partners, and careful demonstration that observed effects are not artifacts of off-target perturbation. The field has matured considerably in its rigor, and the commentary in Cell Research reflects that maturation, emphasizing that the most convincing examples of cross-kingdom RNA communication are those in which the transferred RNA is detected in the recipient, its target is identified, and a functional consequence is demonstrated.

The translational implications are substantial. Host long noncoding RNAs that promote antiviral or antibacterial defense could serve as biomarkers that distinguish active infection from convalescence, or as predictors of disease severity. Therapeutically, RNA-based drugs have finally come of age: antisense oligonucleotides and small interfering RNA therapeutics have been approved for a range of conditions, and the mRNA vaccine success of the COVID-19 pandemic demonstrated that RNA delivery technologies can be scaled to global public health needs. Applying these tools to infection biology, whether by enhancing protective host noncoding RNAs or by directly silencing pathogen transcripts, is a logical next step. In agriculture, RNA-based crop protection strategies are already moving from the laboratory to the field, and a deeper understanding of cross-kingdom RNA exchange will inform both the design of such products and the assessment of their ecological effects on the wider microbiome.

Significant questions remain open. The mechanisms by which RNAs cross cellular boundaries, survive extracellular environments, and enter recipient cells are still incompletely understood, and the physiological relevance of some reported transfers continues to be debated. Dosage is a critical issue: RNA communication depends on molecules reaching functional concentrations in recipient cells, and measuring that accurately in vivo is technically demanding. Specificity is another challenge, since long noncoding RNAs often act at low levels through partial complementarity, raising the risk of unintended interactions when RNAs are manipulated therapeutically. Nonetheless, the conceptual shift is clear and consequential. Host and pathogen are no longer best understood as two organisms exchanging only molecular blows at the protein level; they are two transcriptomes in conversation, each reading and misreading the other’s RNA messages. The commentary’s central message, that long noncoding RNAs broaden the host–pathogen dialogue across kingdoms, captures a field in the midst of redefining itself, and it points toward a future in which the language of RNA becomes as central to infection biology as the language of proteins has always been.

Subject of Research: The role of long noncoding RNAs in cross-kingdom host–pathogen communication and infection biology.

Article Title: Long noncoding RNAs cross kingdoms to broaden host–pathogen dialogue

Article References: Halilovic, L., & Jin, H. (2026). Long noncoding RNAs cross kingdoms to broaden host–pathogen dialogue. Cell Research. https://doi.org/10.1038/s41422-026-01289-7

Image Credits: AI Generated

DOI: 10.1038/s41422-026-01289-7

Keywords: long noncoding RNAs, host-pathogen interactions, cross-kingdom RNA, infection biology, antiviral immunity, gene regulation, RNA therapeutics, plant pathology, viral replication, interferon signaling, host-induced gene silencing, Cell Research