RNA Silencing Mechanisms in Fungal Systems

RNA silencing in fungi encompasses a collection of post-transcriptional and transcriptional pathways that regulate gene expression, maintain genome integrity and defend against invasive nucleic acids. Central to these pathways is the processing of double-stranded RNA by Dicer enzymes into small interfering RNAs (siRNAs) or microRNA-like RNAs (milRNAs), which are then incorporated into an Argonaute-containing RNA-induced silencing complex (RISC). Guided by base-pair complementarity, RISC mediates cleavage or translational repression of target transcripts. Beyond the canonical Dicer-dependent pathway, fungi also exploit non-canonical routes involving RNA-dependent RNA polymerases, phased siRNAs (phasiRNAs) and Dicer-independent nucleases to generate diverse classes of regulatory small RNAs. These mechanisms underpin control of transposon activity, modulation of developmental programmes such as sexual reproduction, and adaptation to environmental stresses. Furthermore, cross-kingdom trafficking of fungal small RNAs into plant hosts exemplifies the broader ecological and practical relevance of fungal RNA silencing, paving the way for RNA-based disease management strategies.

Research from Nature Portfolio

Seminal work has defined the core RNA silencing machinery in a major plant-pathogenic fungus, demonstrating that hairpin RNA constructs efficiently trigger gene knock-down and that specific Dicer and Argonaute proteins are indispensable for siRNA biogenesis. Functional dissection revealed that one Argonaute protein cooperates with a Dicer homologue to generate microRNA-like species, while a second Dicer is required for the production of a distinct subset of small RNAs. This foundational study established hairpin-induced gene silencing as a versatile genetic tool and clarified the roles of individual RNAi components in fungal gene regulation.

RNA Silencing Mechanisms in Fungal Systems publication trend

The graph below shows the total number of articles in rna silencing mechanisms in fungal systems across all publications each year (not limited to Nature Index journals).

Technical terms

Dicer: An RNase III enzyme that cleaves double-stranded RNA into siRNAs or milRNAs of characteristic lengths.

Argonaute: The core protein of the RNA-induced silencing complex (RISC) that binds small RNAs and mediates target RNA cleavage or translational repression.

Small interfering RNA (siRNA): A 20–24 nucleotide RNA generated by Dicer that guides RISC to degrade complementary mRNA.

MicroRNA-like RNA (milRNA): Fungal small RNAs resembling animal or plant microRNAs in biogenesis and function, often arising from hairpin precursors.

Phased siRNA (phasiRNA): A class of siRNAs produced in register from a precursor transcript, generating a series of small RNAs at defined intervals.

RNA-induced silencing complex (RISC): A multiprotein assembly centred on Argonaute that uses small RNAs as guides to recognise and silence complementary RNAs.

References

1. The Evolutionary Significance of RNAi in the Fungal Kingdom. International Journal of Molecular Sciences (2020).
2. Characterization of RNA silencing components in the plant pathogenic fungus Fusarium graminearum. Scientific Reports (2015).
3. Global Analysis of microRNA-like RNAs Reveals Differential Regulation of Pathogenicity and Development in Fusarium oxysporum HS2 Causing Apple Replant Disease. Journal of Fungi (2024).
4. Genome-wide identification of Sclerotinia sclerotiorum small RNAs and their endogenous targets. BMC Genomics (2023).
5. Unveiling microRNA-like small RNAs implicated in the initial infection of Fusarium oxysporum f. sp. cubense through small RNA sequencing. Mycology: An International Journal on Fungal Biology (2024).