Small RNA Profiling Platform for Identifying Plant Gene Targets Modulated by Viral Silencing Suppressors
A computational and experimental platform that identifies host-derived small RNAs bound by viral silencing suppressors and maps their gene targets to reveal proviral and antiviral regulatory mechanisms. Enables discovery of gene targets for crop protection strategies against viral infections.
Overview
This research platform investigates how plant viruses manipulate host RNA silencing pathways to promote infection. By identifying which host-derived small interfering RNAs (siRNAs) are bound and inactivated by viral silencing suppressors, the platform reveals genes that regulate viral replication, movement, and symptom development. Understanding these mechanisms enables the development of targeted crop protection strategies and improved plant resilience against viral pathogens.
The approach combines small RNA sequencing with protein binding analysis to distinguish active versus inactive siRNA populations in virus-infected plants. This addresses a critical gap in plant virology, as previous studies mapped siRNAs to targets without first determining whether those siRNAs remained functional after viral suppressor binding.
Technical specifications
Core methodology:
- Comparative profiling of host-derived siRNAs between healthy and Turnip mosaic virus-infected Arabidopsis thaliana
- Analysis of 21–24 nucleotide siRNA populations and their differential expression patterns
- Identification of viral silencing suppressor HC-Pro-bound siRNAs using immunoprecipitation approaches
- Gene ontology mapping to determine biological targets of suppressor-bound siRNAs
- Arabidopsis thaliana mutant generation with over- and underexpression of target genes for functional validation
Key findings to date:
- Severe reduction of host-derived siRNAs in infected plants, particularly the 24-nucleotide class
- Differential expression observed across shared siRNA populations between healthy and infected conditions
- 7.5 thousand host-derived siRNAs identified as bound by TuMV HC-Pro suppressor
- HC-Pro preferentially binds 21-nucleotide siRNAs despite 24-nucleotide siRNAs being most abundant
Technology readiness level
The platform has completed initial validation with replicated experiments demonstrating reproducible siRNA profiling data and suppressor binding patterns. Computational analysis of HC-Pro-bound siRNA targets is currently underway using gene ontology approaches. The next phase involves experimental validation through mutant generation and infection assays to confirm gene function in proviral and antiviral activity. The research team is actively seeking partnership support for mutant development and supply procurement within the next year.
About University of Nebraska, Lincoln
The University of Nebraska–Lincoln is a comprehensive public research university and the flagship campus of the University of Nebraska system, combining land-grant reach with a collaborative, industry-engaged culture. A research and technology park adjacent to campus provides modern wet and dry labs, greenhouses, offices, and conferencing, enabling companies to co-locate with faculty and access shared equipment and pilot environments. A statewide extension network links university expertise with producers and communities, creating rapid pathways for field trials, demonstrations, and workforce pipelines. Research is supported by competitive federal funding from NSF, USDA, DOE, and NIH. A dedicated technology transfer office manages IP, licensing, agreements, and startup formation with industry-friendly terms.
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