VipariNama: RNA viral vectors to rapidly elucidate the relationship between gene expression and phenotype

Arjun Khakhar, Cecily Wang, Ryan Swanson, Sydney Stokke, Furva Rizvi, Surbhi Sarup, John Hobbs, Daniel F. Voytas

Research output: Contribution to journalArticlepeer-review

3 Scopus citations


Synthetic transcription factors have great promise as tools to help elucidate relationships between gene expression and phenotype by allowing tunable alterations of gene expression without genomic alterations of the loci being studied. However, the years-long timescales, high cost, and technical skill associated with plant transformation have limited their use. In this work, we developed a technology called VipariNama (ViN) in which vectors based on the tobacco rattle virus are used to rapidly deploy Cas9-based synthetic transcription factors and reprogram gene expression in planta. We demonstrate that ViN vectors can implement activation or repression of multiple genes systemically and persistently over several weeks in Nicotiana benthamiana, Arabidopsis (Arabidopsis thaliana), and tomato (Solanum lycopersicum). By exploring strategies including RNA scaffolding, viral vector ensembles, and viral engineering, we describe how the flexibility and efficacy of regulation can be improved. We also show how this transcriptional reprogramming can create predictable changes to metabolic phenotypes, such as gibberellin biosynthesis in N. benthamiana and anthocyanin accumulation in Arabidopsis, as well as developmental phenotypes, such as plant size in N. benthamiana, Arabidopsis, and tomato. These results demonstrate how ViN vector-based reprogramming of different aspects of gibberellin signaling can be used to engineer plant size in a range of plant species in a matter of weeks. In summary, ViN accelerates the timeline for generating phenotypes from over a year to just a few weeks, providing an attractive alternative to transgenesis for synthetic transcription factor-enabled hypothesis testing and crop engineering.

Original languageEnglish (US)
Pages (from-to)2222-2238
Number of pages17
JournalPlant physiology
Issue number4
Early online dateMay 1 2021
StatePublished - Aug 3 2021
Externally publishedYes

Bibliographical note

Funding Information:
This work was supported by the Department of Energy Grant DE-SC0018277 and a grant from DARPA. The University of Minnesota is part of a team supporting DARPA’s Insect Allies Program under agreement HR0011-17-2-0053. A.K. was supported by the Grand Challenges in Biology Postdoctoral Program administered by the College of Biological Sciences at the University of Minnesota.

Publisher Copyright:
© 2021 American Society of Plant Biologists. All rights reserved.

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  • Journal Article


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