In plants, small RNA (sRNA)-directed gene silencing pathways control key biological processes such as development, chromatin remodeling, stress responses and antiviral defense. ARGONAUTES (AGOs) are the effector proteins. They interact with other proteins, load sRNAs, and target and silence specific RNAs through sequence-specific interactions conferred by their guide sRNA.
Our group seeks to develop both new basic knowledge and biotechnological tools for crop improvement while addressing major gaps in the plant small RNA/AGO silencing field.
Our group main research interests are:
1. To better understand how silencing information is processed and expressed at the AGO complex level on a genome-wide scale, particularly in response to stress. AGO function is ultimately determined by its selective association with sRNA, target RNA and protein interactors, and this association changes in response to stresses. Extensive analyses by several laboratories have revealed the highly abundant, complex landscape of multiple sRNAs across plant genomes, and how these sRNAs associate with particular AGOs to exert their function. But, once AGO-sRNA complexes form, which are active to target mRNA and non-coding RNA? Are AGO sRNA-loading and/or mRNA targeting processes regulated by other protein bound to AGOs? The identification of the complete repertoire of AGO target RNAs and protein interactors is key to understand RNA-based silencing on a genome-wide scale. Also, to what extent are active complexes dynamic during physiologic responses to stress or environmental change?
2. To develop next-generation artificial sRNA-based RNAi (art-sRNAi) tools to control gene expression and induce antiviral resistance in plants. AGOs can be programmed with highly-specific, computationally-designed artificial sRNAs (art-sRNAs) to silence the desired gene(s) in gene function studies or for crop improvement. We have recently developed a new platform for high-throughput design and generation of art-sRNA constructs. We are using these tools to develop strategies for next-generation art-sRNAi. These strategies include fine-tuning the degree of art-sRNAi, inducing systemic silencing at the whole-plant level, controlling art-sRNAi in a spatio-temporal manner, increasing art-sRNA efficacy by targeting structurally accessible (TAM-including) sites, and developing GMO-free art-sRNAi approaches such as the exogenous application of art-sRNA precursors or their expression using viral vectors, as well as the possibility of using CRISPR to edit endogenous sRNA precursor genes to express art-sRNAs.