Dissection of RNA Silencing Through Chemical Genomics

Small RNAs are short non-coding RNA elements that can suppress gene expression in a phenomenon called RNA silencing which operates in plants and animals. In plants, they are involved in a diverse range of pathways and processes including development, genome maintenance, genomic imprinting, and abiotic and biotic stress response. In the model plant Arabidopsis thaliana, one small RNA pathway is involved in plant immunity against a bacterial pathogen. Not all of the proteins involved in this pathway are known. To complement genetic studies, we conducted a screen for compounds that interrupt this small RNA pathway using a luciferase transgenic line exhibiting silencing. Chemicals from the “Library of AcTive Compounds on Arabidopsis” were used to perturb the silencing pathway to identify silencing-inhibition chemicals and new proteins or receptors involved in the biogenesis or function of these small RNAs. This approach was used due to its ability to overcome problems found in traditional genetic screens, such as duplicate or essential genes. After several rounds of screening, we found 11 putative hits, currently under further study. Bioinformatics tools are used to characterize the compounds. One to two molecules effective at perturbing this pathway will be further studied to discover their mode(s) of action. This cross-disciplinary project exemplifies the discovery potential that lies at the interface between biology, chemistry and computer science.