Whole-genome miRNA activity at single cell-type resolution
How microRNA activity is spatially coordinated within and across the various cell types of an intact organ had not been elucidated in any species to date. Publishing in the EMBO Journal, the Voinnet team has now addressed this challenging issue in the model plant Arabidopsis thaliana
The team chose to establish the proof-of-concept of their method using the root tip of Arabidopsis, taking advantage of its stereotypical organisation around concentric cell layers of well-defined identities. They developed minimally invasive techniques to preserve the sampled cell layers from stress, a potential source of unwanted small RNAs and transcripts contaminations. They first established cell-type-specific repertoires of functional miRNAs called “miRNAomes” acquired via cell-type-specific immunoprecipitation of the main plant microRNA effector, AGO1. They then established exhaustive, cell-type-specific repertoires of miRNA target transcripts, called “targetomes”, using cell-type-specific immunoprecipitation of the RPL18 ribosomal protein in wild-type versus miRNA-deficient roots. miRNAomes and targetomes were then integrated into a unique, custom-built browser called miRoot, allowing user-friendly data interrogation. The study go on to describe how the use of miRoot coupled to single-cell experimentation uncovered many new modes of miRNA action in space, including via the unexpectedly widespread movement of these molecules between cells. This tour de force should now help the community understand better the biology of microRNAs and their roles in stress adaptation and development in plants. It may also inspire others to adapt the approach to whole model animals or organs thereof.
Link to the publication in external page The EMBO Journal.