Whole-genome miRNA activity at single cell-type resolution

Genome‐scale, single‐cell‐type resolution of microRNA activities within a whole plant organ

Authors: Christopher Andrew Brosnan, Alexis Sarazin, PeiQi Lim, Nicolas Gerardo Bologna, Matthias Hirsch‐Hoffmann, Olivier Voinnet

external pagehttps://www.embopress.org/doi/10.15252/embj.2018100754call_made

miRoot:

Direct access to this project’s data: https://www.miroot.ethz.ch/

Abstract:

Loaded into ARGONAUTE(AGO) proteins, eukaryotic micro(mi)RNAs regulate gene expression via cleavage, translational repression, and/or accelerated decay of sequence‐complementary target transcripts. Despite their importance in development, cell identity maintenance and stress responses, how individual miRNAs contribute to spatial gene regulation within the complex cell mosaics formed in tissues/organs has remained inaccessible in any organism to date. We have developed a non‐invasive methodology to examine, at single‐cell‐type resolution, the AGO‐loading and activity patterns of entire miRNA cohorts in intact organs, applied here to the Arabidopsis root tip. A dual miRNAome–targetome analytical interface allowing intuitive data integration/visualization was developed as the basis for in‐depth investigations via single‐cell‐type experimentation. These uncovered an array of so far speculative or hitherto unknown types of spatial miRNA‐mediated gene regulation schemes, including via widespread cell‐to‐cell movement between contiguous layers of distinct identities. This study provides the proof of principle that minimally invasive, genome‐scale analysis of miRNA activities within and between single‐cell types of whole organs is achievable.

Raw Data Access:

Raw data can be retrieved from the NCBI Gene Expression Omnibus under the accession number (external pageGSE104117call_made).