Detection of transcriptome-wide microRNA-target interactions in single cells with agoTRIBE.

Sekar V, Mármol-Sánchez E, Kalogeropoulos P, Stanicek L, Sagredo EA, Widmark A, Doukoumopoulos E, Bonath F, Biryukova I, Friedländer MR

Nat. Biotechnol. - (-) - [2023-09-21; online 2023-09-21]

MicroRNAs (miRNAs) exert their gene regulatory effects on numerous biological processes based on their selection of target transcripts. Current experimental methods available to identify miRNA targets are laborious and require millions of cells. Here we have overcome these limitations by fusing the miRNA effector protein Argonaute2 to the RNA editing domain of ADAR2, allowing the detection of miRNA targets transcriptome-wide in single cells. miRNAs guide the fusion protein to their natural target transcripts, causing them to undergo A>I editing, which can be detected by sensitive single-cell RNA sequencing. We show that agoTRIBE identifies functional miRNA targets, which are supported by evolutionary sequence conservation. In one application of the method we study microRNA interactions in single cells and identify substantial differential targeting across the cell cycle. AgoTRIBE also provides transcriptome-wide measurements of RNA abundance and allows the deconvolution of miRNA targeting in complex tissues at the single-cell level.

Bioinformatics Support for Computational Resources [Service]

NGI Short read [Service]

NGI Single cell [Service]

NGI Stockholm (Genomics Applications) [Service]

NGI Stockholm (Genomics Production) [Service]

National Genomics Infrastructure [Service]

PubMed 37735263

DOI 10.1038/s41587-023-01951-0

Crossref 10.1038/s41587-023-01951-0

pii: 10.1038/s41587-023-01951-0

Publications 9.5.0