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

Autor: Sekar V; Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden., Mármol-Sánchez E; Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.; Centre for Palaeogenetics, Stockholm, Sweden., Kalogeropoulos P; Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden., Stanicek L; Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden., Sagredo EA; Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden., Widmark A; Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden., Doukoumopoulos E; Department of Medicine, Karolinska Institutet, Solna, Sweden., Bonath F; Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden., Biryukova I; Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden. inna.biryukova@scilifelab.se., Friedländer MR; Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden. marc.friedlander@scilifelab.se.
Jazyk: angličtina
Zdroj: Nature biotechnology [Nat Biotechnol] 2024 Aug; Vol. 42 (8), pp. 1296-1302. Date of Electronic Publication: 2023 Sep 21.
DOI: 10.1038/s41587-023-01951-0
Abstrakt: 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.
(© 2023. The Author(s).)
Databáze: MEDLINE
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