MapToCleave: High-throughput profiling of microRNA biogenesis in living cells

Wenjing Kang; Bastian Fromm; Anna J Houben; Eirik Høye; Daniela Bezdan; Carme Arnan; Kim Thrane; Michaela Asp; Rory Johnson; Inna Biryukova; Marc R Friedländer

doi:10.1016/j.celrep.2021.110015

MapToCleave: High-throughput profiling of microRNA biogenesis in living cells

Cell Rep. 2021 Nov 16;37(7):110015. doi: 10.1016/j.celrep.2021.110015.

Authors

Affiliations

¹ Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.
² Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden; The Arctic University Museum of Norway, UiT - The Arctic University of Norway, Tromsø, Norway.
³ Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona (BIST), Catalonia, Spain.
⁴ Department of Tumor Biology, Oslo Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.
⁵ Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona (BIST), Catalonia, Spain; Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany; NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, Germany.
⁶ Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden.
⁷ Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Department for BioMedical Research, University of Bern, Bern, Switzerland; School of Biology and Environmental Science, University College Dublin, Dublin, Ireland; Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.
⁸ Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden. Electronic address: marc.friedlander@scilifelab.se.

PMID: 34788611
DOI: 10.1016/j.celrep.2021.110015

Abstract

Previous large-scale studies have uncovered many features that determine the processing of microRNA (miRNA) precursors; however, they have been conducted in vitro. Here, we introduce MapToCleave, a method to simultaneously profile processing of thousands of distinct RNA structures in living cells. We find that miRNA precursors with a stable lower basal stem are more efficiently processed and also have higher expression in vivo in tissues from 20 animal species. We systematically compare the importance of known and novel sequence and structural features and test biogenesis of miRNA precursors from 10 animal and plant species in human cells. Lastly, we provide evidence that the GHG motif better predicts processing when defined as a structure rather than sequence motif, consistent with recent cryogenic electron microscopy (cryo-EM) studies. In summary, we apply a screening assay in living cells to reveal the importance of lower basal stem stability for miRNA processing and in vivo expression.

Keywords: RNA structure; biogenesis; comparative biology; large-scale; miRNA; microRNA.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
High-Throughput Nucleotide Sequencing / methods*
Humans
MicroRNAs / biosynthesis*
MicroRNAs / genetics*
Plants / genetics
RNA Precursors / metabolism
RNA Processing, Post-Transcriptional / genetics

Substances

MicroRNAs
RNA Precursors