MiREDiBase, a manually curated database of validated and putative editing events in microRNAs

Gioacchino P Marceca,Alfredo Ferro,Federica Calore,Luisa Tomasello,Carlo M Croce,Qin Ma,Marina Bagnoli,Alessandro Lagana,Giulia Romano,Francesco Russo,Rosario Distefano,Pierluigi Gasparini,Mario Acunzo,Giovanni Nigita

doi:10.1038/s41597-021-00979-8

Abstract

MicroRNAs (miRNAs) are regulatory small non-coding RNAs that function as translational repressors. MiRNAs are involved in most cellular processes, and their expression and function are presided by several factors. Amongst, miRNA editing is an epitranscriptional modification that alters the original nucleotide sequence of selected miRNAs, possibly influencing their biogenesis and target-binding ability. A-to-I and C-to-U RNA editing are recognized as the canonical types, with the A-to-I type being the predominant one. Albeit some bioinformatics resources have been implemented to collect RNA editing data, it still lacks a comprehensive resource explicitly dedicated to miRNA editing. Here, we present MiREDiBase, a manually curated catalog of editing events in miRNAs. The current version includes 3,059 unique validated and putative editing sites from 626 pre-miRNAs in humans and three primates. Editing events in mature human miRNAs are supplied with miRNA-target predictions and enrichment analysis, while minimum free energy structures are inferred for edited pre-miRNAs. MiREDiBase represents a valuable tool for cell biology and biomedical research and will be continuously updated and expanded at https://ncrnaome.osumc.edu/miredibase.

Highlights

MiRNAs are the most studied class of small non-coding RNAs involved in gene expression regulation
Pre-miRNAs are exported to the cytoplasm, where they are processed by Dicer into ~22 nucleotides long single-stranded RNAs1
Statistical significance was taken into consideration when possible, eventually maintaining only significant editing events

Summary

Introduction

MiRNAs are the most studied class of small non-coding RNAs involved in gene expression regulation. The first step occurs within the nucleus, where the Drosha-DGCR8 enzymatic complex cleaves pri-miRNAs into ~70 nucleotide long transcripts. These typically maintain the stem-loop conformation and represent the precursors of miRNAs (pre-miRNAs). Pre-miRNAs are exported to the cytoplasm, where they are processed by Dicer into ~22 nucleotides long single-stranded RNAs (mature miRNAs)[1]. These can be found as −5p or −3p forms, depending on which miRNA’s arm they derive from[1]. It is estimated that more than 1,900 pre-miRNAs are expressed in humans, giving rise to over 2,600 different mature miRNAs2

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