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

Abstract

MicroRNAs (miRNAs) are a class of regulatory small non-coding RNAs that modulate gene expression. As such, miRNAs are indirectly involved in most cellular mechanisms, including cell differentiation, proliferation, survival, and homeostasis. Several different mechanisms finely regulate miRNA expression levels and functions. Among these, miRNA editing is a type of epitranscriptomic modification that alters the original nucleotide sequence of selected miRNAs, possibly influencing their conformational state and target-binding ability. To date, adenosine-to-inosine (A-to-I) and cytosine-to-uracil (C-to-U) RNA editing are recognized as the "canonical" editing types, with the A-to-I type being the predominant one. A comprehensive resource explicitly dedicated to miRNA editing data collection is still missing. Here we present MiREDiBase, a manually curated catalog of editing events in miRNAs. Overall, the current version includes 3059 unique A-to-I and C-to-U editing sites occurring in 626 human miRNA transcripts and three different species of non-human primates. Each editing event is provided with essential information and key relevant details, including biological sample, detection method, enzyme-dependent affinity, editing level, and biological function. Editing events in human mature miRNAs were provided with miRNA-target predictions and enrichment analysis. Minimum free energy structures were inferred for editing events falling into pre-miRNA regions, aiming to help users to interpret the biological information. MiREDiBase represents a valuable tool for cell biology and biomedical research, continuously updated, improved, and expanded with new data from the literature. MiREDiBase is available at https://ncrnaome.osumc.edu/miredibase.

Detecting and Characterizing A-To-I microRNA Editing in Cancer

“…MiRNAs can undergo A-to-I RNA editing, which alters their primary structure. Based on the current literature, the A-to-I editing phenomenon has been reported to occur in over 550 human miRNA transcripts, with the majority of edited sites having been detected at very low levels (<5%) [ 41 ].…”

“…Aside from these mentioned case reports, only a few other studies have demonstrated the importance of miRNA editing at the pathophysiological level [ 41 ]. Indeed, the vast majority (>99%) of miRNA editing events reported until nowadays in both humans and mice have remained functionally uncharacterized, despite their potential in determining the shift between physiological and pathological status [ 41 ]. Moreover, it still remains to elucidate the impact of miRNA expression on the physiological consequences of miRNA editing.…”

A-to-I RNA Editing in Cancer: From Evaluating the Editing Level to Exploring the Editing Effects

“…There are a large number of RNA editing phenomena in ncRNAs ( 114 ), and researchers have identified many RNA editing sites located in ncRNAs, such as lncRNAs ( 112 ). In addition, several specific databases aimed at ncRNAs have been built, including MiREDiBase ( ) (for miRNA) ( 115 ) and LNCediting ( ) (for lncRNA) ( 110 ). Several typical editing effects that occur on ncRNAs are listed below.…”

Detecting and Characterizing A-to-I MicroRNA Editing in Cancer

“…MiRNAs can undergo A-to-I RNA editing, which alters their primary structure. Based on the current literature, the A-to-I editing phenomenon has been reported to occur in over 550 human miRNA transcripts, with the majority of edited sites having been detected at very low levels (<5%) [30].…”

“…Aside from these mentioned case reports, only a few other studies have demonstrated the importance of miRNA editing at the pathophysiological level [30]. Indeed, the vast majority (>99%) of miRNA editing events reported until nowadays in both humans and mice have remained functionally uncharacterized, despite their potential in determining the shift between physiological and pathological status [30]. Moreover, it still remains to elucidate the impact of miRNA expression on the physiological consequences of miRNA editing.…”