The cell line A-to-I RNA editing catalogue

Schaffer, Amos A.; Kopel, Eli; Hendel, Ayal; Picardi, Ernesto; Levanon, Erez Y.; Eisenberg, Eli

doi:10.1093/nar/gkaa305

Cited by 54 publications

(49 citation statements)

References 78 publications

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“…The current REDIportal release allows searches at sample level, provides overviews of RNA editing profiles per each RNAseq experiment, implements a Gene View module to look at individual events in their genic context, hosts the CLAIRE resource ( 28 ) and collects non-human RNA editing changes.…”

Section: Conclusion and Future Plansmentioning

confidence: 99%

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REDIportal: millions of novel A-to-I RNA editing events from thousands of RNAseq experiments

Mansi

Tangaro

Giudice

et al. 2020

Nucleic Acids Research

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RNA editing is a relevant epitranscriptome phenomenon able to increase the transcriptome and proteome diversity of eukaryotic organisms. ADAR mediated RNA editing is widespread in humans in which millions of A-to-I changes modify thousands of primary transcripts. RNA editing has pivotal roles in the regulation of gene expression or modulation of the innate immune response or functioning of several neurotransmitter receptors. Massive transcriptome sequencing has fostered the research in this field. Nonetheless, different aspects of the RNA editing biology are still unknown and need to be elucidated. To support the study of A-to-I RNA editing we have updated our REDIportal catalogue raising its content to about 16 millions of events detected in 9642 human RNAseq samples from the GTEx project by using a dedicated pipeline based on the HPC version of the REDItools software. REDIportal now allows searches at sample level, provides overviews of RNA editing profiles per each RNAseq experiment, implements a Gene View module to look at individual events in their genic context and hosts the CLAIRE database. Starting from this novel version, REDIportal will start collecting non-human RNA editing changes for comparative genomics investigations. The database is freely available at http://srv00.recas.ba.infn.it/atlas/index.html.

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Section: Conclusion and Future Plansmentioning

confidence: 99%

“…The REDIportal resource also includes the Cell Line A-to-I Rna Editing (CLAIRE) database ( http://srv00.recas.ba.infn.it/atlas/claire.html ) ( 28 ), making our portal a reference point for the scientific community and all researchers involved in the RNA editing field.…”

Section: Introductionmentioning

confidence: 99%

REDIportal: millions of novel A-to-I RNA editing events from thousands of RNAseq experiments

Mansi

Tangaro

Giudice

et al. 2020

Nucleic Acids Research

Self Cite

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“…In 2017, Picardi and colleagues developed REDIportal, which today is the most extensive collection of RNA editing in humans, including more than 4.5 million of A-to-I modification events detected across 55 body sites from thousands of RNA-seq experiments (Picardi et al 2017). Moreover, with its last update, REDIportal also includes ∼90,000 putative A-to-I editing events from the mouse brain transcriptome and incorporates CLAIRE, a searchable catalog of RNA editing levels across cell lines (Schaffer et al 2020). Although these three mentioned online resources are undoubtedly the most authoritative repositories of RNA editing events, none of them is strictly dedicated to miRNA editing.…”

Section: Discussionmentioning

confidence: 99%

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

Marceca

Distefano

Tomasello

et al. 2020

Preprint

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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.

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“…A-to-I RNA editing, which is catalyzed by the adenosine deaminase, acts on RNA (ADAR) family of enzymes, is one of the most prevalent type of post-transcriptional modification in metazoans (25,26). In eukaryotes, this modification has been proved to play an important role in all aspects of regulatory processes such as splicing, microRNA targeting and processing and mRNA stability (27). The editing of nuclear protein-coding transcripts was long thought to be absent in bacterial species until recently that several cases were discovered (11,12).…”

Section: Discussionmentioning

confidence: 99%

A-to-I mRNA editing in a ferric siderophore receptor improves competition for iron inXanthomonas oryzae

Nie

Wang

Huang

et al. 2020

Preprint

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Iron is an essential element for growth and survival of pathogenic bacteria. However, how these bacteria sense and respond to iron starvation or excess is still not fully understood. Here, we show that xfeA (a homolog of fepA) in Xanthomonas oryzae, can sense the extra-cytoplasmic iron concentration and change the 3D structure of ligand channel domain by A-to-I RNA editing. The percentage of A-to-I RNA editing was increased to 76.87% under iron-starvation, facilitating iron to pass through the XfeA channel without any interference to the strongest Iron(III)–siderophore [Fe-(Ent)]3−. However, under high iron concentration, the percentage of A-to-I editing to xfeA was reduced, thereby restricting the Fe-Ent to pass iron through the channel of XfeA. The variations in concentration of Fe-Ent was sensed by methyl-accepting chemotaxis proteins (MCPs) at cytoplasmic membrane, which influences the expression of a number of chemotaxis related genes. This regulation drives the bacteria to move further towards the iron-rich direction. Overall, our results revealed a new signaling mechanism that bacterial iron sense and homeostasis are modulated through A-to-I RNA editing.IMPORTANCEA-to-I RNA editing, which is catalyzed by the adenosine deaminase, acts on RNA family of enzymes, is one of the most prevalent type of post-transcriptional modification in metazoans. However, the research of A-to-I editing in bacteria is limited and the importance of this editing is still underestimated. In this study, we found that bacteria may use A-to-I editing (xfeA, a homolog of fepA) as an alternative strategy in iron metabolic uptake, as the editing event level can precisely regulate the RNA and the protein sequence within relatively short physiological time scales comparing with the traditional switch “on” and “off” regulation. To best of our knowledge, it is a new identified inching-switch-like mechanism by which pathogens may absorb iron better in order to compete with the hosts.

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The cell line A-to-I RNA editing catalogue

Cited by 54 publications

References 78 publications

REDIportal: millions of novel A-to-I RNA editing events from thousands of RNAseq experiments

REDIportal: millions of novel A-to-I RNA editing events from thousands of RNAseq experiments

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

A-to-I mRNA editing in a ferric siderophore receptor improves competition for iron inXanthomonas oryzae

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