Abstract
RNA editing is an important epigenetic mechanism by which genome-encoded transcripts are modified by substitutions, insertions and/or deletions. It was first discovered in kinetoplastid protozoa followed by its reporting in a wide range of organisms. In plants, RNA editing occurs mostly by cytidine (C) to uridine (U) conversion in translated regions of organelle mRNAs and tends to modify affected codons restoring evolutionary conserved aminoacid residues. RNA editing has also been described in non-protein coding regions such as group II introns and structural RNAs. Despite its impact on organellar transcriptome and proteome complexity, current primary databases still do not provide a specific field for RNA editing events. To overcome these limitations, we developed REDIdb a specialized database for RNA editing modifications in plant organelles. Hereafter we describe its third release containing more than 26,000 events in a completely novel web interface to accommodate RNA editing in its genomics, biological and evolutionary context through whole genome maps and multiple sequence alignments. REDIdb is freely available at http://srv00.recas.ba.infn.it/redidb/index.html
Highlights
RNA editing is an essential co/post transcriptional process able to expand transcriptome and proteome diversity in addition to alternative splicing
The most prevalent type of RNA editing event is the deamination of adenosine (A) in inosine (I) in double RNA strands through the catalytic activity of the adenosine deaminase (ADAR) family of enzymes
After 10 years of massively parallel sequencing, we present here REDIdb 3.0, an upgraded release that annotates 26,618 RNA editing events distributed among 281 organisms and 85 complete organellar genomes
Summary
RNA editing is an essential co/post transcriptional process able to expand transcriptome and proteome diversity in addition to alternative splicing. The term RNA editing was first introduced in 1986 to describe the addition and deletion of uridine nucleotides to and from mRNAs in trypanosome mitochondria (Benne et al, 1986). Modifications due to RNA editing comprise nucleotide substitutions and insertions or deletions that can affect both protein coding and Non-protein coding RNAs (Maier et al, 1996; Steinhauser et al, 1999). The most prevalent type of RNA editing event is the deamination of adenosine (A) in inosine (I) in double RNA strands (dsRNAs) through the catalytic activity of the adenosine deaminase (ADAR) family of enzymes. More than 4 million events have been collected and annotated in dedicated resources such as DARNED, RADAR, and REDIportal (Kiran et al, 2013; Ramaswami and Li, 2014; Picardi et al, 2017)
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