Databases for RNA Editing Collections

Giudice, Claudio Lo; Mansi, Luigi; Pesole, Graziano; Picardi, Ernesto

doi:10.1007/978-1-0716-1307-8_25

Cited by 2 publications

(2 citation statements)

References 30 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…C‐to‐U RNA editing in animals occurs only sporadically and is catalyzed by members of the APOBEC (Apolipoprotein B mRNA editing catalytic polypeptide‐like) family (Salter et al., 2016; Yang et al., 2000), which has not expanded in size as the PPR gene families in plants and whose members appear to be much more specific in target recognition. In contrast, the deamination of adenosines to inosines by ADARs (Adenosine Deaminases Acting on RNAs) and ADATs (Adenosine Deaminases acting on transfer RNAs; Torres et al., 2014) represents the predominant type of RNA editing in animals, highly outnumbering C‐to‐U RNA editing frequencies with more than a million sites in humans (Lo Giudice et al., 2021; Picardi et al., 2017). Target recognition by members of the ADAR family, however, operates completely different from the protein‐based target recognition in C‐to‐U RNA editing.…”

Section: Discussionmentioning

confidence: 99%

Conquering new grounds: plant organellar C‐to‐U RNA editing factors can be functional in the plant cytosol

Thielen,

Gärtner,

Knoop

et al. 2024

The Plant Journal

View full text Add to dashboard Cite

SUMMARYPlant mitochondrial and chloroplast transcripts are subject to numerous events of specific cytidine‐to‐uridine (C‐to‐U) RNA editing to correct genetic information. Key protein factors for this process are specific RNA‐binding pentatricopeptide repeat (PPR) proteins, which are encoded in the nucleus and post‐translationally imported into the two endosymbiotic organelles. Despite hundreds of C‐to‐U editing sites in the plant organelles, no comparable editing has been found for nucleo‐cytosolic mRNAs raising the question why plant RNA editing is restricted to chloroplasts and mitochondria. Here, we addressed this issue in the model moss Physcomitrium patens, where all PPR‐type RNA editing factors comprise specific RNA‐binding and cytidine deamination functionalities in single proteins. To explore whether organelle‐type RNA editing can principally also take place in the plant cytosol, we expressed PPR56, PPR65 and PPR78, three editing factors recently shown to also function in a bacterial setup, together with cytosolic co‐transcribed native targets in Physcomitrium. While we obtained unsatisfying results upon their constitutive expression, we found strong cytosolic RNA editing under hormone‐inducible expression. Moreover, RNA‐Seq analyses revealed varying numbers of up to more than 900 off‐targets in other cytosolic transcripts. We conclude that PPR‐mediated C‐to‐U RNA editing is not per se incompatible with the plant cytosol but that its limited target specificity has restricted its occurrence to the much less complex transcriptomes of mitochondria and chloroplast in the course of evolution.

show abstract

Section: Discussionmentioning

confidence: 99%

Conquering new grounds: plant organellar C‐to‐U RNA editing factors can be functional in the plant cytosol

Thielen,

Gärtner,

Knoop

et al. 2024

The Plant Journal

View full text Add to dashboard Cite

show abstract

“…We highlight the necessity of dedicated projects, which could leverage on existing approaches and implement them to species having specific genome structure, plasticity, repeat contents, and distributions, as bivalves ( 21 ). By producing individual paired DNA/RNA-seq data, useful to discriminate ADAR edits from genomic/transcriptomic variations, it will be possible to develop dedicated SNP databases, such as the human/mouse REDI portal ( 22 ). The use of rRNA-depleted, stranded RNA libraries can allow the identification of strand-specific edits beyond coding genes and improve the identification of ADAR-editing versus other variation sources.…”

Section: Discussionmentioning

confidence: 99%