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FairBase: a comprehensive database of fungal A-to-I RNA editing
Jinding Liu1,2,3, Dongbo Wang1,2, Yinna Su2,3
1College of Information Science and Technology, Nanjing Agricultural University, Nanjing, China.
Abstract:
Frequent A-to-I RNA editing has recently been identified in fungi despite the absence of recognizable homologues of metazoan ADARs ("Adenosine Deaminases Acting on RNA"). In particular, there is emerging evidence showing that A-to-I editing is involved in sexual reproduction of filamentous fungi. Here, we report on the creation of FairBase - a fungal A-to-I RNA editing database that provides a platform for deep exploration of fungal RNA editing to relevant academic communities. This database includes a comprehensive collection of A-to-I editing sites in six filamentous fungal species, together with extensive annotations for each editing site. In FairBase, users can conveniently search editing sites and obtain editing levels for each editing site in various RNA-seq samples. In addition, the pathways involving RNA editing are built in FairBase to help users understand the functions of RNA editing. Furthermore, each fungal species has a genome browser (JBrowse) that allows users to explore A-to-I editing in a genomic context. FairBase is the first fungal RNA editing database.
Insights
FairBase is a new database for exploring fungal A-to-I RNA editing, particularly its role in sexual reproduction. It offers comprehensive data and tools for researchers studying this phenomenon in filamentous fungi.
Area of Science:
- Molecular Biology
- Mycology
- Bioinformatics
Background:
- Adenosine to Inosine (A-to-I) RNA editing is prevalent in fungi, despite lacking metazoan ADAR enzymes.
- Evidence suggests A-to-I editing plays a role in the sexual reproduction of filamentous fungi.
Purpose of the Study:
- To introduce FairBase, the first comprehensive database dedicated to fungal A-to-I RNA editing.
- To provide a platform for in-depth exploration of fungal RNA editing data.
Main Methods:
- Compilation of A-to-I editing sites from six filamentous fungal species.
- Inclusion of detailed annotations for each editing site.
- Integration of RNA-seq data for editing level quantification.
Main Results:
- FairBase offers a searchable collection of fungal A-to-I editing sites with associated editing levels.
- Pathways involving RNA editing are integrated to elucidate functional roles.
- Each species includes a JBrowse genome browser for genomic context exploration.
Conclusions:
- FairBase serves as a valuable resource for the scientific community to study fungal RNA editing.
- The database facilitates research into the function and mechanisms of A-to-I editing in fungi.
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