Closing the circle – current state and perspectives of circular RNA databases

Circular RNAs (circRNAs) are covalently closed RNA molecules that have been linked to various diseases, including cancer. However, a precise function and working mechanism are lacking for the larger majority. Following many different experimental and computational approaches to identify circRNAs, multiple circRNA databases were developed as well. Unfortunately, there are several major issues with the current circRNA databases, which substantially hamper progression in the field. First, as the overlap in content is limited, a true reference set of circRNAs is lacking. This results from the low abundance and highly specific expression of circRNAs, and varying sequencing methods, data-analysis pipelines, and circRNA detection tools. A second major issue is the use of ambiguous nomenclature. Thus, redundant or even conflicting names for circRNAs across different databases contribute to the reproducibility crisis. Third, circRNA databases, in essence, rely on the position of the circRNA back-splice junction, whereas alternative splicing could result in circRNAs with different length and sequence. To uniquely identify a circRNA molecule, the full circular sequence is required. Fourth, circRNA databases annotate circRNAs’ microRNA binding and protein-coding potential, but these annotations are generally based on presumed circRNA sequences. Finally, several databases are not regularly updated, contain incomplete data or suffer from connectivity issues.

Ghent University researchers present a comprehensive overview of the current circRNA databases and their content, features, and usability. In addition to discussing the current issues regarding circRNA databases, they come with important suggestions to streamline further research in this growing field.

Varying degrees of overlap among circRNA databases

rna-seq

To assess the content of circRNA databases, the overlap within (A) noncurated and within (B) curated databases was calculated. First, all non-hg19-based databases were converted to hg19 using LiftOver (UCSC Genome Browers [21]), and subsequently a Euler plot was computed. Of note, while an Euler plot is helpful for vizualisation, it is not entirely accurate and the plotted overlap is the approximation with the smallest error. For example, 35% of circRNAs present in CircRiC are also present in at least one of the other noncurated databases, however it was not possible to show this in the Euler plot. 

Vromman M, Vandesompele J, Volders PJ. (2020) Closing the circle: current state and perspectives of circular RNA databases. Brief Bioinform [Epub ahead of print]. [article]

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