Abstract
Circular RNAs (circRNAs) are a large class of noncoding RNAs with functions that, in most cases, remain unknown. Recent genome-wide analysis of circRNAs using RNA-Seq has revealed that circRNAs are abundant and some of them conserved in plants. Furthermore, it has been shown that the expression of circRNAs in plants is regulated in a tissue-specific manner. Arabidopsis thaliana circular RNA database is a new resource designed to integrate and standardize the data available for circRNAs in a model plant A. thaliana, which is currently the best-characterized plant in terms of circRNAs. The resource integrates all applicable publicly available RNA-seq datasets. These datasets were subjected to extensive reanalysis and curation, yielding results in a unified format. Moreover, all data were normalized according to our optimized approach developed for circRNA identification in plants. As a result, the database accommodates circRNAs identified across organs and seedlings of wild-type A. thaliana and its single-gene knockout mutants for genes related to splicing. The database provides free access to unified data and search functionalities, thus enabling comparative analyses of A. thaliana circRNAs between organs, variants and studies for the first time.Database URLhttps://plantcircrna.ibch.poznan.pl/
Highlights
IntroductionCircular RNAs (circRNAs) are a class of noncoding alternatively spliced transcripts. It has been shown that circRNAs are present across the eukaryotic tree of life [1]
Circular RNAs are a class of noncoding alternatively spliced transcripts
It is worth mentioning that we introduced a novel ‘reproducibility’ criterion in At-C-RNA, as in our previous studies, and we showed that most circRNAs in A. thaliana are produced spontaneously and possibly carry no biological function [11]
Summary
Circular RNAs (circRNAs) are a class of noncoding alternatively spliced transcripts. It has been shown that circRNAs are present across the eukaryotic tree of life [1]. Next-generation sequencing technology can provide a comprehensive distribution of circRNAs in the whole organism and its particular organs This situation is reflected in an increasing number of RNA-seq-based reports on plant circRNAs. A. thaliana circRNAs have been characterized in multiple studies, a comparison of their results reveals clear discrepancies. The isolation, sequencing and bioinformatics protocols were rarely optimized for circRNA research and differed significantly between studies This led to the situation that the results published on circRNAs were inconsistent and impossible to comprehensively analyze. Comprehensive comparative analyses of circRNAs in this model species have been significantly hampered To change this situation, we reanalyzed RNA-seq raw data available in the public domain with our protocol for circRNA identification in plants [11] and developed At-C-RNA database to integrate and standardize the available circRNA data (see Figure 1)
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