FL-circAS--Home

Welcome to FL-circAS!

Circular RNAs (circRNAs) are a class of functional RNA molecules with a continuous loop structure characterized by back-splice junctions (BSJs). Analyses of short-read RNA sequencing (RNA-seq) have identified millions of BSJ events in various species and developed numerous databases. However, it is inherently challenging for such short-read-based strategies to determine exact full-length circle sequences and alternatively spliced (AS) isoforms of circRNAs. Recent advances in nanopore long-read sequencing with circRNA enrichment bring an unprecedented opportunity for investigating the above issues. Here we developed FL-circAS, which collected such log-read sequencing data of 20 cell lines/tissues and thereby identified 884,636 BSJs with 1,853,692 full-length circRNA isoforms in human and 115,173 BSJs with 135,617 full-length circRNA isoforms in mouse. With the full-length circRNA sequences, FL-circAS further provides multiple types of features related to circRNA expression, biogenesis, and function. For circRNA expression, FL-circAS calculates expression levels for each circRNA isoform, cell line/tissue specificity at both the BSJ and isoform levels, and AS entropy for each BSJ across samples. For circRNA biogenesis, we identified reverse complementary sequences and RNA binding protein (RBP) binding sites residing in flanking sequences of BSJs. For functional patterns, we identified potential microRNA/RBP binding sites and several types of evidence for circRNA translation (circRNA specific open reading frames, internal ribosome entry sites, N-6-methyladenosine sites, and experimentally supported translation initiation sites) on each full-length circRNA isoform. FL-circAS provides user-friendly web interfaces for browsing, searching, analyzing and downloading data freely, presenting the first resource to discover full-length circRNAs at the isoform level.

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Citation

Tai-Wei Chiang, Song-En Jhong, Yu-Chen Chen, Chia-Ying Chen, Wei-Sheng Wu, Trees-Juen Chuang (2024) FL-circAS: an integrative resource and analysis for full-length sequences and alternative splicing of circular RNAs with nanopore sequencing. Nucleic Acids Research, 52: D115-D123.