FL-circAS

FL-circAS catalogs and analyzes full-length circular RNAs (circRNAs) to characterize back-splice junctions (BSJs), isoform sequences, expression, alternative splicing, biogenesis features, and potential functions using nanopore long-read sequencing data.

Key Features:

• Comprehensive catalog: Contains 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 derived from nanopore long-read sequencing of 20 cell lines and tissues.
• Expression analysis: Calculates expression levels for each circRNA isoform across cell lines and tissues and reports cell line/tissue specificity at both BSJ and isoform levels.
• Alternative splicing quantification: Computes alternative splicing (AS) entropy for each BSJ across samples.
• Biogenesis insights: Identifies reverse complementary sequences and RNA binding protein (RBP) binding sites within flanking sequences of BSJs.
• Functional annotation: Detects potential microRNA and RBP binding sites on full-length circRNA isoforms and provides evidence for circRNA translation.

Scientific Applications:

• Full-length isoform characterization: Enables identification and cataloging of complete circRNA isoforms derived from nanopore long reads.
• Tissue and cell-type expression profiling: Supports comparative analysis of circRNA and isoform expression and specificity across 20 cell lines and tissues.
• CircRNA biogenesis studies: Facilitates investigation of mechanisms via reverse complementary sequences and RBP binding site patterns in BSJ flanking regions.
• Functional inference: Allows assessment of microRNA/RBP interactions and translation potential of full-length circRNA isoforms.
• Cross-species resource: Provides comparative datasets for human and mouse circRNA BSJs and isoforms.

Methodology:

Integrates nanopore long-read sequencing from 20 cell lines and tissues to identify and catalog BSJs and full-length circRNA isoforms, calculates expression levels and AS entropy, identifies reverse complementary sequences and RBP binding sites in BSJ flanking sequences, detects microRNA and RBP binding sites on isoforms, and provides evidence for circRNA translation.