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isoCirc catalogs full-length circular RNA isoforms in human transcriptomes
- Source :
- Nature Communications, Vol 12, Iss 1, Pp 1-11 (2021), Nature Communications
- Publication Year :
- 2021
- Publisher :
- Nature Portfolio, 2021.
-
Abstract
- Circular RNAs (circRNAs) have emerged as an important class of functional RNA molecules. Short-read RNA sequencing (RNA-seq) is a widely used strategy to identify circRNAs. However, an inherent limitation of short-read RNA-seq is that it does not experimentally determine the full-length sequences and exact exonic compositions of circRNAs. Here, we report isoCirc, a strategy for sequencing full-length circRNA isoforms, using rolling circle amplification followed by nanopore long-read sequencing. We describe an integrated computational pipeline to reliably characterize full-length circRNA isoforms using isoCirc data. Using isoCirc, we generate a comprehensive catalog of 107,147 full-length circRNA isoforms across 12 human tissues and one human cell line (HEK293), including 40,628 isoforms ≥500 nt in length. We identify widespread alternative splicing events within the internal part of circRNAs, including 720 retained intron events corresponding to a class of exon-intron circRNAs (EIciRNAs). Collectively, isoCirc and the companion dataset provide a useful strategy and resource for studying circRNAs in human transcriptomes.<br />Circular RNAs have been identified using short-read RNA sequencing. Here, the authors report isoCirc, a long-read sequencing method to characterize full-length circRNA isoforms and generate a catalogue of full-length circRNA isoforms in 12 human tissues and one human cell line.
- Subjects :
- 0301 basic medicine
Science
General Physics and Astronomy
RNA-Seq
Computational biology
Biology
General Biochemistry, Genetics and Molecular Biology
Article
Non-coding RNAs
Transcriptome
03 medical and health sciences
0302 clinical medicine
Circular RNA
Databases, Genetic
RNA Isoforms
Humans
Transcriptomics
Multidisciplinary
Alternative splicing
Intron
RNA
RNA sequencing
General Chemistry
RNA, Circular
Non-coding RNA
Computational biology and bioinformatics
Alternative Splicing
030104 developmental biology
HEK293 Cells
Rolling circle replication
030217 neurology & neurosurgery
Subjects
Details
- Language :
- English
- ISSN :
- 20411723
- Volume :
- 12
- Issue :
- 1
- Database :
- OpenAIRE
- Journal :
- Nature Communications
- Accession number :
- edsair.doi.dedup.....70228ebb93ae83bac692ace81aa6ad75