Application Note
CIRCexplorer3: A CLEAR Pipeline for Direct Comparison of Circular and Linear RNA Expression

https://doi.org/10.1016/j.gpb.2019.11.004Get rights and content
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Abstract

Sequences of circular RNAs (circRNAs) produced from back-splicing of exon(s) completely overlap with those from cognate linear RNAs transcribed from the same gene loci with the exception of their back-splicing junction (BSJ) sites. Therefore, examination of global circRNA expression from RNA-seq datasets generally relies on the detection of RNA-seq fragments spanning BSJ sites, which is different from the quantification of linear RNA expression by normalized RNA-seq fragments mapped to whole gene bodies. Thus, direct comparison of circular and linear RNA expression from the same gene loci in a genome-wide manner has remained challenging. Here, we update the previously-reported CIRCexplorer pipeline to version 3 for circular and linear RNA expression analysis from ribosomal-RNA depleted RNA-seq (CIRCexplorer3-CLEAR). A new quantitation parameter, fragments per billion mapped bases (FPB), is applied to evaluate circular and linear RNA expression individually by fragments mapped to circRNA-specific BSJ sites or to linear RNA-specific splicing junction (SJ) sites. Comparison of circular and linear RNA expression levels is directly achieved by dividing FPBcirc by FPBlinear to generate a CIRCscore, which indicates the relative circRNA expression level using linear RNA expression level as the background. Highly-expressed circRNAs with low cognate linear RNA expression background can be readily identified by CIRCexplorer3-CLEAR for further investigation. CIRCexplorer3-CLEAR is publically available at https://github.com/YangLab/CLEAR.

Keywords

Circular RNA
Back-splicing
Linear RNA
Pre-mRNA splicing
Ribo RNA-seq

Cited by (0)

Peer review under responsibility of Beijing Institute of Genomics, Chinese Academy of Sciences and Genetics Society of China.

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Present address: Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.

a

ORCID: 0000-0003-3779-4070.

b

ORCID: 0000-0002-9281-9501.

c

ORCID: 0000-0002-6725-8327.

d

ORCID: 0000-0003-0985-6211.

e

ORCID: 0000-0002-0379-6580.

f

ORCID: 0000-0001-9501-0305.

g

ORCID: 0000-0001-8833-7473.