SRCP: a comprehensive pipeline for accurate annotation and quantification of circRNAs

• Published in: Genome Biology Vol. 22; no. 1; p. 277
• Main Authors: Rabin, Avigayel, Zaffagni, Michela, Ashwal-Fluss, Reut, Patop, Ines Lucia, Jajoo, Aarti, Shenzis, Shlomo, Carmel, Liran, Kadener, Sebastian
• Format: Journal Article
• Language: English
• Published: England BioMed Central 23-09-2021; BMC
• Subjects: AGO2; Animals; Annotations; Argonaute 2 protein; Argonaute Proteins - metabolism; Brain - metabolism; CircRNAs; Circular RNA; Databases, Nucleic Acid; Datasets; Exoribonucleases; Genomics; Humans; Method; Mice; miRNA; Molecular Sequence Annotation; Pipeline; Pipelines; Rats; RNA metabolism; RNA, Circular - analysis; RNA, Circular - genetics; RNA, Circular - metabolism; RNA-Seq; Software; Splicing; Circular RNA; CircRNAs; Splicing; AGO2; Pipeline; RNA metabolism
• ISSN: 1474-760X; 1474-7596; 1474-760X
• DOI: 10.1186/s13059-021-02497-7

Here we describe a new integrative approach for accurate annotation and quantification of circRNAs named Short Read circRNA Pipeline (SRCP). Our strategy involves two steps: annotation of validated circRNAs followed by a quantification step. We show that SRCP is more sensitive than other individual pipelines and allows for more comprehensive quantification of a larger number of differentially expressed circRNAs. To facilitate the use of SRCP, we generate a comprehensive collection of validated circRNAs in five different organisms, including humans. We then utilize our approach and identify a subset of circRNAs bound to the miRNA-effector protein AGO2 in human brain samples.