circFL-seq – identification and quantification of full-length circRNAs for large-scale screening of functional circRNAs

Circular RNAs (circRNAs) act through multiple mechanisms via their sequence features to fine-tune gene expression networks. Due to overlapping sequences with linear cognates, identifying internal sequences of circRNAs remains a challenge, which hinders a comprehensive understanding of circRNA functions and mechanisms. Here, based on rolling circular reverse transcription and nanopore sequencing, researchers at Peking University Health Science Center have developed circFL-seq, a full-length circRNA sequencing method, to profile circRNA at the isoform level. With a customized computational pipeline to directly identify full-length sequences from rolling circular reads, the researchers reconstructed 77,606 high-quality circRNAs from seven human cell lines and two human tissues. circFL-seq benefits from rolling circles and long-read sequencing, and the results showed more than tenfold enrichment of circRNA reads and advantages for both detection and quantification at the isoform level compared to those for short-read RNA sequencing. The concordance of the RT-qPCR and circFL-seq results for the identification of differential alternative splicing suggested wide application prospects for functional studies of internal variants in circRNAs. Moreover, the detection of fusion circRNAs at the omics scale may further expand the application of circFL-seq. Taken together, the accurate identification and quantification of full-length circRNAs make circFL-seq a potential tool for large-scale screening of functional circRNAs.

Diagram of circFL-seq workflow

(A) Experimental operation of circFL-seq consisted of circRNA enrichment, library construction, and nanopore sequencing. (B) PCR validation of rolling circle products from the circFL-seq cDNA library. The yellow and green lines indicate the positions of the PCR primers. The upward triangle, downward triangle, and circle symbols denote the 0-circle, 1-circle, and 2-circle cDNA products. (C) Computational pipeline of circFL-seq. circFL-seq clean reads were directly used in RG mode or were self-corrected for consensus sequences in cRG mode to reconstruct full-length circRNAs. circRNA, circular RNA.

Liu Z, Tao C, Li S, Du M, Bai Y, Hu X, Li Y, Chen J, Yang E. (2021) circFL-seq reveals full-length circular RNAs with rolling circular reverse transcription and nanopore sequencing. Elife 10:e69457. [article]

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