isoCirc catalogs full-length circular RNA isoforms in human transcriptomes

Xin, Ruijiao; Gao, Yan; Gao, Yuan; Wang, Robert; Kadash-Edmondson, Kathryn E.; Liu, Bo; Wang, Yadong; Lin, Lan; Xing, Yi

doi:10.1038/s41467-020-20459-8

Cited by 117 publications

(93 citation statements)

References 47 publications

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“…In these cases, all circRNA identification and quantification pipelines, including SRCP, will quantify the sum of all the different isoforms. Therefore, the detection and quantification of those isoforms would require a different type of experimental procedure, like the ones recently described utilizing full sequencing of circRNAs [ 51 , 52 ] or a computational approach, as described for CIRIFULL [ 53 ].…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2021

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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.

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Section: Discussionmentioning

confidence: 99%

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

et al. 2021

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“…Compared to short-read sequencing, which is limited to reconstructing short circRNAs (< 500 nt), long-read sequencing of circFL-seq has shown advances in comprehensively identifying full-length circRNAs of all sizes (64 nt to 2334 nt in our data and more than 40% identified isoforms > 500 nt). Very recently, isoCirc 13 and CIRI-long 28 also employed nanopore sequencing to identify full-length circRNAs by utilizing rolling circles. Both circFL-seq and CIRI-long employed RCRT to produce rolling circles during first-strand synthesis, but circFL-seq synthesized second-strand cDNA with an anchor primer instead of template switching of CIRI-long.…”

Section: Discussionmentioning

confidence: 99%

“…Pacific Biosciences (PacBio) sequencing was applied to PCR products for target full-length circRNA sequences in a low-throughput and high-cost way 12 . In contrast, rolling circular amplification (RCA) for circular cDNA of circRNA followed by Oxford Nanopore Technologies (ONT) sequencing can be used to reconstruct genome-wide full-length circRNA 13 . However, the method is limited by the use of ligation, which may also generate circular cDNA from linear residuals.…”

Section: Introductionmentioning

confidence: 99%

circFL-seq reveals full-length circular RNAs with rolling circular reverse transcription and nanopore sequencing

Liu

Tao

et al. 2021

Preprint

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Circular RNAs (circRNAs) act through multiple mechanisms with their sequence features to fine-tune gene expression networks. Due to overlapping sequences with linear cognates, identifying internal sequences of circRNAs remains a great challenge, which hinders comprehensive understanding of circRNA functions and mechanisms. Here, based on rolling circular reverse transcription (RCRT) and nanopore sequencing, we developed circFL-seq, a full-length circRNA sequencing method, to profile circRNA at the isoform level. With a customized computational pipeline circfull to directly identify full-length sequences from rolling circular reads, we reconstructed 77,606 high-quality circRNAs from seven human cell lines and two human tissues. Benefiting from rolling circles and long-read sequencing, circFL-seq showed more than tenfold enrichment of circRNA reads and advantages for both detection and quantification at the isoform level compared to short-read RNA sequencing. The concordance of 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 cancer-related fusion circRNAs at the omics scale may further expand the application of circFL-seq. Together, the accurate identification and quantification of full-length circRNAs make circFL-seq a potential tool for large-scale screening of functional circRNAs.

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“…As with structural genomics, organelle transcriptomics and mitochondrial disorders are also related to non-coding RNA [37]. Recently, TGS has allowed the sequencing of a class of them known as circular RNA (circRNA), which was previously refractory to sequencing [124].…”

Section: Functional Genomicsmentioning

confidence: 99%

Analyzing Modern Biomolecules: The Revolution of Nucleic-Acid Sequencing – Review

et al. 2021

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Recent developments have revolutionized the study of biomolecules. Among them are molecular markers, amplification and sequencing of nucleic acids. The latter is classified into three generations. The first allows to sequence small DNA fragments. The second one increases throughput, reducing turnaround and pricing, and is therefore more convenient to sequence full genomes and transcriptomes. The third generation is currently pushing technology to its limits, being able to sequence single molecules, without previous amplification, which was previously impossible. Besides, this represents a new revolution, allowing researchers to directly sequence RNA without previous retrotranscription. These technologies are having a significant impact on different areas, such as medicine, agronomy, ecology and biotechnology. Additionally, the study of biomolecules is revealing interesting evolutionary information. That includes deciphering what makes us human, including phenomena like non-coding RNA expansion. All this is redefining the concept of gene and transcript. Basic analyses and applications are now facilitated with new genome editing tools, such as CRISPR. All these developments, in general, and nucleic-acid sequencing, in particular, are opening a new exciting era of biomolecule analyses and applications, including personalized medicine, and diagnosis and prevention of diseases for humans and other animals.

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isoCirc catalogs full-length circular RNA isoforms in human transcriptomes

Cited by 117 publications

References 47 publications

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

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

circFL-seq reveals full-length circular RNAs with rolling circular reverse transcription and nanopore sequencing

Analyzing Modern Biomolecules: The Revolution of Nucleic-Acid Sequencing – Review

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