Full-length circular RNA profiling by nanopore sequencing with CIRI-long

Lingling Hou, Jinyang Zhang, Fangqing Zhao

Published: 2023-04-11 DOI: 10.1038/s41596-023-00815-w

circRNA

nanopore sequencing

CIRI-long

full-length circular RNA

long-read sequencing

AI 解读

Supplementary information

Supplementary Code 1

Code used in the paper.

Purification of infection-associated macropinosomes by magnetic isolation for proteomic characterization

Hi-CO: 3D genome structure analysis with nucleosome resolution

Practical and concise synthesis of nucleoside analogs

Comprehensive analysis of glycosphingolipid glycans by lectin microarrays and MALDI-TOF mass spectrometry

Human primordial germ cell-like cells specified from resetting precursors develop in human hindgut organoids

KAS-seq: genome-wide sequencing of single-stranded DNA by N3-kethoxal–assisted labeling

Detecting chromosomal interactions in Capture Hi-C data with CHiCAGO and companion tools

Capture of the newly transcribed RNA interactome using click chemistry

Design, assembly, and characterization of membrane-spanning DNA nanopores

Transcriptome-wide identification of RNA-binding protein binding sites using seCLIP-seq

查看全部

Sections

Figures

References

Supplementary information

Kristensen, L. S. et al. The biogenesis, biology and characterization of circular RNAs. Nat. Rev. Genet. 20, 675–691 (2019).
Liu, C.-X. & Chen, L.-L. Circular RNAs: characterization, cellular roles, and applications. Cell 185, 2016–2034 (2022).
Wu, W., Ji, P. & Zhao, F. CircAtlas: an integrated resource of one million highly accurate circular RNAs from 1070 vertebrate transcriptomes. Genome Biol. 21, 101 (2020).
Gao, Y., Wang, J. & Zhao, F. CIRI: an efficient and unbiased algorithm for de novo circular RNA identification. Genome Biol. 16, 4 (2015).
Zhang, J., Chen, S., Yang, J. & Zhao, F. Accurate quantification of circular RNAs identifies extensive circular isoform switching events. Nat. Commun. 11, 90 (2020).
Wu, W., Zhang, J., Cao, X., Cai, Z. & Zhao, F. Exploring the cellular landscape of circular RNAs using full-length single-cell RNA sequencing. Nat. Commun. 13, 3242 (2022).
Ji, P. et al. Expanded expression landscape and prioritization of circular RNAs in mammals. Cell Rep. 26, 3444–3460 e3445 (2019).
Dong, R., Ma, X. K., Li, G. W. & Yang, L. CIRCpedia v2: an updated database for comprehensive circular RNA annotation and expression comparison. Genom. Proteom. Bioinform. 16, 226–233 (2018).
Gan, X. et al. CircMUC16 promotes autophagy of epithelial ovarian cancer via interaction with ATG13 and miR-199a. Mol. Cancer 19, 45 (2020).
Kristensen, L. S. et al. Spatial expression analyses of the putative oncogene ciRS-7 in cancer reshape the microRNA sponge theory. Nat. Commun. 11, 4551 (2020).
Chen, S. et al. circVAMP3 drives CAPRIN1 phase separation and inhibits hepatocellular carcinoma by suppressing c-Myc translation. Adv. Sci. 9, e2103817 (2022).
Liu, C. X. et al. RNA circles with minimized immunogenicity as potent PKR inhibitors. Mol. Cell. 82, 420–434 e426 (2022).
Chen, S., Zhang, J. & Zhao, F. Screening linear and circular RNA transcripts from stress granules. Genom. Proteom. Bioinform. https://doi.org/10.1016/j.gpb.2022.01.003 (2022).
Yang, Y. et al. Extensive translation of circular RNAs driven by N(6)-methyladenosine. Cell Res. 27, 626–641 (2017).
Li, Y. et al. HNRNPL circularizes ARHGAP35 to produce an oncogenic protein. Adv. Sci. 8, 2001701 (2021).
Zhang, M. et al. A peptide encoded by circular form of LINC-PINT suppresses oncogenic transcriptional elongation in glioblastoma. Nat. Commun. 9, 4475 (2018).
Dal Molin, A. et al. CRAFT: a bioinformatics software for custom prediction of circular RNA functions. Brief. Bioinform. https://doi.org/10.1093/bib/bbab601 (2022).
Gao, Y., Zhang, J. & Zhao, F. Circular RNA identification based on multiple seed matching. Brief. Bioinform. 19, 803–810 (2018).
Gao, Y. et al. Comprehensive identification of internal structure and alternative splicing events in circular RNAs. Nat. Commun. 7, 12060 (2016).
Zheng, Y., Ji, P., Chen, S., Hou, L. & Zhao, F. Reconstruction of full-length circular RNAs enables isoform-level quantification. Genome Med. 11, 2 (2019).
Zhang, X. O. et al. Diverse alternative back-splicing and alternative splicing landscape of circular RNAs. Genome Res. 26, 1277–1287 (2016).
Zhang, J. et al. Comprehensive profiling of circular RNAs with nanopore sequencing and CIRI-long. Nat. Biotechnol. 39, 836–845 (2021).
Zhang, J. et al. Evaluation of circRNA sequence assembly methods using long reads. Front. Genet. 13, 816825 (2022).
Soutschek, M., Gross, F., Schratt, G. & Germain, P.-L. scanMiR: a biochemically based toolkit for versatile and efficient microRNA target prediction. Bioinformatics 38, 2466–2473 (2022).
Wu, J. et al. CircAST: full-length assembly and quantification of alternatively spliced isoforms in circular RNAs. Genom. Proteom. Bioinform. 17, 522–534 (2019).
Ye, C. Y. et al. Full-length sequence assembly reveals circular RNAs with diverse non-GT/AG splicing signals in rice. RNA Biol. 14, 1055–1063 (2017).
Metge, F., Czaja-Hasse, L. F., Reinhardt, R. & Dieterich, C. FUCHS-towards full circular RNA characterization using RNAseq. PeerJ 5, e2934 (2017).
Hossain, M. T., Peng, Y., Feng, S. & Wei, Y. FcircSEC: an R package for full length circRNA sequence extraction and classification. Int. J. Genom. 2020, 9084901 (2020).
Qin, Y. et al. Reference-free and de novo identification of circular RNAs. Preprint at bioRxiv https://doi.org/10.1101/2020.04.21.050617 (2020).
Zheng, Y. & Zhao, F. Visualization of circular RNAs and their internal splicing events from transcriptomic data. Bioinformatics 36, 2934–2935 (2020).
Zhang, J. & Zhao, F. Reconstruction of circular RNAs using Illumina and Nanopore RNA-seq datasets. Methods 196, 17–22 (2021).
Zhang, J. & Zhao, F. Characterizing circular RNAs using Nanopore sequencing. Trends Biochem. Sci. 46, 785–786 (2021).
Jeck, W. R. et al. Circular RNAs are abundant, conserved, and associated with ALU repeats. RNA 19, 141–157 (2013).
Pandey, P. R., Rout, P. K., Das, A., Gorospe, M. & Panda, A. C. RPAD (RNase R treatment, polyadenylation, and poly(A)+ RNA depletion) method to isolate highly pure circular RNA. Methods 155, 41–48 (2019).
Panda, A. C. et al. High-purity circular RNA isolation method (RPAD) reveals vast collection of intronic circRNAs. Nucleic Acids Res. 45, e116 (2017).
Zhang, Z. & Han, L. Circular RNAs sequenced at last. Nat. Biotechnol. 39, 811–812 (2021).
Vo, J. N. et al. The landscape of circular RNA in cancer. Cell 176, 869–881 e813 (2019).
Xin, R. et al. isoCirc catalogs full-length circular RNA isoforms in human transcriptomes. Nat. Commun. 12, 266 (2021).
Liu, Z. et al. circFL-seq reveals full-length circular RNAs with rolling circular reverse transcription and nanopore sequencing. eLife https://doi.org/10.7554/eLife.69457 (2021).
Rahimi, K., Veno, M. T., Dupont, D. M. & Kjems, J. Nanopore sequencing of brain-derived full-length circRNAs reveals circRNA-specific exon usage, intron retention and microexons. Nat. Commun. 12, 4825 (2021).
Jeck, W. R. & Sharpless, N. E. Detecting and characterizing circular RNAs. Nat. Biotechnol. 32, 453–461 (2014).
Vincent, H. A. & Deutscher, M. P. Substrate recognition and catalysis by the exoribonuclease RNase R. J. Biol. Chem. 281, 29769–29775 (2006).
Xiao, M. S. & Wilusz, J. E. An improved method for circular RNA purification using RNase R that efficiently removes linear RNAs containing G-quadruplexes or structured 3′ ends. Nucleic Acids Res. 47, 8755–8769 (2019).
Fukasawa, Y., Ermini, L., Wang, H., Carty, K. & Cheung, M. S. LongQC: a quality control tool for third generation sequencing long read data. G3 (Bethesda) 10, 1193–1196 (2020).
Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. Preprint at https://doi.org/10.48550/arXiv.1303.3997 (2013).
Wang, Y. et al. GSA: Genome Sequence Archive. Genom. Proteom. Bioinform. 15, 14–18 (2017).
Zhang, J. Full-length circular RNA profiling by nannopore sequencing with CIRI-long. https://github.com/bioinfo-biols/CIRI-long, https://doi.org/10.5281/zenodo.7399826 (2022).
Thorvaldsdottir, H., Robinson, J. T. & Mesirov, J. P. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief. Bioinform. 14, 178–192 (2013).
Diesh, C. et al. JBrowse 2: a modular genome browser with views of synteny and structural variation. Preprint at https://doi.org/10.1101/2022.07.28.501447 (2022).

Full-length circular RNA profiling by nanopore sequencing with CIRI-long

Supplementary information

推荐阅读