isoCirc catalogs full-length circular RNA isoforms in human transcriptomes
Circular RNAs (circRNAs) have emerged as an important class of functional RNA molecules. Short-read RNA sequencing (RNA-seq) is a widely used strategy to identify circRNAs. However, an inherent limitation of short-read RNA-seq is that it does not experimentally determine the full-length sequences and exact exonic compositions of circRNAs. Here, we report isoCirc, a strategy for sequencing full-length circRNA isoforms, using rolling circle amplification followed by nanopore long-read sequencing. We describe an integrated computational pipeline to reliably characterize full-length circRNA isoforms using isoCirc data. Using isoCirc, we generate a comprehensive catalog of 107,147 full-length circRNA isoforms across 12 human tissues and one human cell line (HEK293), including 40,628 isoforms ≥500 nt in length. We identify widespread alternative splicing events within the internal part of circRNAs, including 720 retained intron events corresponding to a class of exon-intron circRNAs (EIciRNAs). Collectively, isoCirc and the companion dataset provide a useful strategy and resource for studying circRNAs in human transcriptomes.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2021 |
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| Erschienen: |
2021 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:12 |
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| Enthalten in: |
Nature communications - 12(2021), 1 vom: 12. Jan., Seite 266 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Xin, Ruijiao [VerfasserIn] |
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| Links: |
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| Themen: |
Journal Article |
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| Anmerkungen: |
Date Completed 21.01.2021 Date Revised 30.03.2024 published: Electronic Citation Status MEDLINE |
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| doi: |
10.1038/s41467-020-20459-8 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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NLM31999967X |
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| 245 | 1 | 0 | |a isoCirc catalogs full-length circular RNA isoforms in human transcriptomes |
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| 500 | |a Date Revised 30.03.2024 | ||
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| 500 | |a Citation Status MEDLINE | ||
| 520 | |a Circular RNAs (circRNAs) have emerged as an important class of functional RNA molecules. Short-read RNA sequencing (RNA-seq) is a widely used strategy to identify circRNAs. However, an inherent limitation of short-read RNA-seq is that it does not experimentally determine the full-length sequences and exact exonic compositions of circRNAs. Here, we report isoCirc, a strategy for sequencing full-length circRNA isoforms, using rolling circle amplification followed by nanopore long-read sequencing. We describe an integrated computational pipeline to reliably characterize full-length circRNA isoforms using isoCirc data. Using isoCirc, we generate a comprehensive catalog of 107,147 full-length circRNA isoforms across 12 human tissues and one human cell line (HEK293), including 40,628 isoforms ≥500 nt in length. We identify widespread alternative splicing events within the internal part of circRNAs, including 720 retained intron events corresponding to a class of exon-intron circRNAs (EIciRNAs). Collectively, isoCirc and the companion dataset provide a useful strategy and resource for studying circRNAs in human transcriptomes | ||
| 650 | 4 | |a Journal Article | |
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| 650 | 7 | |a RNA Isoforms |2 NLM | |
| 650 | 7 | |a RNA, Circular |2 NLM | |
| 700 | 1 | |a Gao, Yan |e verfasserin |4 aut | |
| 700 | 1 | |a Gao, Yuan |e verfasserin |4 aut | |
| 700 | 1 | |a Wang, Robert |e verfasserin |4 aut | |
| 700 | 1 | |a Kadash-Edmondson, Kathryn E |e verfasserin |4 aut | |
| 700 | 1 | |a Liu, Bo |e verfasserin |4 aut | |
| 700 | 1 | |a Wang, Yadong |e verfasserin |4 aut | |
| 700 | 1 | |a Lin, Lan |e verfasserin |4 aut | |
| 700 | 1 | |a Xing, Yi |e verfasserin |4 aut | |
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