Design and use of a back splicing junction probe for pulldown of circular RNA-binding proteins in cell lines
Summary: Due to the unique structure of circular RNAs, it is challenging to use traditional pulldown approaches. Here, we describe the design and use of a probe that spans the back splicing junction (BSJ), enabling interaction with circular RNAs. The probe repeats four times, allowing efficient and...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2022-12-01
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| Series: | STAR Protocols |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166722005822 |
| _version_ | 1811292694389981184 |
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| author | Feiya Li Nan Wu Qiwei Yang William W. Du Javeria Qadir Burton B. Yang |
| author_facet | Feiya Li Nan Wu Qiwei Yang William W. Du Javeria Qadir Burton B. Yang |
| author_sort | Feiya Li |
| collection | DOAJ |
| description | Summary: Due to the unique structure of circular RNAs, it is challenging to use traditional pulldown approaches. Here, we describe the design and use of a probe that spans the back splicing junction (BSJ), enabling interaction with circular RNAs. The probe repeats four times, allowing efficient and specific pulldown of circular RNAs and their binding partners. This protocol describes the steps for mouse cardiac fibroblast (MCF) cells; we have also verified the protocol in other cell types.For complete details on the use and execution of this protocol, please refer to Wu et al. (2021). : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. |
| first_indexed | 2024-04-13T04:49:17Z |
| format | Article |
| id | doaj.art-e66caa3d4ba5476ea7d42e1431a3c8fa |
| institution | Directory Open Access Journal |
| issn | 2666-1667 |
| language | English |
| last_indexed | 2024-04-13T04:49:17Z |
| publishDate | 2022-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj.art-e66caa3d4ba5476ea7d42e1431a3c8fa2022-12-22T03:01:45ZengElsevierSTAR Protocols2666-16672022-12-0134101702Design and use of a back splicing junction probe for pulldown of circular RNA-binding proteins in cell linesFeiya Li0Nan Wu1Qiwei Yang2William W. Du3Javeria Qadir4Burton B. Yang5Sunnybrook Research Institute, and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Corresponding authorSunnybrook Research Institute, and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, CanadaSunnybrook Research Institute, and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, CanadaSunnybrook Research Institute, and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, CanadaSunnybrook Research Institute, and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, CanadaSunnybrook Research Institute, and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Corresponding authorSummary: Due to the unique structure of circular RNAs, it is challenging to use traditional pulldown approaches. Here, we describe the design and use of a probe that spans the back splicing junction (BSJ), enabling interaction with circular RNAs. The probe repeats four times, allowing efficient and specific pulldown of circular RNAs and their binding partners. This protocol describes the steps for mouse cardiac fibroblast (MCF) cells; we have also verified the protocol in other cell types.For complete details on the use and execution of this protocol, please refer to Wu et al. (2021). : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.http://www.sciencedirect.com/science/article/pii/S2666166722005822RNAseqMolecular biologyMolecular/Chemical probes |
| spellingShingle | Feiya Li Nan Wu Qiwei Yang William W. Du Javeria Qadir Burton B. Yang Design and use of a back splicing junction probe for pulldown of circular RNA-binding proteins in cell lines STAR Protocols RNAseq Molecular biology Molecular/Chemical probes |
| title | Design and use of a back splicing junction probe for pulldown of circular RNA-binding proteins in cell lines |
| title_full | Design and use of a back splicing junction probe for pulldown of circular RNA-binding proteins in cell lines |
| title_fullStr | Design and use of a back splicing junction probe for pulldown of circular RNA-binding proteins in cell lines |
| title_full_unstemmed | Design and use of a back splicing junction probe for pulldown of circular RNA-binding proteins in cell lines |
| title_short | Design and use of a back splicing junction probe for pulldown of circular RNA-binding proteins in cell lines |
| title_sort | design and use of a back splicing junction probe for pulldown of circular rna binding proteins in cell lines |
| topic | RNAseq Molecular biology Molecular/Chemical probes |
| url | http://www.sciencedirect.com/science/article/pii/S2666166722005822 |
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