Design and use of a back splicing junction probe for pulldown of circular RNA-binding proteins in cell lines

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...

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Detalles Bibliográficos
Autores principales: Li, Feiya, Wu, Nan, Yang, Qiwei, Du, William W., Qadir, Javeria, Yang, Burton B.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2022
Materias:
Protocol
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9519607/
https://www.ncbi.nlm.nih.gov/pubmed/36149796
http://dx.doi.org/10.1016/j.xpro.2022.101702
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author Li, Feiya
Wu, Nan
Yang, Qiwei
Du, William W.
Qadir, Javeria
Yang, Burton B.
author_facet Li, Feiya
Wu, Nan
Yang, Qiwei
Du, William W.
Qadir, Javeria
Yang, Burton B.
author_sort Li, Feiya
collection PubMed
description 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).
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spelling pubmed-95196072022-09-30 Design and use of a back splicing junction probe for pulldown of circular RNA-binding proteins in cell lines Li, Feiya Wu, Nan Yang, Qiwei Du, William W. Qadir, Javeria Yang, Burton B. STAR Protoc Protocol 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). Elsevier 2022-09-22 /pmc/articles/PMC9519607/ /pubmed/36149796 http://dx.doi.org/10.1016/j.xpro.2022.101702 Text en © 2022 The Author(s) https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Protocol
Li, Feiya
Wu, Nan
Yang, Qiwei
Du, William W.
Qadir, Javeria
Yang, Burton B.
Design and use of a back splicing junction probe for pulldown of circular RNA-binding proteins in cell lines
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 Protocol
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9519607/
https://www.ncbi.nlm.nih.gov/pubmed/36149796
http://dx.doi.org/10.1016/j.xpro.2022.101702
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