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  FLASH: ultra-fast protocol to identify RNA-protein interactions in cells

Ilik, I. A., Aktas, T., Maticzka, D., Backofen, R., & Akhtar, A. (2020). FLASH: ultra-fast protocol to identify RNA-protein interactions in cells. Nucelic Acids Research, 48, e15. doi:10.1093/nar/gkz1141.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0005-7039-D Version Permalink: http://hdl.handle.net/21.11116/0000-0005-DA1C-7
Genre: Journal Article

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 Creators:
Ilik, Ibrahim Avsar1, Author              
Aktas, Tugce1, Author              
Maticzka, Daniel2, Author
Backofen, Rolf2, Author
Akhtar, Asifa3, Author              
Affiliations:
1Quantitative RNA Biology (Tugce Aktas), Independent Junior Research Groups (OWL), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_3014184              
2External Organizations, ou_persistent22              
3Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society, ou_2243643              

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 Abstract: Determination of the in vivo binding sites of RNA-binding proteins (RBPs) is paramount to understanding their function and how they affect different aspects of gene regulation. With hundreds of RNA-binding proteins identified in human cells, a flexible, high-resolution, high-throughput, highly multiplexible and radioactivity-free method to determine their binding sites has not been described to date. Here we report FLASH (Fast Ligation of RNA after some sort of Affinity Purification for High-throughput Sequencing), which uses a special adapter design and an optimized protocol to determine protein-RNA interactions in living cells. The entire FLASH protocol, starting from cells on plates to a sequencing library, takes 1.5 days. We demonstrate the flexibility, speed and versatility of FLASH by using it to determine RNA targets of both tagged and endogenously expressed proteins under diverse conditions in vivo.

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Language(s): eng - English
 Dates: 2019-12-032020-02-20
 Publication Status: Published in print
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 Rev. Type: Peer
 Identifiers: DOI: 10.1093/nar/gkz1141
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Title: Nucelic Acids Research
  Alternative Title : NAR
Source Genre: Journal
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Publ. Info: Oxford : Oxford University Press
Pages: - Volume / Issue: 48 Sequence Number: - Start / End Page: e15 Identifier: n.a.: /journals/resource/110992357379342_1