Identifying essential long non-coding RNAs in cancer using CRISPRi-based dropout screens

Oscar Bril; Laura J. Schwarzmueller; Leandro F. Moreno; Louis Vermeulen; Nicolas Léveillé

doi:10.1016/j.xpro.2023.102588

Identifying essential long non-coding RNAs in cancer using CRISPRi-based dropout screens

Oscar Bril
, Laura J. Schwarzmueller
, Leandro F. Moreno
, Louis Vermeulen
, Nicolas Léveillé^*

^*Corresponding author for this work

Oncode Institute, Amsterdam, the Netherlands
University of Amsterdam

Research output: Contribution to journal › Article › Academic › peer-review

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Abstract

Long non-coding RNAs (lncRNAs) are emerging as key regulators in the initiation, growth, and progression of cancer. High-throughput CRISPR-based techniques systematically assess the function of genes or regulatory elements present in the human genome. Here, we present a protocol for identifying essential lncRNAs in cancer using CRISPRi-based dropout screens. We describe steps to select target sites, design guide RNAs, and generate CRISPRi cell lines. We then detail the execution and analysis of CRISPRi-based dropout screens.

Original language	English
Article number	102588
Journal	STAR Protocols
Volume	4
Issue number	4
DOIs	https://doi.org/10.1016/j.xpro.2023.102588
Publication status	Published - 15 Dec 2023

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

Keywords

Bioinformatics
CRISPR
Cell Biology
Genomics
Molecular Biology

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10.1016/j.xpro.2023.102588

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title = "Identifying essential long non-coding RNAs in cancer using CRISPRi-based dropout screens",

abstract = "Long non-coding RNAs (lncRNAs) are emerging as key regulators in the initiation, growth, and progression of cancer. High-throughput CRISPR-based techniques systematically assess the function of genes or regulatory elements present in the human genome. Here, we present a protocol for identifying essential lncRNAs in cancer using CRISPRi-based dropout screens. We describe steps to select target sites, design guide RNAs, and generate CRISPRi cell lines. We then detail the execution and analysis of CRISPRi-based dropout screens.",

keywords = "Bioinformatics, CRISPR, Cell Biology, Genomics, Molecular Biology",

author = "Oscar Bril and Schwarzmueller, \{Laura J.\} and Moreno, \{Leandro F.\} and Louis Vermeulen and Nicolas L{\'e}veill{\'e}",

note = "Funding Information: This work is supported by Oncode Institute , The New York Stem Cell Foundation , grants from the European Research Council (ERC- CoG 101045612 - NIMICRY) and ZonMw ( Vici 09-15018-21-10029 ) to L.V. and KWF ( 12228 \& 15052 ) to N.L. L.V. is a New York Stem Cell Foundation—Robertson Investigator. Funding Information: This work is supported by Oncode Institute, The New York Stem Cell Foundation, grants from the European Research Council (ERC-CoG 101045612 - NIMICRY) and ZonMw (Vici 09-15018-21-10029) to L.V. and KWF (12228 \& 15052) to N.L. L.V. is a New York Stem Cell Foundation—Robertson Investigator. O.B. wrote parts of the manuscript, designed figures, and proofread the manuscript. L.J.S. wrote parts of the manuscript, designed figures, and proofread the manuscript. L.F.M. wrote part 2.1 of the manuscript and proofread the manuscript. L.V. proofread the manuscript. N.L. proofread the manuscript. L.V. received consultancy fees from Bayer, Genentech Inc, MSD, Servier, and Pierre Fabre, but these have no relation to the content of this publication. Currently L.V. is an employee of Genentech-Roche. Publisher Copyright: {\textcopyright} 2023 The Authors",

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doi = "10.1016/j.xpro.2023.102588",

language = "English",

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AU - Schwarzmueller, Laura J.

AU - Moreno, Leandro F.

AU - Vermeulen, Louis

AU - Léveillé, Nicolas

N1 - Funding Information: This work is supported by Oncode Institute , The New York Stem Cell Foundation , grants from the European Research Council (ERC- CoG 101045612 - NIMICRY) and ZonMw ( Vici 09-15018-21-10029 ) to L.V. and KWF ( 12228 & 15052 ) to N.L. L.V. is a New York Stem Cell Foundation—Robertson Investigator. Funding Information: This work is supported by Oncode Institute, The New York Stem Cell Foundation, grants from the European Research Council (ERC-CoG 101045612 - NIMICRY) and ZonMw (Vici 09-15018-21-10029) to L.V. and KWF (12228 & 15052) to N.L. L.V. is a New York Stem Cell Foundation—Robertson Investigator. O.B. wrote parts of the manuscript, designed figures, and proofread the manuscript. L.J.S. wrote parts of the manuscript, designed figures, and proofread the manuscript. L.F.M. wrote part 2.1 of the manuscript and proofread the manuscript. L.V. proofread the manuscript. N.L. proofread the manuscript. L.V. received consultancy fees from Bayer, Genentech Inc, MSD, Servier, and Pierre Fabre, but these have no relation to the content of this publication. Currently L.V. is an employee of Genentech-Roche. Publisher Copyright: © 2023 The Authors

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N2 - Long non-coding RNAs (lncRNAs) are emerging as key regulators in the initiation, growth, and progression of cancer. High-throughput CRISPR-based techniques systematically assess the function of genes or regulatory elements present in the human genome. Here, we present a protocol for identifying essential lncRNAs in cancer using CRISPRi-based dropout screens. We describe steps to select target sites, design guide RNAs, and generate CRISPRi cell lines. We then detail the execution and analysis of CRISPRi-based dropout screens.

AB - Long non-coding RNAs (lncRNAs) are emerging as key regulators in the initiation, growth, and progression of cancer. High-throughput CRISPR-based techniques systematically assess the function of genes or regulatory elements present in the human genome. Here, we present a protocol for identifying essential lncRNAs in cancer using CRISPRi-based dropout screens. We describe steps to select target sites, design guide RNAs, and generate CRISPRi cell lines. We then detail the execution and analysis of CRISPRi-based dropout screens.

KW - Bioinformatics

KW - CRISPR

KW - Cell Biology

KW - Genomics

KW - Molecular Biology

UR - https://www.scopus.com/pages/publications/85172335644

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M1 - 102588

ER -

Identifying essential long non-coding RNAs in cancer using CRISPRi-based dropout screens

Abstract

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Keywords

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