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

STAR Protoc. 2023 Dec 15;4(4):102588. doi: 10.1016/j.xpro.2023.102588. Epub 2023 Sep 28.

Authors

Oscar Bril¹, Laura J Schwarzmueller¹, Leandro F Moreno¹, Louis Vermeulen¹, Nicolas Léveillé²

Affiliations

¹ Center for Experimental and Molecular Medicine, Cancer Center Amsterdam and Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam 1105AZ, The Netherlands; Oncode Institute, Meibergdreef 9, Amsterdam 1105AZ, The Netherlands.
² Center for Experimental and Molecular Medicine, Cancer Center Amsterdam and Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam 1105AZ, The Netherlands; Oncode Institute, Meibergdreef 9, Amsterdam 1105AZ, The Netherlands. Electronic address: n.leveille@amsterdamumc.nl.

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.

MeSH terms

CRISPR-Cas Systems / genetics
Genome, Human
Humans
Neoplasms* / diagnosis
Neoplasms* / genetics
RNA, Guide, CRISPR-Cas Systems
RNA, Long Noncoding* / genetics

Substances

RNA, Guide, CRISPR-Cas Systems
RNA, Long Noncoding