Paired guide RNA CRISPR-Cas9 screening for protein-coding genes and lncRNAs involved in transdifferentiation of human B-cells to macrophages

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• dc.contributor.author Arnan Ros, Carme
• dc.contributor.author Ullrich, Sebastian, 1984-
• dc.contributor.author Pulido-Quetglas, Carlos
• dc.contributor.author Nurtdinov, Ramil
• dc.contributor.author Esteban, Alexandre
• dc.contributor.author Blanco-Fernandez, Joan
• dc.contributor.author Aparicio-Prat, Estel
• dc.contributor.author Johnson, Rory
• dc.contributor.author Pérez-Lluch, Sílvia
• dc.contributor.author Guigó Serra, Roderic
• dc.date.accessioned 2022-06-17T10:31:45Z
• dc.date.available 2022-06-17T10:31:45Z
• dc.date.issued 2022
• dc.description.abstract CRISPR-Cas9 screening libraries have arisen as a powerful tool to identify protein-coding (pc) and non-coding genes playing a role along different processes. In particular, the usage of a nuclease active Cas9 coupled to a single gRNA has proven to efficiently impair the expression of pc-genes by generating deleterious frameshifts. Here, we first demonstrate that targeting the same gene simultaneously with two guide RNAs (paired guide RNAs, pgRNAs) synergistically enhances the capacity of the CRISPR-Cas9 system to knock out pc-genes. We next design a library to target, in parallel, pc-genes and lncRNAs known to change expression during the transdifferentiation from pre-B cells to macrophages. We show that this system is able to identify known players in this process, and also predicts 26 potential novel ones, of which we select four (two pc-genes and two lncRNAs) for deeper characterization. Our results suggest that in the case of the candidate lncRNAs, their impact in transdifferentiation may be actually mediated by enhancer regions at the targeted loci, rather than by the lncRNA transcripts themselves. The CRISPR-Cas9 coupled to a pgRNAs system is, therefore, a suitable tool to simultaneously target pc-genes and lncRNAs for genomic perturbation assays.
• dc.description.sponsorship The research leading to these results has received funding from the Ministerio de Economía y Competitividad and FEDER funds under reference number BIO2015-70777-P and from the European Union Seventh Framework Programme (FP7/2007‐2013) under grant agreement nº ERC-2011-AdG-294653-RNA-MAPS. We also acknowledge the support of the Spanish Ministry of Science and Innovation to the EMBL partnership, Centro de Excelencia Severo Ochoa and CERCA Programme / Generalitat de Catalunya
• dc.format.mimetype application/pdf
• dc.identifier.citation Arnan C, Ullrich S, Pulido-Quetglas C, Nurtdinov R, Esteban A, Blanco-Fernandez J et al. Paired guide RNA CRISPR-Cas9 screening for protein-coding genes and lncRNAs involved in transdifferentiation of human B-cells to macrophages. BMC Genomics. 2022 May 26;23(1):402. DOI:10.1186/s12864-022-08612-7
• dc.identifier.doi http://dx.doi.org/10.1186/s12864-022-08612-7
• dc.identifier.issn 1471-2164
• dc.identifier.uri http://hdl.handle.net/10230/53519
• dc.language.iso eng
• dc.publisher BioMed Central
• dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/294653
• dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BIO2015-70777-P
• dc.rights © Carme Arnan et al 2022. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri https://creativecommons.org/licenses/by/4.0/
• dc.subject.other Genètica
• dc.subject.other Gens
• dc.subject.other RNA
• dc.subject.other Proteïnes
• dc.title Paired guide RNA CRISPR-Cas9 screening for protein-coding genes and lncRNAs involved in transdifferentiation of human B-cells to macrophages
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion