Welcome to the UPF Digital Repository

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

Show simple item record

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.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.issn 1471-2164
dc.identifier.uri http://hdl.handle.net/10230/53519
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.language.iso eng
dc.publisher BioMed Central
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.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.identifier.doi http://dx.doi.org/10.1186/s12864-022-08612-7
dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/294653
dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BIO2015-70777-P
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion

Thumbnail

This item appears in the following Collection(s)

Show simple item record

Search DSpace


Advanced Search

Browse

My Account

Statistics

In collaboration with Compliant to Partaking