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Mutant resources for functional genomics in Dictyostelium discoideum using REMI-seq technology

Gruenheit, N; Baldwin, A; Stewart, B; Jaques, S; Keller, T; Parkinson, K; Salvidge, W; ... Thompson, CRL; + view all (2021) Mutant resources for functional genomics in Dictyostelium discoideum using REMI-seq technology. BMC Biology , 19 , Article 172. 10.1186/s12915-021-01108-y. Green open access

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Abstract

Background: Genomes can be sequenced with relative ease, but ascribing gene function remains a major challenge. Genetically tractable model systems are crucial to meet this challenge. One powerful model is the social amoeba Dictyostelium discoideum, a eukaryotic microbe widely used to study diverse questions in the cell, developmental and evolutionary biology. Results: We describe REMI-seq, an adaptation of Tn-seq, which allows high throughput, en masse, and quantitative identification of the genomic site of insertion of a drug resistance marker after restriction enzyme-mediated integration. We use REMI-seq to develop tools which greatly enhance the efficiency with which the sequence, transcriptome or proteome variation can be linked to phenotype in D. discoideum. These comprise (1) a near genome-wide resource of individual mutants and (2) a defined pool of ‘barcoded’ mutants to allow large-scale parallel phenotypic analyses. These resources are freely available and easily accessible through the REMI-seq website that also provides comprehensive guidance and pipelines for data analysis. We demonstrate that integrating these resources allows novel regulators of cell migration, phagocytosis and macropinocytosis to be rapidly identified. Conclusions: We present methods and resources, generated using REMI-seq, for high throughput gene function analysis in a key model system.

Type: Article
Title: Mutant resources for functional genomics in Dictyostelium discoideum using REMI-seq technology
Open access status: An open access version is available from UCL Discovery
DOI: 10.1186/s12915-021-01108-y
Publisher version: https://doi.org/10.1186/s12915-021-01108-y
Language: English
Additional information: © The Author(s). 2021 Open Access 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. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
Keywords: Science & Technology, Life Sciences & Biomedicine, Biology, Life Sciences & Biomedicine - Other Topics, Dictyostelium discoideum, Functional genomics, Genome-wide mutant resource, Parallel phenotypic analysis, REMI-seq, ENZYME-MEDIATED INTEGRATION, SOCIAL AMEBA, CELL MOTILITY, COOPERATION, GENES, RECOMBINATION, CYTOKINESIS, COMPLEXITY, RESISTANCE, MECHANISM
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment
URI: https://discovery.ucl.ac.uk/id/eprint/10133859
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