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

Gruenheit, Nicole, Baldwin, Amy, Stewart, Balint, Jaques, Sarah, Keller, Thomas, Parkinson, Katie, Salvidge, William, Baines, Robert, Brimson, Chris, Wolf, Jason B., Chisholm, Rex, Harwood, Adrian J. and Thompson, Christopher R. L. 2021. Mutant resources for functional genomics in Dictyostelium discoideum using REMI-seq technology. BMC Biology 19 (1) , 172. 10.1186/s12915-021-01108-y

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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.

Item Type: Article
Date Type: Publication
Status: Published
Schools: Biosciences
Additional Information: 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.
Publisher: BioMed Central
ISSN: 1741-7007
Date of First Compliant Deposit: 2 September 2021
Date of Acceptance: 22 July 2021
Last Modified: 10 Nov 2021 02:23
URI: http://orca.cardiff.ac.uk/id/eprint/143829

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