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

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...

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Bibliographic Details
Published in:	BMC biology Vol. 19; no. 1; p. 172
Main Authors:	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, Thompson, Christopher R L
Format:	Journal Article
Language:	English
Published:	England BioMed Central Ltd 24-08-2021 BioMed Central BMC
Subjects:	Amoeba Analysis Biological effects Cell migration Data analysis Dictyostelium Dictyostelium - genetics Dictyostelium discoideum Drug resistance Enzymes Function analysis Functional genomics Genes Genetic aspects Genome Genome-wide mutant resource Genomes Genomics Insertion Methodology Methods Mutagenesis Mutants Mutation Parallel phenotypic analysis Phagocytosis Phenotypes Plasmids Proteomes REMI-seq Restriction enzymes, DNA Technology Transcriptomes Websites United Kingdom Dictyostelium discoideum Functional genomics Genome-wide mutant resource Parallel phenotypic analysis REMI-seq
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Summary:	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. 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. We present methods and resources, generated using REMI-seq, for high throughput gene function analysis in a key model system.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	1741-7007 1741-7007
DOI:	10.1186/s12915-021-01108-y