Cargando…

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

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...

Descripción completa

Detalles Bibliográficos
Autores principales: 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.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8386026/
https://www.ncbi.nlm.nih.gov/pubmed/34429112
http://dx.doi.org/10.1186/s12915-021-01108-y
_version_ 1783742186083319808
author 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.
author_facet 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.
author_sort Gruenheit, Nicole
collection PubMed
description 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12915-021-01108-y.
format Online
Article
Text
id pubmed-8386026
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-83860262021-08-26 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. Thompson, Christopher R. L. BMC Biol Methodology Article 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12915-021-01108-y. BioMed Central 2021-08-24 /pmc/articles/PMC8386026/ /pubmed/34429112 http://dx.doi.org/10.1186/s12915-021-01108-y Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis 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/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://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.
spellingShingle Methodology Article
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.
Mutant resources for functional genomics in Dictyostelium discoideum using REMI-seq technology
title Mutant resources for functional genomics in Dictyostelium discoideum using REMI-seq technology
title_full Mutant resources for functional genomics in Dictyostelium discoideum using REMI-seq technology
title_fullStr Mutant resources for functional genomics in Dictyostelium discoideum using REMI-seq technology
title_full_unstemmed Mutant resources for functional genomics in Dictyostelium discoideum using REMI-seq technology
title_short Mutant resources for functional genomics in Dictyostelium discoideum using REMI-seq technology
title_sort mutant resources for functional genomics in dictyostelium discoideum using remi-seq technology
topic Methodology Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8386026/
https://www.ncbi.nlm.nih.gov/pubmed/34429112
http://dx.doi.org/10.1186/s12915-021-01108-y
work_keys_str_mv AT gruenheitnicole mutantresourcesforfunctionalgenomicsindictyosteliumdiscoideumusingremiseqtechnology
AT baldwinamy mutantresourcesforfunctionalgenomicsindictyosteliumdiscoideumusingremiseqtechnology
AT stewartbalint mutantresourcesforfunctionalgenomicsindictyosteliumdiscoideumusingremiseqtechnology
AT jaquessarah mutantresourcesforfunctionalgenomicsindictyosteliumdiscoideumusingremiseqtechnology
AT kellerthomas mutantresourcesforfunctionalgenomicsindictyosteliumdiscoideumusingremiseqtechnology
AT parkinsonkatie mutantresourcesforfunctionalgenomicsindictyosteliumdiscoideumusingremiseqtechnology
AT salvidgewilliam mutantresourcesforfunctionalgenomicsindictyosteliumdiscoideumusingremiseqtechnology
AT bainesrobert mutantresourcesforfunctionalgenomicsindictyosteliumdiscoideumusingremiseqtechnology
AT brimsonchris mutantresourcesforfunctionalgenomicsindictyosteliumdiscoideumusingremiseqtechnology
AT wolfjasonb mutantresourcesforfunctionalgenomicsindictyosteliumdiscoideumusingremiseqtechnology
AT chisholmrex mutantresourcesforfunctionalgenomicsindictyosteliumdiscoideumusingremiseqtechnology
AT harwoodadrianj mutantresourcesforfunctionalgenomicsindictyosteliumdiscoideumusingremiseqtechnology
AT thompsonchristopherrl mutantresourcesforfunctionalgenomicsindictyosteliumdiscoideumusingremiseqtechnology