Mutant resources for functional genomics in Dictyostelium discoideum using REMI-seq technology.
Mutant resources for functional genomics in Dictyostelium discoideum using REMI-seq technology.
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DOI：
10.1186/s12915-021-01108-y
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发表时间：
2021-08-24
期刊：
影响因子：
5.4
通讯作者：
Thompson CRL
中科院分区：
文献类型：
--
作者：
Gruenheit N;Baldwin A;Stewart B;Jaques S;Keller T;Parkinson K;Salvidge W;Baines R;Brimson C;Wolf JB;Chisholm R;Harwood AJ;Thompson CRL
基因组测序可以相对容易地进行，但确定基因功能仍然是一个重大挑战。基因上易于处理的模型系统对于迎接这一挑战至关重要。一个强大的模型是社会阿米巴Dictyostelialdiscoideum，一种真核微生物，广泛用于研究细胞、发育和进化生物学的各种问题。我们描述了REMI-SEQ，它是TN-SEQ的一种改进型，它允许在限制酶介导的整合后高通量、整体和定量地鉴定插入耐药标记的基因组位置。我们使用REMI-SEQ开发工具，极大地提高了将序列、转录组或蛋白质组变异与盘状芽孢杆菌表型联系起来的效率。这些资源包括(1)接近全基因组范围的个体突变资源和(2)确定的“条形码”突变体库，以便进行大规模的并行表型分析。这些资源可以通过REMI-SEQ网站免费获得和轻松获取，该网站还为数据分析提供了全面的指导和渠道。我们证明，整合这些资源可以快速识别细胞迁移、吞噬和巨噬细胞吞噬的新调节因子。我们提出了使用REMI-SEQ生成的方法和资源，用于在关键模型系统中进行高通量基因功能分析。网上版载有补充材料，可在10.1186/s12915-021-01108-y查阅。
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. The online version contains supplementary material available at 10.1186/s12915-021-01108-y.
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影响因子：
11.8
作者：
Gruenheit N;Parkinson K;Brimson CA;Kuwana S;Johnson EJ;Nagayama K;Llewellyn J;Salvidge WM;Stewart B;Keller T;van Zon W;Cotter SL;Thompson CRL
通讯作者：
Thompson CRL
DOI：
10.1006/bbrc.1994.2880
发表时间：
1994-12-30
影响因子：
3.1
作者：
ADACHI, H;HASEBE, T;SUTOH, K
通讯作者：
SUTOH, K
影响因子：
64.8
作者：
Foster, KR;Shaulsky, G;Thompson, CRL
通讯作者：
Thompson, CRL
影响因子：
7.7
作者：
Bloomfield G;Traynor D;Sander SP;Veltman DM;Pachebat JA;Kay RR
通讯作者：
Kay RR
影响因子：
2.6
作者：
Keim, M;Williams, RSB;Harwood, AJ
通讯作者：
Harwood, AJ