Genome-Wide Insertional Mutagenesis of Arabidopsis thaliana

@article{Alonso2003GenomeWideIM,
  title={Genome-Wide Insertional Mutagenesis of Arabidopsis thaliana},
  author={Jos{\'e} M. Alonso and Anna N. Stepanova and Thomas J Leisse and Christopher J Kim and Huaming Chen and Paul Shinn and Denise K Stevenson and Justin Zimmerman and Pascual Barajas and Rosa Cheuk and Carmelita Gadrinab and Collen Heller and Albert Jeske and Eric Koesema and Cristina C Meyers and Holly Parker and Lance Prednis and Yasser Ansari and Nathan Choy and Hashim Deen and Michael Geralt and Nisha Hazari and Emily Hom and Meagan Karnes and Celene Mulholland and Ral Ndubaku and Ian Schmidt and Plinio Guzm{\'a}n and Laura Aguilar-Henonin and Markus Schmid and Detlef Weigel and David E Carter and Trudy Marchand and Eddy P. Risseeuw and Debra Brogden and Albana Zeko and William Crosby and Charles C. Berry and Joseph R. Ecker},
  journal={Science},
  year={2003},
  volume={301},
  pages={653 - 657}
}
Over 225,000 independent Agrobacterium transferred DNA (T-DNA) insertion events in the genome of the reference plant Arabidopsis thaliana have been created that represent near saturation of the gene space. [] Key Result The precise locations were determined for more than 88,000 T-DNA insertions, which resulted in the identification of mutations in more than 21,700 of the approximately 29,454 predicted Arabidopsis genes.
Insertional mutagenesis with Tos17 for functional analysis of rice genes
Genomic sequencing of rice followed by curated genome annotation predicted that the rice genome carries ~32,000 genes. To reveal functions of all the predicted genes is the next important challenge.
A non-canonical transferred DNA insertion at the BRI1 locus in Arabidopsis thaliana.
TLDR
This work reports on a locus showing a complex mutation associated with T-DNA insertion at the BRI1 gene in Arabidopsis thaliana, revealing non-canonical T- DNA insertion, implicating horizontal gene transfer and cautioning the use ofT-DNA as mutagen in transgenic research.
Forward genetic screening of insertional mutants.
TLDR
Protocols for the identification and confirmation of mutations by forward genetics, the isolation of insertion/genome junctions, and the stabilization of transposon-induced mutations are provided, together with an overview of available insertional mutant collections and of their characteristics.
Linking genotype to phenotype using the Arabidopsis unimutant collection.
TLDR
The large collections of Arabidopsis thaliana sequence-indexed T-DNA insertion mutants are among the most important resources to emerge from the sequencing of the genome and are poised to have a larger impact on the understanding of gene function.
Large scale genomic rearrangements in selected Arabidopsis thaliana T-DNA lines are caused by T-DNA insertion mutagenesis
TLDR
Long read sequencing was demonstrated to be an effective way to resolve complex T-DNA insertions and chromosome fusions and local assembly of selected reads was shown to be a computationally effective method to resolve the structure of T- DNA insertion loci.
Gene Site-Specific Insertion in Plants
TLDR
The recent development of engineered nucleases represents an important step forward towards allowing the insertion of a transgene at any given locus in the genome.
Identification of components in disease-resistance signaling in Arabidopsis by map-based cloning.
TLDR
Detailed protocols for each step on general scheme of map-based cloning, from mutagenesis to genetic analysis, from rough mapping to fine mapping, and at the end to cloning the gene are described.
The complex architecture of plant transgene insertions
TLDR
An unprecedented nucleotide-level definition of T-DNA insertions enabled the mapping of epigenome data and the utility of state-of-the-art long-range sequencing technologies to rapidly identify unanticipated genomic changes.
Reverse Genetic Approaches for Functional Genomics of Rice
TLDR
DNA pools of the T-DNA tagged lines and Tos17 lines have been prepared for PCR screening of insertional mutants in a given gene and Tag end sequences (TES) of the inserts have also been produced.
...
...

References

SHOWING 1-10 OF 24 REFERENCES
Insertional mutagenesis of genes required for seed development in Arabidopsis thaliana.
TLDR
The 350 tagged embryo-defective mutants identified to date represent a significant advance toward saturation mutagenesis of EMB genes in Arabidopsis and are consistent with a relatively small number of essential (EMB) genes with nonredundant functions during seed development.
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
TLDR
This is the first complete genome sequence of a plant and provides the foundations for more comprehensive comparison of conserved processes in all eukaryotes, identifying a wide range of plant-specific gene functions and establishing rapid systematic ways to identify genes for crop improvement.
Large-scale analysis of the yeast genome by transposon tagging and gene disruption
TLDR
This work has developed a transposon-tagging strategy for the genome-wide analysis of disruption phenotypes, gene expression and protein localization, and has applied this method to the large-scale analysis of gene function in the budding yeast Saccharomyces cerevisiae.
Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis.
TLDR
A total of 6925 Saccharomyces cerevisiae strains were constructed, by a high-throughput strategy, each with a precise deletion of one of 2026 ORFs (more than one-third of the ORFs in the genome), finding that 17 percent were essential for viability in rich medium.
Systematic functional analysis of the Caenorhabditis elegans genome using RNAi
TLDR
It is found that genes of similar functions are clustered in distinct, multi-megabase regions of individual chromosomes; genes in these regions tend to share transcriptional profiles.
The maternal chromosome set is the target of the T-DNA in the in planta transformation of Arabidopsis thaliana.
TLDR
Results point to the chromosome set of the female gametophyte as the main target for the T-DNA in planta transformation methods used to transform Arabidopsis thaliana by Agrobacterium tumefaciens.
Functional profiling of the Saccharomyces cerevisiae genome
TLDR
It is shown that previously known and new genes are necessary for optimal growth under six well-studied conditions: high salt, sorbitol, galactose, pH 8, minimal medium and nystatin treatment, and less than 7% of genes that exhibit a significant increase in messenger RNA expression are also required for optimal Growth in four of the tested conditions.
From host recognition to T-DNA integration: the function of bacterial and plant genes in the Agrobacterium-plant cell interaction.
TLDR
This work discusses the molecular interactions among these bacterial and plant factors and their role in the A. tumefaciens-plant cell interaction and discusses the widest host ranges known among plant pathogens.
...
...