Transposon Insertion Sequencing, a Global Measure of Gene Function
- 23 November 2020
- journal article
- review article
- Published by Annual Reviews in Annual Review of Genetics
- Vol. 54 (1), 337-365
- https://doi.org/10.1146/annurev-genet-112618-043838
Abstract
The goal of genomics and systems biology is to understand how complex systems of factors assemble into pathways and structures that combine to form living organisms. Great advances in understanding biological processes result from determining the function of individual genes, a process that has classically relied on characterizing single mutations. Advances in DNA sequencing has made available the complete set of genetic instructions for an astonishing and growing number of species. To understand the function of this ever-increasing number of genes, a high-throughput method was developed that in a single experiment can measure the function of genes across the genome of an organism. This occurred approximately 10 years ago, when high-throughput DNA sequencing was combined with advances in transposon-mediated mutagenesis in a method termed transposon insertion sequencing (TIS). In the subsequent years, TIS succeeded in addressing fundamental questions regarding the genes of bacteria, many of which have been shown to play central roles in bacterial infections that result in major human diseases. The field of TIS has matured and resulted in studies of hundreds of species that include significant innovations with a number of transposons. Here, we summarize a number of TIS experiments to provide an understanding of the method and explanation of approaches that are instructive when designing a study. Importantly, we emphasize critical aspects of a TIS experiment and highlight the extension and applicability of TIS into nonbacterial species such as yeast.Keywords
This publication has 109 references indexed in Scilit:
- Genome-Wide Detection of Fitness Genes in Uropathogenic Escherichia coli during Systemic InfectionPLoS Pathogens, 2013
- Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental dataBioinformatics, 2011
- Global gene disruption in human cells to assign genes to phenotypes by deep sequencingNature Biotechnology, 2011
- Integrative genomics viewerNature Biotechnology, 2011
- The essential genome of a bacteriumMolecular Systems Biology, 2011
- Aligning Short Sequencing Reads with BowtieCurrent Protocols in Bioinformatics, 2010
- edgeR: a Bioconductor package for differential expression analysis of digital gene expression dataBioinformatics, 2009
- Tracking insertion mutants within libraries by deep sequencing and a genome-wide screen for Haemophilus genes required in the lungProceedings of the National Academy of Sciences of the United States of America, 2009
- Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganismsNature Methods, 2009
- Identifying Genetic Determinants Needed to Establish a Human Gut Symbiont in Its HabitatCell Host & Microbe, 2009