Advances in bacterial transcriptome and transposon insertion-site profiling using second-generation sequencing

Febrer, Melanie; McLay, Kirsten; Cáccamo, Mario; Twomey, Kate B.; Ryan, Robert P.

doi:10.1016/j.tibtech.2011.06.004

Cited by 25 publications

(12 citation statements)

References 65 publications

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“…Compared with DNA microarray analysis, whole-transcriptome sequencing has a more extensive detection range with no background and allows the absolute quantification of gene expression (55). Moreover, data obtained from different RNA-seq experiments can also be easily normalized and compared (56). Our analysis revealed several metabolic and regulatory pathways with altered expression in the rsiR mutant, which suggested that rsiR may possess a global regulatory function across many physiological pathways.…”

Section: Discussionmentioning

confidence: 92%

Lactobacillus reuteri-Specific Immunoregulatory Gene rsiR Modulates Histamine Production and Immunomodulation by Lactobacillus reuteri

et al. 2013

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Section: Discussionmentioning

confidence: 92%

Lactobacillus reuteri-Specific Immunoregulatory Gene rsiR Modulates Histamine Production and Immunomodulation by Lactobacillus reuteri

et al. 2013

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“…Most Bioconductor components are organized as R packages. These Bioconductor packages and other software for RNA-seq data analysis have been well reviewed elsewhere (Chen et al, 2011;Febrer et al, 2011;Oshlack et al, 2010). Nowadays, researchers can routinely combine these tools to form the best analysis pipeline per their research interests.…”

Section: Qian Et Almentioning

confidence: 99%

RNA-Seq Technology and Its Application in Fish Transcriptomics

Qian

Ba²,

Zhuang³

et al. 2014

OMICS: A Journal of Integrative Biology

290

147

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High-throughput sequencing technologies, also known as next-generation sequencing (NGS) technologies, have revolutionized the way that genomic research is advancing. In addition to the static genome, these state-of-art technologies have been recently exploited to analyze the dynamic transcriptome, and the resulting technology is termed RNA sequencing (RNA-seq). RNA-seq is free from many limitations of other transcriptomic approaches, such as microarray and tag-based sequencing method. Although RNA-seq has only been available for a short time, studies using this method have completely changed our perspective of the breadth and depth of eukaryotic transcriptomes. In terms of the transcriptomics of teleost fishes, both model and non-model species have benefited from the RNA-seq approach and have undergone tremendous advances in the past several years. RNA-seq has helped not only in mapping and annotating fish transcriptome but also in our understanding of many biological processes in fish, such as development, adaptive evolution, host immune response, and stress response. In this review, we first provide an overview of each step of RNA-seq from library construction to the bioinformatic analysis of the data. We then summarize and discuss the recent biological insights obtained from the RNA-seq studies in a variety of fish species.

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“…The second challenge to implementing such a system is to identify Tnp insertion sites that become underrepresented when counterselected with inhibitor. High density oligonucleotide tiled microarrays 45 - 47 and more recently next generation sequencing technologies 48 , 49 are proving to be highly efficient in mapping Tnp junction sites among large transposant pools with base pair resolution. When disrupted by Tnp insertion, genes that confer sensitivity to aminoglycosides in Pseudomonas aeruginosa 50 and to bile acid in Salmonella typhymurium 51 have been identified using this approach.…”

Section: Textmentioning

confidence: 99%

Harnessing the power of transposon mutagenesis for antibacterial target identification and evaluation

Meredith

Wang

Beaulieu

et al. 2012

Mobile Genetic Elements

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Determining the mechanism of action of bacterial growth inhibitors can be a formidable challenge in the progression of small molecules into antibacterial therapies. To help address this bottleneck, we have developed a robust transposon mutagenesis system using a suite of outward facing promoters in order to generate a comprehensive range of expression genotypes in Staphylococcus aureus from which to select defined compound-resistant transposon insertion mutants. Resistance stemming from either gene or operon over/under-expression, in addition to deletion, provides insight into multiple factors that contribute to a compound’s observed activity, including means of cell envelope penetration and susceptibility to efflux. By profiling the entire resistome, the suitability of an antibacterial target itself is also evaluated, sometimes with unanticipated results. We herein show that for the staphylococcal signal peptidase (SpsB) inhibitors, modulating expression of lipoteichoic acid synthase (LtaS) confers up to a 100-fold increase in the minimal inhibitory concentration. As similarly efficient transposition systems are or will become established in other bacteria and cell types, we discuss the utility, limitations and future promise of Tnp mutagenesis for determining both a compound’s mechanism of action and in the evaluation of novel targets.

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Advances in bacterial transcriptome and transposon insertion-site profiling using second-generation sequencing

Cited by 25 publications

References 65 publications

Lactobacillus reuteri-Specific Immunoregulatory Gene rsiR Modulates Histamine Production and Immunomodulation by Lactobacillus reuteri

Lactobacillus reuteri-Specific Immunoregulatory Gene rsiR Modulates Histamine Production and Immunomodulation by Lactobacillus reuteri

RNA-Seq Technology and Its Application in Fish Transcriptomics

Harnessing the power of transposon mutagenesis for antibacterial target identification and evaluation

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