Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

CRISPR/dCas-based modulation of bacterial IS-transposition

ABSTRACT: In this work, a plasmid-based system is applied to inhibit the transposition of bacterial insertion sequences (IS). Using multiple guide RNAs, inactivated Cas9 was directed to simultaneously bind to the left end of IS1, IS5, IS3 and IS150 in Escherichia coli, in vivo. As a result, the transcription of IS1, and IS5 was successfully silenced, in certain cases by two orders of magnitude. The transposition rate of all four targeted elements nevertheless dropped to negligible levels, as verified at the cycA and bgl chromosomal loci. A GFP-expressing plasmid, known to be predominantly inactivated by insertion mutations also displayed a significant increase in stability. The transposition-silencing effect was easily transferable between various E. coli strains by plasmid transformation. Our portable system, or other plasmids constructed likewise can serve as useful tools to eliminate insertion mutagenesis or selectively study distinct transposable elements in numerous prokaryotic species.

ORGANISM(S): Escherichia coli str. K-12 substr. MG1655

PROVIDER: GSE110946 | GEO | 2019/02/21

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Targets of Ty3 transposition in Saccharomyces cerevisiae

Project description:The goal of these experiments was to define the targets of Ty3 transposition in Saccharomyces cerevisiae. Ty3 is a retroviruslike element that is found at the transcription initiation site of chromosomal tRNA genes. A Ty3 that can be induced by growth in galactose-containing medium and which was marked by an insertion of HIS3 downstream of the second open reading frame of the element (POL3) was induced to undergo transposition by plating cells onto galactose containing medium and replica-plating onto medium selective for cells that had undergone transposition. These cells were collected, DNA was extracted, and inverse PCR was performed using primers inside the Ty3 element in order to generate a library of insertion sites flanked by Illumina sequence-compatible primers.

2011-09-02 | E-GEOD-31820 | biostudies-arrayexpress

Selective recruitment of the AAA+ ATPase TnsC increases the fidelity of Type I-F CRISPR RNA-guided transposition

Project description:Bacterial transposons are pervasive mobile genetic elements that exploit distinct DNA binding proteins for their horizontal spread. For example, E. coli Tn7 homes to a specific attachment site using a TniQ family protein, whereas diverse Tn7-like transposons employ Type I or Type V CRISPR-Cas systems to insert downstream of target sites specified by a guide RNA. Despite this targeting pathway diversity, transposition invariably requires TnsB, a DDE superfamily transposase that catalyses DNA excision and insertion, and TnsC, a AAA+ ATPase that is thought to communicate between the transposase and targeting proteins. How TnsC mediates this communication and thereby regulates transposition fidelity has remained elusive. Here we apply chromatin immunoprecipitation sequencing (ChIP-seq) to monitor in vivo formation of the Vibrio cholerae RNA-guided transpososome, allowing us to unambiguously resolve distinct protein recruitment events prior to integration. DNA targeting by the TniQ-Cascade complex is surprisingly promiscuous, leading to binding at hundreds of genomic off-target sites, but only a subset of those sites are licensed for TnsC and TnsB recruitment, revealing a crucial proofreading checkpoint that controls transposition fidelity. To advance the mechanistic understanding of interactions responsible for transpososome assembly, we analysed V. cholerae TnsC by cryo-EM and found that TnsC forms ATP-dependent heptameric rings, which are likely to play a critical architectural role in positioning DNA substrates for downstream integration. Collectively, our results highlight the molecular specificity imparted by consecutive binding of distinct factors to genomic target sites during RNA-guided transposition, and provide a structural roadmap to guide future engineering efforts.

2021-10-31 | GSE183114 | GEO

Complete genome sequence of Escherichia coli C - old model organism with a new application in biofilm research

Project description:Escherichia coli strain C is the last of five E. coli strains (C, K12, B, W, Crooks) designated as safe for laboratory purposes whose genome has not been sequenced. We found that E. coli C forms more robust biofilms than the other four laboratory strains. Here we present the complete genomic sequence of this strain in which we utilized high resolution optical mapping to confirm a large inversion in comparison to other strains. DNA sequence comparison revealed the absence of several genes involved in biofilm formation, such as antigen 43, waaSBOJYZUL for LPS synthesis, and cpsB for curli synthesis. The main difference affecting biofilm formation is the presence of an IS3-like insertion sequence in front of the carbon storage regulator csrA gene. This insertion is located 86 bp upstream of the csrA start codon inside the -35 region of P4 promoter and blocks the transcription from the sigma32 and sigma70 promoters P1-P3 located further upstream. Analysis of gene expression profiles in planktonic and biofilm attached cells by the RNAseq method allows better understanding of this regulatory pathway in E. coli.

2020-01-01 | GSE125110 | GEO

Somatic piRNA pathway prevents transgenerational germline transposition [smallRNA-seq]

Project description:Transposable elements (TEs) are genomic parasite that threat genome integrity. One major strategy organisms evolved to balance TE activity in the germline is the Piwi-interacting RNAs (piRNAs) pathway. It prevents transposition by repressing TE at transcriptional and/or post-transcriptional level. However, evidence that TE derepression caused by piRNA pathway impairment is actually followed by bursts of transposition is still lacking. Here we present a genome-wide TE-analyses of the replicative TE life cycle (their expression, their translation to their transposition in the germline) after piRNA pathway impairment in the somatic follicle cells. We observed a high transposition-rate in the germline, leading to a 10-fold increase in genomic TE-load after 70 successive generations of piRNA pathway impairment. Moreover, we demonstrate that siRNAs co-regulate TE activity at post transcriptional level in follicle cells. These observations demonstrate that the small RNA-mediated TE repression in follicle cells contribute to genome homeostasis.

2018-08-09 | GSE112971 | GEO

Somatic piRNA pathway prevents transgenerational germline transposition [circularDNA-seq]

2018-08-09 | GSE112968 | GEO

Somatic piRNA pathway prevents transgenerational germline transposition [RNA-seq]

2018-08-09 | GSE112966 | GEO

Somatic piRNA pathway prevents transgenerational germline transposition [DNA-seq]

2018-08-09 | GSE112925 | GEO

The Rhox gene cluster suppresses germline LINE1 transposition

Project description:Transposable elements (TEs) are mobile sequences that engender widespread mutations and thus are a major hazard that must be silenced. The most abundant active class of TEs in mammalian genomes is long interspersed element class 1 (LINE1). Here, we report that LINE1 transposition is suppressed in the male germline by transcription factors encoded by a rapidly evolving X-linked homeobox gene cluster. LINE1 transposition is repressed by many members of this RHOX transcription factor family, including those with different patterns of expression during spermatogenesis. One family member—RHOX10—suppresses LINE1 transposition during fetal development in vivo when the germline would otherwise be susceptible to LINE1 activation because of epigenetic reprogramming. We provide evidence that RHOX10 suppresses LINE transposition by inducing Piwil2, which encodes a key component in the Piwi-interacting (pi) RNA pathway that protects against TEs. The ability of RHOX transcription factors to suppress LINE1 is conserved in humans, but is lost in RHOXF2 mutants from several infertile human patients, raising the possibility that loss of RHOXF2 causes human infertility by allowing uncontrolled LINE1 expression in the germline. Together, our results support a model in which the Rhox gene cluster is in an evolutionary arms race with TEs, resulting in expansion of the Rhox gene cluster to suppress TEs in different biological contexts.

2021-05-20 | GSE160600 | GEO

somatic-transposition-drosophila

Project description:Unravelling the features of somatic transposition in the Drosophila intestine

| PRJEB41757 | ENA

Zinc-Induced Transposition of Insertion Sequence Elements Contributes to Increased Adaptability of Cupriavidus metallidurans

Project description:Bacteria can respond to adverse environments by increasing their genomic variability and subsequently facilitating adaptive evolution. To demonstrate this, the contribution of Insertion Sequence (IS) elements to the genetic adaptation of Cupriavidus metallidurans AE126 to toxic zinc concentrations was determined. This derivative of type strain CH34, devoid of its main zinc resistance determinant, is still able to increase its zinc resistance level. Specifically, upon plating on toxic zinc medium, resistant variants arose in which a compromised cnrYX regulatory locus caused derepression of CnrH sigma factor activity and concomitant induction of the corresponding RND-driven cnrCBA efflux system. Late-occurring zinc resistant variants likely arose in response to the selective conditions, as they were enriched in cnrYX disruptions caused by specific IS elements whose transposase expression was found to be zinc-responsive. Interestingly, deletion of cnrH, and consequently CnrH-dependent adaptation potential, still enabled adaptation by transposition of IS elements (ISRme5 and IS1086) that provided outward-directed promoters driving cnrCBAT transcription. Finally, adaptation to zinc by IS reshuffling can also enhance the adaptation to subsequent environmental challenges. Thus, transposition of IS elements can be induced by stress conditions and play a multifaceted, pivotal role in the adaptation to these and subsequent stress conditions.

2016-12-31 | GSE74091 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data