Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

CRISPR Cas3 Plasmid degradation assays

ABSTRACT: CRISPR Cas3 Plasmid degradation assays

PROVIDER: PRJEB13999 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Sequence Requirements for Cascade Function in a Type I-E CRISPR System: Plasmid Loss

Project description:We generated a collection of 13 plasmids, with each plasmid containing a variant of a CRISPR protospacer targeted by spacer 8 of the E. coli CRISPR-I array. We transformed the plasmids as a pool into delta cas3 E. coli cells expressing all other cas genes constitutively. We then transformed these cells with either an empty vector or a plasmid expressing the Cas3 nuclease. DNA surrounding the protospacers was PCR-amplified and sequenced.

2017-08-24 | E-MTAB-5969 | biostudies-arrayexpress

Sequence Requirements for Cascade Function in a Type I-E CRISPR System: ChIP Library-seq

Project description:We generated a collection of 13 plasmids, with each plasmid containing a variant of a CRISPR protospacer targeted by spacer 8 of the E. coli CRISPR-I array. We transformed the plasmids as a pool into delta cas3 E. coli cells expressing all other cas genes constitutively, with FLAG-tagged casA. We then used ChIP to enrich for CasA-bound protospacers. DNA surrounding the protospacers was PCR-amplified from input (pre-immunocrecipitation) and ChIP (post-immunoprecipitation) samples and sequenced.

2017-08-24 | E-MTAB-5972 | biostudies-arrayexpress

Nus factors prevent premature transcription termination of bacterial CRISPR arrays

Project description:We used ChIP-seq to map binding of the CRISPR surveillance complex, Cascade, in a Salmonella enterica serovar Typhimurium strain lacking the gene encoding the endonuclease Cas3. We performed ChIP-seq in strains with wild-type and mutant sequences upstream of the two CRISPR arrays, and in strains with wild-type and mutant nusE genes to determine the impact of Nus factor antitermination on CRISPR array function.

2018-10-13 | E-MTAB-7242 | biostudies-arrayexpress

Interrogating two extensively self-targeting Type I CRISPR-Cas systems in Xanthomonas albilineans reveals distinct anti-CRISPR proteins that block DNA degradation

Project description:CRISPR-Cas systems store fragments of invader DNA as spacers to recognize and clear those same invaders in the future. Spacers can also be acquired from the host’s genomic DNA, leading to lethal self-targeting. While self-targeting can be circumvented through different mechanisms, natural examples remain poorly explored. Here, we investigate extensive self-targeting by two CRISPR-Cas systems encoding an astonishing 24 self-targeting spacers in the plant pathogen Xanthomonas albilineans. We show, based on transcriptomics analyses, that the native I-C and I-F1 systems are actively expressed and that CRISPR RNAs are properly processed. When expressed in Escherichia coli, each Cascade complex binds its PAM-flanked DNA target to block transcription, while the addition of Cas3 paired with genome targeting induces cell killing. While exploring how X. albilineans survives self-targeting, we predicted putative anti-CRISPR proteins (Acrs) encoded within the bacterium’s genome. Screening of identified candidates with cell-free transcription-translation systems and in E. coli revealed two Acrs, which we named AcrIC11 and AcrIF12Xal, that inhibit Cas3 but not Cascade of the respective system. These findings reveal how a bacterium tolerates extensive self-targeting through two CRISPR-Cas systems and expand the suite of Cas3-inhibiting Acrs.

2023-10-28 | GSE229478 | GEO

Sequence Requirements for Cascade Function in a Type I-E CRISPR System: ChIP-Seq

Project description:We used ChIP-seq to map binding of the CRISPR surveillance complex, Cascade, in an E. coli strain lacking the endonuclease Cas3. These data enabled us to determine the precise sequence requirements for Cascade binding.

2017-08-24 | E-MTAB-5970 | biostudies-arrayexpress

Sequence Requirements for Cascade Function in a Type I-E CRISPR System: RNA-Seq

Project description:We measured global RNA levels using RNA-seq in cas3+ E. coli cells with intact CRISPR arrays or cells with the CRISPR-I array deleted to determine if off-target events driven by endogenous spacers affect RNA levels.

2018-02-10 | E-MTAB-6446 | biostudies-arrayexpress

Sequence Requirements for Cascade Function in a Type I-E CRISPR System: RNA-Seq

Project description:We measured global RNA levels using RNA-seq in cas3 E. coli cells with intact CRISPR arrays or cells with the CRISPR-I array deleted to determine if off-target events driven by endogenous spacers affect local gene expression.

2017-08-24 | E-MTAB-5971 | biostudies-arrayexpress

CRISPR-Cas protein Cas3 controls virulence in the oral pathogen Porphyromonas gingivalis.

Project description:Our results show that compared to wild type, a deletion mutant of the cas3 gene, an essential nuclease part of the class 1 type I CRISPR-Cas system, increases the virulence of P gingivalis.

2020-09-16 | GSE154569 | GEO

Protospacer integration into plasmid DNA by Cas1–Cas2

Project description:We report the integration site specificity of Cas1–Cas2 into target plasmid DNA encoding a CRISPR locus. The goal of this study is to determine the effect of IHF on target site selection of Cas1–Cas2.

2016-05-27 | GSE79992 | GEO

Characterization of primed adaptation in the Escherichia coli type I-E CRISPR-Cas system

Project description:We determined the set of newly acquired CRISPR spacers during naive and primed adaptation in E. coli. We compared primed adaptation when targeting different plasmid and chromosomal sites. These data provide insight into the sequence features that impact the efficiency of primed adaptation in E. coli.

2020-02-06 | E-MTAB-8700 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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