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CRISPR RNA-dependent binding and cleavage of endogenous RNAs by the Campylobacter jejuni Cas9

ABSTRACT: CRISPR RNA-dependent binding and cleavage of endogenous RNAs by the Campylobacter jejuni Cas9

PROVIDER: PRJNA418174 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6286160.fastq.gz	Fastqsanger.gz
	SRR6286161.fastq.gz	Fastqsanger.gz
	SRR6286162.fastq.gz	Fastqsanger.gz
	SRR6286163.fastq.gz	Fastqsanger.gz
	SRR6286155.fastq.gz	Fastqsanger.gz

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CRISPR RNA-dependent binding and cleavage of endogenous RNAs by the Campylobacter jejuni Cas9

Project description:This study investigates the RNA targets and cleavage sites of endogenous Cas9 in the food-borne pathogen Campylobacter jejuni. Direct RNA binding targets of Cas9 in C. jejuni strain NCTC11168 were determined using RIP-seq. The Cleavage sites were then predicted in the RNA targets by comparing total transcriptome data from WT and deletion (cas9, crRNA3, tracrRNA, CRISPR-tracrRNA) strains. PAMs for the CjeCas9 were enriched using the PAM-SCANR platform, which operates through a GFP reporter gene. Upon GFP (and thus functional PAM) enrichment, fluorescing cells were isolated using FACS and prepared plasmid DNA was amplified and prepared for sequencing.

2018-03-01 | GSE106849 | GEO

Campylobacter jejuni Cas9 is necessary for efficient infection of Caco-2 cells and cell stress induction

Project description:Objective: We previously showed that Campylobacter jejuni Cas9 was necessary for full virulence and efficient induction of human cell stress followed by cell death, but no virulence mechanism could be unravelled then. Therefore, we carried out global genome-wide transcriptomics, using RNA samples extracted from cells infected by a wild-type C. jejuni strain and the corresponding cas9 deletion strain. Methods: Caco-2 epithelial cells were infected with C. jejuni wild-type or cas9 deletion strains and RNA was extracted at 5 timepoints post-infection. Results: Wild-type C. jejuni induced cellular stress, DNA damage and cell death pathways in Caco-2 cells continuously from 30 min up to 4 hours after infection, eventually followed by visual cell death induction after 24 hours; the corresponding cas9 deletion strain did also induce cell stress pathways within the first two hours of infection but at later timepoints, stress pathway induction had dropped and after 4 hours of infection, expression of the corresponding stress genes had normalised to near-t=0 (uninfected) expression values; the cas9 deletion strain did not lead to visual cell death induction after 24 hours. Conclusions: Campylobacter jejuni Cas9 is necessary for full virulence of C. jejuni and is involved in the efficient induction of cellular stress pathways and eventually, cell death.

2018-09-30 | GSE89661 | GEO

CRISPR RNA-Dependent Binding and Cleavage of Endogenous RNAs by the Campylobacter jejuni Cas9.

Project description:Cas9 nucleases naturally utilize CRISPR RNAs (crRNAs) to silence foreign double-stranded DNA. While recent work has shown that some Cas9 nucleases can also target RNA, RNA recognition has required nuclease modifications or accessory factors. Here, we show that the Campylobacter jejuni Cas9 (CjCas9) can bind and cleave complementary endogenous mRNAs in a crRNA-dependent manner. Approximately 100 transcripts co-immunoprecipitated with CjCas9 and generally can be subdivided through their base-pairing potential to the four crRNAs. A subset of these RNAs was cleaved around or within the predicted binding site. Mutational analyses revealed that RNA binding was crRNA and tracrRNA dependent and that target RNA cleavage required the CjCas9 HNH domain. We further observed that RNA cleavage was PAM independent, improved with greater complementarity between the crRNA and the RNA target, and was programmable in vitro. These findings suggest that C. jejuni Cas9 is a promiscuous nuclease that can coordinately target both DNA and RNA.

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Campylobacter jejuni butyrate resopnse

Project description:Growth of Campylobacter jejuni in butyrate, including deletions of a TCS involved in sensing this response

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Project description:Campylobacter jejuni is the most prevalent cause of foodborne bacterial enteritis worldwide. This study aims at the characterisation of pathomechanisms and signalling in Campylobacter-induced diarrhoea in the human mucosa. During routine colonoscopy, biopsies were taken from patients suffering from campylobacteriosis. RNA-seq of colon biopsies was performed to describe Campylobacter jejuni-mediated effects. Mucosal mRNA profiles of acutely infected patients and healthy controls were generated by deep sequencing using Illumina HiSeq 2500. This data provide the basis for subsequent upstream regulator analysis.

2017-10-10 | GSE88710 | GEO

Campylobacter jejuni gene expression in germ-free mice

Project description:Expression arrays comparing Campylobacter jejuni NCTC11168 during growth in the cecum of germ-free C57 BL/6 IL-10 knockout mice to C. jejuni NCTC11168 during growth in Bolton broth.

2011-04-14 | GSE28578 | GEO

Transcriptional profile in macrolide susceptible and resistant Campylobacter jejuni

Project description:Campylobacter jejuni is a major zoonotic pathogen transmitted to humans via the food chain. C. jejuni is prevalent in chickens, a natural reservoir for this pathogenic organism. Due to the importance of macrolide antibiotics in clinical therapy of human campylobacteriosis, development of macrolide resistance in Campylobacter has become a concern for public health.To facilitate understanding the molecular basis associated with the fitness difference between Erys and Eryr Campylobacter, we compared the transcriptomes between ATCC 700819 and its isogenic Eryr transformant T.L.101 using DNA microarray.

2011-11-02 | GSE33330 | GEO

Transcriptomic analysis of C. jejuni HPC5 with C. jejuni HPC5 R14, R20, R14A, R14B, R20A, R20B and R20C.

Project description:C. jejuni HPC5 is a Campylobacter strain isolated from chickens. Following bacteriophage CP34 treatment on chickens colonised by C. jejuni HPC5, a series of CP34 insensitive strains like C. jejuni HPC5 R14 and C. jejuni HPC5 R20 were obtained which compromised their ability to colonise chickens. Reintroduction of C. jejuni HPC5 R14 and R20 in to chickens led to reversion of these strains and the MRPs of the revertant strains fell in to different classes termed C. jejuni HPC5 R14A, R14B, R20A, R20B and R20C and these strained were tested positive for colonisation proficient and bacteriophage sensitive.

2015-09-15 | GSE17799 | GEO

Defining stationary phase transcriptomes of Campylobacter jejuni cell morphotypes

Project description:Filamentation, the transition from rod to filamentous cell morphology, has been identified as a response to stressful conditions in many bacterial species. Campylobacter jejuni exhibits filamentation upon entry to stationary phase. This study examines the cell mophotype specific transciptomes (RNAseq) of C. jejuni.

2018-07-07 | GSE116729 | GEO

Gene Expression Changes in Campylobacter jejuni triggered by exposure to Novobiocin

Project description:In order to investigate the gene experssion changes in Campylobacter jejuni triggered by exposure to Novobiocin.

2009-12-28 | GSE18415 | GEO