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RNAseq analysis reveals the transcriptional programme of Clostridium difficile in a biologically relevant faecal–stress environment: implications for pathogenicity

ABSTRACT: RNAseq analysis reveals the transcriptional programme of Clostridium difficile in a biologically relevant faecal–stress environment: implications for pathogenicity

PROVIDER: PRJNA445971 | ENA |

REPOSITORIES: ENA

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RNAseq analysis reveals the transcriptional programme of Clostridium difficile in a biologically relevant faecal–stress environment: implications for pathogenicity

Project description:RNAseq and LC/MS metabolomics analysis of C. difficile strain 630 grown in BHIS media with 50% (vol/vol) faecal water added, compared with control BHIS containing only the additional PBS used for prep of Faecal water. Cells grown in biological triplicates to late log phase (T=6h) prior to harvest. Goal was to determine changes in gene expression caused by exposure to Faecal water, and changes in the metabolite profile of faecal water containing medium when incubated with actively growing C. difficile cells

2018-11-12 | GSE112422 | GEO

Increased sporulation underpins adaptation of Clostridium difficile strain 630 to a biologically-relevant faecal environment, with implications for pathogenicity.

Project description: Not available

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Dnmt2-dependent methylomes lack biologically relevant DNA methylation patterns [Drosophila melanogaster]

Project description:Dnmt2 is a widely conserved protein, which is closely related to eukaryotic DNA methyltransferases. However, Dnmt2 shows a robust tRNA methyltransferase activity and only limited activity towards DNA. Interestingly, a recent study has provided evidence for a biologically important function of Dnmt2-dependent DNA methylation in the blood fluke Schistosoma mansoni, which seemed to contradict the weak activity of the enzyme in other organisms. We now used whole-genome bisulfite sequencing to comprehensively analyze the methylome of adult worms and could not detect any evidence for biologically relevant DNA methylation patterns. We also characterized the methylome of Drosophila melanogaster embryos and did not find any evidence for DNA methylation. Unconverted cytosine residues were detectable only at very low levels and shared many attributes with bisulfite deamination artifacts. Our results thus strongly argue against a DNA methyltransferase activity of Dnmt2 and suggest that Dnmt2-dependent phenotypes are caused by reduced tRNA methylation.

2013-05-06 | GSE39996 | GEO

Dnmt2-dependent methylomes lack biologically relevant DNA methylation patterns [Schistosoma mansoni]

2013-05-06 | GSE39997 | GEO

Dnmt2-dependent methylomes lack biologically relevant DNA methylation patterns

Project description:Several organisms belonging to diverse animal groups have retained Dnmt2 as their only bona fide DNA methyltransferase gene. However, recent studies have shown that Dnmt2 functions as a tRNA methyltransferase, which prompted us to analyze the methylomes of Dnmt2-only organisms at single-base resolution. Using whole-genome bisulfite sequencing we show here that the genomes of Schistosoma mansoni and Drosophila melanogaster lack detectable DNA methylation patterns. Residual unconverted cytosine residues shared many attributes with bisulfite deamination artifacts and were observed at comparable levels in a Dnmt2-deficient fly strain. Furthermore, genetically modified mouse embryonic stem cells that had retained Dnmt2 as their only bona fide DNA methyltransferase gene, did not show any detectable DNA methylation patterns. Our results thus uncover fundamental differences among animal methylomes and suggest that Dnmt2-only organisms lack biologically relevant DNA methylation patterns.

2013-05-06 | GSE42170 | GEO

Dnmt2-dependent methylomes lack biologically relevant DNA methylation patterns [Schistosoma mansoni]

2013-05-06 | E-GEOD-39997 | biostudies-arrayexpress

Dnmt2-dependent methylomes lack biologically relevant DNA methylation patterns [Drosophila melanogaster]

2013-05-06 | E-GEOD-39996 | biostudies-arrayexpress

Integrated Genomics Approach to Identify Biologically Relevant Alterations in Fewer Samples.

Project description:Integrated Genomics Approach to Identify Biologically Relevant Alterations in Fewer Samples.

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Integrated Genomics Approach to Identify Biologically Relevant Alterations in Fewer Samples.

Project description:Integrated Genomics Approach to Identify Biologically Relevant Alterations in Fewer Samples.

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Identification of Biologically Relevant Enhancers in Human Erythroid Cells [ChIP-Seq]

Project description:Identification of cell-type specific enhancers is important for understanding the regulation of programs controlling cellular development and differentiation. Enhancers are typically marked by the co-transcriptional activator protein p300 or by groups of cell-expressed transcription factors. We hypothesized that a unique set of enhancers regulates gene expression in human erythroid cells, a highly specialized cell type evolved to provide adequate amounts of oxygen throughout the body. Using chromatin immunoprecipitation followed by massively parallel sequencing, genome-wide maps of candidate enhancers were constructed for p300 and four transcription factors, GATA1, NF-E2, KLF1, and SCL, using primary human erythroid cells. These data were combined with gene expression analyses and candidate enhancers identified. Consistent with their predicted function as candidate enhancers, there was statistically significant enrichment of p300 and combinations of co-localizing erythroid transcription factors within 1-50 kb of the TSS of genes highly expressed in erythroid cells. Candidate enhancers were also enriched near genes with known erythroid cell function or erythroid cell phenotypes. Candidate enhancers exhibited only moderate conservation with mouse and minimal conservation with nonplacental vertebrates. Candidate enhancers were mapped to a data set of erythroid-associated, biologically relevant, SNPs from the GWAS catalog of the NHGRI. Fourteen candidate enhancers, representing 10 genetic loci, mapped to sites associated with biologically relevant erythroid traits. Fragments from these loci directed statistically significant expression in reporter gene assays. Identification of enhancers in human erythroid cells will allow a better understanding of erythroid cell development, differentiation, structure, and function, and provide insights into inherited and acquired hematologic disease.

2013-01-28 | GSE43625 | GEO

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