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Gene expression "Epigenomic modifications predict active promoters and gene structure in Toxoplasma gondii"

ABSTRACT: total RNA was extracted after 24 hours of development of the RH strain in HFF cells. Keywords: gene expression

OTHER RELATED OMICS DATASETS IN: PRJNA104431PRJNA98019PRJNA104429

ORGANISM(S): Toxoplasma gondii Toxoplasma gondii RH Homo sapiens

PROVIDER: GSE5989 | GEO | 2007/05/22

SECONDARY ACCESSION(S): PRJNA104429

REPOSITORIES: GEO

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Epigenomic modifications predict active promoters and gene structure in Toxoplasma gondii.

Project description:Mechanisms of gene regulation are poorly understood in Apicomplexa, a phylum that encompasses deadly human pathogens like Plasmodium and Toxoplasma. Initial studies suggest that epigenetic phenomena, including histone modifications and chromatin remodeling, have a profound effect upon gene expression and expression of virulence traits. Using the model organism Toxoplasma gondii, we characterized the epigenetic organization and transcription patterns of a contiguous 1% of the T. gondii genome using custom oligonucleotide microarrays. We show that methylation and acetylation of histones H3 and H4 are landmarks of active promoters in T. gondii that allow us to deduce the position and directionality of gene promoters with >95% accuracy. These histone methylation and acetylation "activation" marks are strongly associated with gene expression. We also demonstrate that the pattern of histone H3 arginine methylation distinguishes certain promoters, illustrating the complexity of the histone modification machinery in Toxoplasma. By integrating epigenetic data, gene prediction analysis, and gene expression data from the tachyzoite stage, we illustrate feasibility of creating an epigenomic map of T. gondii tachyzoite gene expression. Further, we illustrate the utility of the epigenomic map to empirically and biologically annotate the genome and show that this approach enables identification of previously unknown genes. Thus, our epigenomics approach provides novel insights into regulation of gene expression in the Apicomplexa. In addition, with its compact genome, genetic tractability, and discrete life cycle stages, T. gondii provides an important new model to study the evolutionarily conserved components of the histone code.

| S-EPMC1891328 | biostudies-literature

Epigenomic modifications predict active promoters and gene structure in Toxoplasma gondii

Project description:This SuperSeries is composed of the SubSeries listed below.

2007-05-21 | GSE7262 | GEO

ChIP on chip "Epigenomic modifications predict active promoters and gene structure in Toxoplasma gondii"

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2007-05-22 | GSE5992 | GEO

Genome-wide analysis of gene expression response upon infection with Toxoplasma gondii

Project description:The in vitro effect of infection with different strains of Toxoplasma gondii was tested 24 hours after infection of Human Foreskin Fibroblasts (HFF) The strains tested include RH, VEG, and transgenic strains of RH overexpressing ROP38 or ROP21

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Gene expression "Epigenomic modifications predict active promoters and gene structure in Toxoplasma gondii"

Project description:Gene expression "Epigenomic modifications predict active promoters and gene structure in Toxoplasma gondii"

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Genome-wide analysis of gene expression response upon infection with Toxoplasma gondii

2010-07-31 | E-GEOD-22402 | biostudies-arrayexpress

Host gene expression response to Toxoplasma gondii infection is not different between RH?ku80 and RH?ku80?rop5 parasites.

Project description:The normally virulent type-I RH parasite is rendered avirulent when lacking ROP5. The avirulent phenotype is a consequence of interaction with the host innate immune system. We sought to understand if ROP5 alters host gene expression in order to escape host defenses. We saw no gene expression differences between host cells infected with wt (RH?ku80) or RH?ku80?rop5 parasites. We have included uninfected HFF samples that were harvested in parallel with the infected samples. Host gene expression in response to infection with Toxoplasma gondii. Two independent samples per sample type. Three sample types: HFF infected with RH?ku80, HFF infected with RH?ku80?rop5, and uninfected HFF.

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RNAseq of intracellular Toxoplasma gondii treated with Tartrolon E

Project description:Tartrolon E is a pan anti-apicomplexan compound derived from a symbiotic bacteria of shipworms. The mechanism of action of the compound is unknown, and attempts to select parasite mutants resistant to the compound has been unsuccessful. In this study, RNAseq was performed on human foreskin fibroblast cells (HFF) infected with Toxoplasma gondii RH strain and treated with Tartrolon E to identify genes targeted by the compound.

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Host gene expression response to Toxoplasma gondii infection is not different between RH∆ku80 and RH∆ku80∆rop5 parasites

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Toxoplasma gondii

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