Ontology highlight
ABSTRACT:
PROVIDER: PRJNA98019 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Gene expression "Epigenomic modifications predict active promoters and gene structure in Toxoplasma gondii"
| PRJNA104429 | ENA
Project description:ChIP on chip "Epigenomic modifications predict active promoters and gene structure in Toxoplasma gondii"
| PRJNA104431 | ENA
Project description:Toxoplasma gondii is a unicellular eukaryote belonging to the Apicomplexa phylum. It is an obligate intracellular parasite of critical importance to primarily infected pregnant women and immunosuppressed patient. ApiAP2 are a family of conserved transcription factors (TF) that play an important role in regulating gene expression in apicomplexan parasites. Previous studies had revealed the ability of one of these TFs, TgAP2XI-5, to bind to transcriptionally active promoters of genes expressed during the S/M phase such as rhoptry and micronemes genes. However, expression of TgAP2XI-5 is constitutive during the tachyzoite cell cycle. To better understand how its function is regulated, we identified proteins interacting with TgAP2XI-5 including a cell cycle regulated ApiAP2 TFs, TgAP2X-5. The purpose of the study is to determine the impact of the absence of a TF (TgAP2X-5) on the wide expression profile of a Toxoplasma gondii strain.
2018-05-30 | GSE106864 | GEO
Project description:The protozoan pathogen Toxoplasma gondii relies on tight regulation of gene expression to invade and establish infection in its host. The divergent gene regulatory mechanisms of Toxoplasma and related apicomplexan pathogens rely heavily on regulators of chromatin structure and histone modifications. The important contribution of histone acetylation for Toxoplasma in both acute and chronic infection has been demonstrated, where histone acetylation increases at active gene loci. However, the direct consequences of specific histone acetylation marks and the chromatin pathway that influences transcriptional regulation in response to the modification is unclear. As a reader of lysine acetylation, the bromodomain serves as a mediator between the acetylated histone and transcriptional regulators. Here we show that the bromodomain protein TgBDP1 which is conserved amongst Apicomplexa and within the Alveolata superphylum, is essential for Toxoplasma asexual proliferation. Using CUT&TAG we demonstrate that TgBDP1 is recruited to transcriptional start sites of a large proportion of parasite genes. Transcriptional profiling during TgBDP1 knockdown revealed that loss of TgBDP1 leads to major dysregulation of gene expression, implying multiple roles for TgBDP1 in both gene activation and repression. This is supported by interactome analysis of TgBDP1 demonstrating that TgBDP1 forms a core complex with two other bromodomain proteins and an ApiAP2 factor. This core complex appears to interact with other epigenetic factors such as nucleosome remodelling complexes. We conclude that TgBDP1 interacts with diverse epigenetic regulators to exert opposing influences on gene expression in the Toxoplasma tachyzoite.
2023-05-31 | GSE228853 | GEO
Project description:The lytic cycle of the protozoan parasite Toxoplasma gondii, which involves a brief sojourn in the extracellular space, is characterized by defined transcriptional profiles. For an obligate intracellular parasite that is shielded from the cytosolic host immune factors by a parasitophorous vacuole, the brief entry into the extracellular space is likely to exert enormous stress. Due to its role in cellular stress response, we hypothesize that translational control plays an important role in regulating gene expression in Toxoplasma during the lytic cycle. Unlike transcriptional profiles, insights into genome-wide translational profiles of Toxoplasma gondii are lacking. We have performed genome-wide ribosome profiling, coupled with high throughput RNA sequencing, in intracellular and extracellular Toxoplasma gondii parasites to investigate translational control during the lytic cycle. Results: Although differences in transcript abundance were mostly mirrored at the translational level, we observed significant differences in the abundance of ribosome footprints between the two parasite stages. Furthermore, our data suggest that mRNA translation in the parasite is potentially regulated by mRNA secondary structure and upstream open reading frames.
2017-11-23 | GSE99395 | GEO
Project description:The purpose of this project is to predict Toxoplasma gondii complexes from cofractionation datasets. In short, T. gondii lysates were fractionated utilizing reagent beads with different biochemical surface properties. 5 beads were utilized with each generating 60 fractions, resulting in a total of 300 fractions. T. gondii lysates were also subjected to fractionation by ion exchange chromatography (IEX), resulting in an additional 120 fractions. These fractions are then analyzed by liquid chromatography-mass spectrometry (LC-MS). Protein fractionation profiles are then utilized to predict protein complexes. See the sample processing protocol for experimental details.
2023-05-30 | MSV000092051 | MassIVE
Project description:Tymoshenko2015 - Genome scale metabolic model
- ToxoNet1
This model is described in the article:
Metabolic Needs and
Capabilities of Toxoplasma gondii through Combined
Computational and Experimental Analysis.
Tymoshenko S, Oppenheim RD, Agren R,
Nielsen J, Soldati-Favre D, Hatzimanikatis V.
PLoS Comput. Biol. 2015 May; 11(5):
e1004261
Abstract:
Toxoplasma gondii is a human pathogen prevalent worldwide
that poses a challenging and unmet need for novel treatment of
toxoplasmosis. Using a semi-automated reconstruction algorithm,
we reconstructed a genome-scale metabolic model, ToxoNet1. The
reconstruction process and flux-balance analysis of the model
offer a systematic overview of the metabolic capabilities of
this parasite. Using ToxoNet1 we have identified significant
gaps in the current knowledge of Toxoplasma metabolic pathways
and have clarified its minimal nutritional requirements for
replication. By probing the model via metabolic tasks, we have
further defined sets of alternative precursors necessary for
parasite growth. Within a human host cell environment, ToxoNet1
predicts a minimal set of 53 enzyme-coding genes and 76
reactions to be essential for parasite replication.
Double-gene-essentiality analysis identified 20 pairs of genes
for which simultaneous deletion is deleterious. To validate
several predictions of ToxoNet1 we have performed experimental
analyses of cytosolic acetyl-CoA biosynthesis. ATP-citrate
lyase and acetyl-CoA synthase were localised and their
corresponding genes disrupted, establishing that each of these
enzymes is dispensable for the growth of T. gondii, however
together they make a synthetic lethal pair.
This model is hosted on
BioModels Database
and identified by:
MODEL1504280000.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2015-07-07 | MODEL1504280000 | BioModels
Project description:The protozoan pathogen Toxoplasma gondii relies on tight regulation of gene expression to invade and establish infection in its host. The divergent gene regulatory mechanisms of Toxoplasma and related apicomplexan pathogens rely heavily on regulators of chromatin structure and histone modifications. The important contribution of histone acetylation for Toxoplasma in both acute and chronic infection has been demonstrated, where histone acetylation increases at active gene loci. However, the direct consequences of specific histone acetylation marks and the signaling pathway that influences transcriptional regulation in response to the modification is unclear. As a reader of lysine acetylation, the bromodomain serves as a mediator between the acetylated histone and transcriptional regulators. Here we show that the bromodomain protein TgBDP1 which is conserved amongst Apicomplexa and within the Alveolata superphylum, is essential for Toxoplasma asexual proliferation. Using CUT&TAG we demonstrate that TgBDP1 is recruited to transcriptional start sites of a large proportion of parasite genes. Transcriptional profiling during TgBDP1 knockdown revealed that loss of TgBDP1 leads to major dysregulation of gene expression, implying multiple roles for TgBDP1 in both gene activation and repression. This is supported by interactome analysis of TgBDP1 demonstrating that TgBDP1 forms a core complex with two other bromodomain proteins and an ApiAP2 factor. This core complex appears to interact with other epigenetic factors such as nucleosome remodelling complexes. We conclude that TgBDP1 interacts with diverse epigenetic regulators to exert opposing influences on gene expression in the Toxoplasma tachyzoite.
2023-06-01 | PXD038848 | Pride
Project description:Toxoplasma gondii (T. gondii) is an obligate intracellular parasite that can infect almost all warm-blooded animals, causing serious public health problems. Lysine crotonylation (Kcr) is a newly discovered posttranslational modification (PTM), which has been proved that is relevant to procreation regulation, active transcription and cell signaling pathway. However, the biological functions of crotonylation have not yet been reported in macrophages infected with T. gondii. In our study, we performed a ChIP-seq analysis of porcine alveolar macrophages infected with T. gondii RH to explore the relationship of histone Kcr with T. gondii infection.
2021-12-31 | GSE167340 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE11437: Expression QTL mapping of Toxoplasma gondii genes, Bradyzoite array GSE11514: Expression QTL mapping of Toxoplasma gondii genes, Tachyzoite array Keywords: SuperSeries Refer to individual Series
2008-05-22 | E-GEOD-11515 | biostudies-arrayexpress