Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of genes regulated by the transcription factor RFX1 (CR_06110C) in the yeast Candida albicans

ABSTRACT: The regulatory factor X (RFX) gene family comprises a functionally diverse group of transcription factors characterized by a highly conserved and unique winged-helix DNA binding domain. The RFX proteins control a variety of processes ranging from genome integrity and cell cycle in model yeasts to immune functions and tissue differentiation in higher eukaryotes. The yeast Candida albicans encodes two RFX homologs, one of which (CR_06110C, termed RFX1) remains uncharacterized. In this study we employed RNA-seq to identify downstream targets of the transcriptional regulator Rfx1 in C. albicans.

ORGANISM(S): Candida albicans

PROVIDER: GSE249927 | GEO | 2023/12/15

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

RNA-seq Analysis of RFX1-dependent Genes in Fusarium graminearum Z-3639

Project description:Fusarium graminearum is a major pathogen of Fusarium head blight in wheat, barley, and rice, as well as ear rot and stalk rot in maize. Regulatory Factor X (RFX) transcription factors are well-conserved in animals and fungi, but their functions are diverse, ranging from DNA-damage response to ciliary gene regulation. We investigated the role of the sole RFX transcription factor, RFX1, in F. graminearum. Deletion of rfx1 resulted in multiple defects in hyphal growth, conidiation, virulence, and sexual development. Deletion mutants of rfx1 were more sensitive to various types of DNA damage than the wild-type strain. Septum formation was inhibited and micronuclei were produced in the rfx1 deletion mutants. The results of the neutral comet assay demonstrated that disruption of rfx1 function caused spontaneous DNA double-strand breaks. To understand regulatory mechanisms of rfx1 in F. graminearum, we obtained and analyzed genome-wide transcription profiles generated from the RNA-sequencing data of the wild-type and M-NM-^Trfx1 strains. RNA-sequencing-based transcriptomic analysis revealed that RFX1 suppressed the expression of many genes, including genes for the repair of DNA damage. 2 samples examined: mycelia harvested 24 h after inoculation of wild-type conidia in complete medium; mycelia harvested 32 h after inoculation of M-NM-^Trfx1 conidia in complete medium

2014-01-28 | E-GEOD-52198 | biostudies-arrayexpress

RNA-seq Analysis of RFX1-dependent Genes in Fusarium graminearum Z-3639

Project description:Fusarium graminearum is a major pathogen of Fusarium head blight in wheat, barley, and rice, as well as ear rot and stalk rot in maize. Regulatory Factor X (RFX) transcription factors are well-conserved in animals and fungi, but their functions are diverse, ranging from DNA-damage response to ciliary gene regulation. We investigated the role of the sole RFX transcription factor, RFX1, in F. graminearum. Deletion of rfx1 resulted in multiple defects in hyphal growth, conidiation, virulence, and sexual development. Deletion mutants of rfx1 were more sensitive to various types of DNA damage than the wild-type strain. Septum formation was inhibited and micronuclei were produced in the rfx1 deletion mutants. The results of the neutral comet assay demonstrated that disruption of rfx1 function caused spontaneous DNA double-strand breaks. To understand regulatory mechanisms of rfx1 in F. graminearum, we obtained and analyzed genome-wide transcription profiles generated from the RNA-sequencing data of the wild-type and Δrfx1 strains. RNA-sequencing-based transcriptomic analysis revealed that RFX1 suppressed the expression of many genes, including genes for the repair of DNA damage.

2014-01-28 | GSE52198 | GEO

ChIP-seq for RFX1

Project description:ChIP-seq for RFX1

| PRJNA866861 | ENA

Study of RFX1 and RFX3 binding sites in the mouse genome

Project description:The aim of the study was to identify RFX1 and RFX2 binding sites in mouse pancreatic beta cells. Chromatin immunoprecipitation experiments were performed with the mouse MIN6 beta cell line and antibodies raised against RFX1 and RFX3. Immunoprecipitated DNA was sequenced using the Genome Analyzer II (Illumina). Antibodies were described in Reith W, Ucla C, Barras E, Gaud A, Durand B, Herrero-Sanchez C, Kobr M, Mach B : RFX1, a transactivator of hepatitis B virus enhancer I, belongs to a novel family of homodimeric and heterodimeric DNA-binding proteins. Mol Cell Biol 1994;14:1230–1244

2015-08-22 | E-GEOD-72272 | biostudies-arrayexpress

Effect of of RFX1 on regene expression in mouse peritoneal macrophages

Project description:To investigate the function of RFX1 in the regulation of macrophage polarization, we overexpressed RFX1 in mouse peritoneal macrophages(PMAs) by lentivirus infections. We then performed gene expression profiling analysis using data obtained from RNA-seq.

2024-08-06 | GSE236155 | GEO

Effect of RFX1 on gene expression and the potential binding target genes in LPS-stimulated macrophages [RNA-seq]

Project description:To investigate the function of RFX1 in the regulation of macrophage polarization, we overexpressed RFX1 in mouse peritoneal macrophages(PMAs) or human CD14+ derived macrophage(hMDMs) by lentivirus infections or reduce RFX1 expression in PMAs from mice with Rfx1 deficiency(CKO) . We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells at two time points.

2023-11-08 | GSE210667 | GEO

Candida albicans CUG codon translation, comparison with other yeasts

Project description:Candida yeasts causing human infections are spread across the yeast phylum with Candida glabrata being related to Saccharomyces cerevisiae, Candida krusei grouping to Pichia spp., and Candida albicans, Candida parapsilosis and Candida tropicalis belonging to the CTG-clade. The latter lineage contains yeasts with an altered genetic code translating CUG codons as serine using a serine-tRNA with a mutated anticodon. It has been suggested that the CTG-clade CUG codons are mistranslated to a small extent as leucine due to mischarging of the serine-tRNA(CAG). The mistranslation was suggested to result in variable surface proteins explaining fast host adaptation and pathogenicity. Here, we re-assessed this potential mistranslation by high-resolution mass spectrometry-based proteogenomics of multiple CTG-clade yeasts, various C. albicans strains, isolated from colonized and from infected human body sites, and C. albicans grown in yeast and hyphal forms.

2021-11-17 | PXD027278 | Pride

Identification of genes regulated by the transcription factor RFX1 (CR_06110C) in the yeast Candida albicans

Project description:Identification of genes regulated by the transcription factor RFX1 (CR_06110C) in the yeast Candida albicans

| PRJNA1051142 | ENA

Study of RFX1 and RFX3 binding sites in the mouse genome

Project description:The aim of the study was to identify RFX1 and RFX2 binding sites in mouse pancreatic beta cells.

2015-08-22 | GSE72272 | GEO

Functions of the Mediator subunit Med31 in Candida albicans support a role in shaping species-specific gene expression.

Project description:Mediator is an essential, evolutionarily conserved co-regulator of RNA polymerase II. Studies in model yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe showed remarkably conserved roles for Mediator despite high species divergence, and thus whether Mediator contributed to establishment of species-specific gene expression programs within related fungal species remains an open question. Here we show that in the fungal pathogen Candida albicans, the Mediator middle domain subunit Med31 has a conserved role with non-pathogenic model yeasts in regulation of Ace2-dependent cytokinesis genes and stress responses, but also additional roles in the transcription of genes associated with virulence traits: genes related to filamentous growth and gene families expanded in pathogenic vs non-pathogenic yeasts, such as the ALS adhesins and the FGR6 family of filamentous growth regulators. Consistently, Med31 is required for two key virulence attributes of C. albicans: filamentous growth and biofilm formation. Unlike our data in C. albicans, no role for Med31 in adhesin expression has been reported in model yeasts. To show biological relevance for the control over adhesin gene expression, we demonstrate that ALS1 is a relevant Med31 target for development of biofilms. Collectively, our data supports a role for Med31 in shaping species-specific gene expression in related fungal species.

2012-02-20 | GSE31632 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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