Differentially expressed genes in absence of histone H3K4 methyltransferase Set1 in Candida albicans
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ABSTRACT:
PROVIDER: PRJNA665387 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12703157_1.fastq.gz | Fastqsanger.gz | |||
| SRR12703157_2.fastq.gz | Fastqsanger.gz | |||
| SRR12703158_1.fastq.gz | Fastqsanger.gz | |||
| SRR12703158_2.fastq.gz | Fastqsanger.gz | |||
| SRR12703159_1.fastq.gz | Fastqsanger.gz |
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Project description:Candida albicans is an opportunistic human fungal pathogen. It exists as a member of human normal flora but can cause infection in immunocompromised individuals. Transition to pathogenic C. albicans requires a change in gene expression of various genes. As the histone-modifying enzymes can regulate gene expression, they can be considered as a factor controlling the virulence of C. albicans. Among them, it has been reported that the absence of H3K4 methyltransferase Set1 reduces the virulence of C. albicans. However, Set1-regulated genes responsible for this attenuated virulence phenotype are unknown. Here, we identified that the Set1 positively regulates the expression of mitochondrial protein genes and oxidative stress response-related genes through the methylation of H3K4. Levels of cellular mitochondrial reactive oxygen species (ROS) in Δset1 are also higher than those in the wild-type. Furthermore, Set1 deletion increases sensitivity to hydrogen peroxide (H2O2). Set1 deleted mutant also does not form its colony properly when it interacts with macrophage in vitro, in agreement with its attenuated virulence in vivo. Therefore, Set1 is required to inhibit cellular ROS production by positive regulation of mitochondrial protein genes and oxidative stress response-related genes expression, and consequently, the Set1-mediated gene expression assists C. albicans in defending against ROS generated from the host more rapidly.
2021-11-03 | GSE158481 | GEO
Project description:Set1 H3K4 methyltransferase and Jhd2 H3K4 demethylase
| PRJNA296896 | ENA
Project description:Histone H3K4 methylation is connected to gene transcription from yeast to humans, but its mechanistic role in transcription and chromatin dynamics remains poorly understood. Here, we investigated the functions for Set1 and Jhd2, the sole H3K4 methyltransferase and H3K4 demethylase, respectively, in S. cerevisiae. Our data show that Set1 and Jhd2 predominantly co-regulate transcription. To further understand the role for H3K4 methylation, we overexpressed Flag epitope-tagged SET1-G990E (a dominant hyperactive allele of SET1) in yeast using the constitutive ADH1 promoter (ADH1p). As a control, we also overexpressed Flag epitope-tagged wild type SET1 in yeast. Analysis of gene expression in set1-null, jhd2-null and wild type SET1 or hypeactive SET1-G990E overexpressing mutants together revealed that the transcriptional regulation at a sub-set of genes, inclduing those governing glycogen metabolism and ribosome biogenesis, is highly sensitive to any change (i.e., loss or gain) in H3K4 methylation levels. Overall, we find combined activities of Set1 and Jhd2 via dynamic modulation of H3K4 methylation contribute to positive or negative transcriptional regulation at shared target genes. Gene expression changes were generated from five different yeast strains representing wild type control, set1 null and jhd2 null mutants, and wild type SET1 or dominant hyperacive SET1-G990E overexpressing mutants. Three independent biological samples were grown for each strain, total RNA was isolated, libraries were prepared, sequenced, and analyzed separately.
2016-06-15 | E-GEOD-73406 | biostudies-arrayexpress
Project description:Histone H3K4 methylation is connected to gene transcription from yeast to humans, but its mechanistic role in transcription and chromatin dynamics remains poorly understood. Here, we investigated the functions for Set1 and Jhd2, the sole H3K4 methyltransferase and H3K4 demethylase, respectively, in S. cerevisiae. Our data show that Set1 and Jhd2 predominantly co-regulate transcription. To further understand the role for H3K4 methylation, we overexpressed Flag epitope-tagged SET1-G990E (a dominant hyperactive allele of SET1) in yeast using the constitutive ADH1 promoter (ADH1p). As a control, we also overexpressed Flag epitope-tagged wild type SET1 in yeast. Analysis of gene expression in set1-null, jhd2-null and wild type SET1 or hypeactive SET1-G990E overexpressing mutants together revealed that the transcriptional regulation at a sub-set of genes, inclduing those governing glycogen metabolism and ribosome biogenesis, is highly sensitive to any change (i.e., loss or gain) in H3K4 methylation levels. Overall, we find combined activities of Set1 and Jhd2 via dynamic modulation of H3K4 methylation contribute to positive or negative transcriptional regulation at shared target genes.
2016-06-15 | GSE73406 | GEO
Project description:Histone H3K4 methylation is connected to gene transcription from yeast to humans, but its mechanistic role in transcription and chromatin dynamics remains poorly understood. Here, we investigated the functions for Set1 and Jhd2, the sole H3K4 methyltransferase and H3K4 demethylase, respectively, in S. cerevisiae. Our data show that Set1 and Jhd2 predominantly co-regulate transcription. We find combined activities of Set1 and Jhd2 via H3K4 methylation contribute to positive or negative transcriptional regulation at shared target genes. Providing mechanistic insights, our data reveal that Set1 and Jhd2 together control nucleosomal occupancy during transcriptional co-regulation. Moreover, we find a remarkable genome-wide co-regulation of nucleosome and chromatin structure by Set1 and Jhd2 at different groups of transcriptionally active or inactive genes and at different regions within yeast genes. Overall, our study prompts a model wherein combined actions of Set1 and Jhd2 via H3K4 methylationâdemethylation control chromatin dynamics during various facets of transcriptional regulation. Genome-wide nucleosome maps were generated from three different yeast strains representing wild type control, set1 null and jhd2 null mutants. Three independent biological samples were grown for each strain, nucleosomes were prepared by micrococcal nuclease digestion, libraries were prepared, mononculeosomal DNA was isolated, sequenced, and analyzed separately.
2016-06-15 | E-GEOD-73404 | biostudies-arrayexpress
Project description:Histone H3K4 methylation is connected to gene transcription from yeast to humans, but its mechanistic role in transcription and chromatin dynamics remains poorly understood. Here, we investigated the functions for Set1 and Jhd2, the sole H3K4 methyltransferase and H3K4 demethylase, respectively, in S. cerevisiae. Our data show that Set1 and Jhd2 predominantly co-regulate transcription. We find combined activities of Set1 and Jhd2 via H3K4 methylation contribute to positive or negative transcriptional regulation at shared target genes. Providing mechanistic insights, our data reveal that Set1 and Jhd2 together control nucleosomal occupancy during transcriptional co-regulation. Moreover, we find a remarkable genome-wide co-regulation of nucleosome and chromatin structure by Set1 and Jhd2 at different groups of transcriptionally active or inactive genes and at different regions within yeast genes. Overall, our study prompts a model wherein combined actions of Set1 and Jhd2 via H3K4 methylation−demethylation control chromatin dynamics during various facets of transcriptional regulation.
2016-06-15 | GSE73404 | GEO
Project description:Histone H3K4 methylation is connected to gene transcription from yeast to humans, but its mechanistic role in transcription and chromatin dynamics remains poorly understood. Here, we investigated the functions for Set1 and Jhd2, the sole H3K4 methyltransferase and H3K4 demethylase, respectively, in S. cerevisiae. Our data show that Set1 and Jhd2 predominantly co-regulate transcription. We find combined activities of Set1 and Jhd2 via H3K4 methylation contribute to positive or negative transcriptional regulation at shared target genes. Providing mechanistic insights, our data reveal that Set1 and Jhd2 together control nucleosomal occupancy during transcriptional co-regulation. Moreover, we find a remarkable genome-wide co-regulation of nucleosome and chromatin structure by Set1 and Jhd2 at different groups of transcriptionally active or inactive genes and at different regions within yeast genes. Overall, our study prompts a model wherein combined actions of Set1 and Jhd2 via H3K4 methylationâdemethylation control chromatin dynamics during various facets of transcriptional regulation. Genome-wide nucleosome maps were generated from three different yeast strains representing no tag control, 8V5-Set1 and Jhd2-12V5. Cells were cross-linked with formaldehyde, spheroplasted, nuclei were isolated and chromatin was prepared using micrococcal nuclease digestion, chromatin immunoprecipitation was performed using an epitope-tag specific antibody, libraries were prepared from ChIP and input DNA, sequenced, and analyzed separately.
2016-06-15 | E-GEOD-81021 | biostudies-arrayexpress
Project description:Histone H3K4 methylation is connected to gene transcription from yeast to humans, but its mechanistic role in transcription and chromatin dynamics remains poorly understood. Here, we investigated the functions for Set1 and Jhd2, the sole H3K4 methyltransferase and H3K4 demethylase, respectively, in S. cerevisiae. Our data show that Set1 and Jhd2 predominantly co-regulate transcription. We find combined activities of Set1 and Jhd2 via H3K4 methylation contribute to positive or negative transcriptional regulation at shared target genes. Providing mechanistic insights, our data reveal that Set1 and Jhd2 together control nucleosomal occupancy during transcriptional co-regulation. Moreover, we find a remarkable genome-wide co-regulation of nucleosome and chromatin structure by Set1 and Jhd2 at different groups of transcriptionally active or inactive genes and at different regions within yeast genes. Overall, our study prompts a model wherein combined actions of Set1 and Jhd2 via H3K4 methylationâ??demethylation control chromatin dynamics during various facets of transcriptional regulation. Genome-wide nucleosome maps were generated from three different yeast strains representing no tag control, 8V5-Set1 and Jhd2-12V5. Cells were cross-linked with formaldehyde, spheroplasted, nuclei were isolated and chromatin was prepared using micrococcal nuclease digestion , chromatin immunoprecipitation was performed using an epitope-tag specific antibody, libraries were prepared from ChIP and input DNA, sequenced, and analyzed separately.
2016-06-15 | E-GEOD-81022 | biostudies-arrayexpress
Project description:Histone H3K4 methylation is connected to gene transcription from yeast to humans, but its mechanistic role in transcription and chromatin dynamics remains poorly understood. Here, we investigated the functions for Set1 and Jhd2, the sole H3K4 methyltransferase and H3K4 demethylase, respectively, in S. cerevisiae. Our data show that Set1 and Jhd2 predominantly co-regulate transcription. We find combined activities of Set1 and Jhd2 via H3K4 methylation contribute to positive or negative transcriptional regulation at shared target genes. Providing mechanistic insights, our data reveal that Set1 and Jhd2 together control nucleosomal occupancy during transcriptional co-regulation. Moreover, we find a remarkable genome-wide co-regulation of nucleosome and chromatin structure by Set1 and Jhd2 at different groups of transcriptionally active or inactive genes and at different regions within yeast genes. Overall, our study prompts a model wherein combined actions of Set1 and Jhd2 via H3K4 methylation−demethylation control chromatin dynamics during various facets of transcriptional regulation.
2016-06-15 | GSE81022 | GEO
Project description:Histone H3K4 methylation is connected to gene transcription from yeast to humans, but its mechanistic role in transcription and chromatin dynamics remains poorly understood. Here, we investigated the functions for Set1 and Jhd2, the sole H3K4 methyltransferase and H3K4 demethylase, respectively, in S. cerevisiae. Our data show that Set1 and Jhd2 predominantly co-regulate transcription. We find combined activities of Set1 and Jhd2 via H3K4 methylation contribute to positive or negative transcriptional regulation at shared target genes. Providing mechanistic insights, our data reveal that Set1 and Jhd2 together control nucleosomal occupancy during transcriptional co-regulation. Moreover, we find a remarkable genome-wide co-regulation of nucleosome and chromatin structure by Set1 and Jhd2 at different groups of transcriptionally active or inactive genes and at different regions within yeast genes. Overall, our study prompts a model wherein combined actions of Set1 and Jhd2 via H3K4 methylation−demethylation control chromatin dynamics during various facets of transcriptional regulation.
2016-06-15 | GSE81021 | GEO