MNase-Seq analysis of wild-type Candida glabrata strain in RPMI-growth and macrophage-internalized conditions at 2 h and 10 h post-infection.
Ontology highlight
ABSTRACT:
ORGANISM(S): Nakaseomyces glabratus
PROVIDER: GSE234671 | GEO | 2024/04/16
REPOSITORIES: GEO
Similar Datasets
Project description:To delineate the interaction of Candida glabrata with host immune cells, we performed genome-wide transcriptional profiling analysis on THP-1 macrophage-internalized wild-type and chromatin remodeling defective mutant (Cgrsc3-a∆ and Cgrtt109∆) yeasts. Genes implicated in ergosterol biosynthesis, and high-affinity iron uptake and homeostasis were found to be down-regulated in C. glabrata wild-type and mutant cells upon macrophage internalization. Additionally, global gene expression profiles of RPMI-grown and macrophage-ingested Cgrsc3-a∆ and Cgrtt109∆ cells revealed down-regulation of genes involved in mitochondrial respiration under normal growth conditions and induction of genes required for generation of precursors of metabolites and energy upon macrophage internalization. To examine the behavior of Candida glabrata wild-type and chromatin remodeling defective mutants upon internalization by differentiated human monocytic THP-1 cells, we compared the transcript profiles of 10 hour RPMI-grown with those of 10 hour THP-1 macrophage internalized C. glabrata cells. Additionally, early transcriptional response of C. glabrata wild-type cells to macrophage internal milieu was examined post 2 hour THP-1 macrophage infection.
2012-08-18 | GSE38953 | GEO
Project description:Mapping of nucleosomes, the basic DNA packaging unit in eukaryotes, is fundamental for understanding genome regulation as nucleosomes modulate DNA access by their positioning along the genome. A cell population nucleosome map requires two observables: nucleosome positions along the DNA (“Where?”) and nucleosome occupancies across the population (“In how many cells?”). All available genome-wide nucleosome mapping techniques are yield methods as they score either nucleosomal (e.g., MNase-seq, chemical cleavage-seq) or non-nucleosomal (e.g., ATAC-seq) DNA but lose track of the total DNA population for each genomic region. Therefore, they only provide nucleosome positions and maybe compare relative occupancies between positions but cannot measure absolute nucleosome occupancy, which is the fraction of all DNA molecules occupied at a given position and time by a nucleosome. Here, we established two orthogonal and thereby crossvalidating approaches to measure absolute nucleosome occupancy across the Saccharomyces cerevisiae genome via restriction enzymes and DNA methyltransferases. The resulting high-resolution (9 bp) map shows uniform absolute occupancies. Most nucleosome positions are occupied in most cells: 97% of all nucleosomes called by chemical cleavage-seq have a mean absolute occupancy of 90 ± 6% (± SD). Depending on nucleosome position calling procedures, there are 57-60,000 nucleosomes per yeast cell. The few low absolute occupancy nucleosomes do not correlate with highly transcribed gene bodies, but with increased presence of the nucleosome-evicting RSC chromatin remodeling complex there and are enriched upstream of highly transcribed or regulated genes. Our work provides a quantitative method and reference frame in absolute terms for future chromatin studies.
2019-11-27 | GSE141043 | GEO
Project description:To delineate the interaction of Candida glabrata with host immune cells, we performed genome-wide transcriptional profiling analysis on THP-1 macrophage-internalized wild-type and chromatin remodeling defective mutant (Cgrsc3-aM-bM-^HM-^F and Cgrtt109M-bM-^HM-^F) yeasts. Genes implicated in ergosterol biosynthesis, and high-affinity iron uptake and homeostasis were found to be down-regulated in C. glabrata wild-type and mutant cells upon macrophage internalization. Additionally, global gene expression profiles of RPMI-grown and macrophage-ingested Cgrsc3-aM-bM-^HM-^F and Cgrtt109M-bM-^HM-^F cells revealed down-regulation of genes involved in mitochondrial respiration under normal growth conditions and induction of genes required for generation of precursors of metabolites and energy upon macrophage internalization. To examine the behavior of Candida glabrata wild-type and chromatin remodeling defective mutants upon internalization by differentiated human monocytic THP-1 cells, we compared the transcript profiles of 10 hour RPMI-grown with those of 10 hour THP-1 macrophage internalized C. glabrata cells. Additionally, early transcriptional response of C. glabrata wild-type cells to macrophage internal milieu was examined post 2 hour THP-1 macrophage infection. Agilent one-color experiment, Organism: Yeast (Candida glabrata)
2012-08-18 | E-GEOD-38953 | biostudies-arrayexpress
Project description:Chromatin has a highly organized structure with the repeating nucleosome subunits. The position of nucleosomes on the chromatin is dynamically regulated by ATP-dependent chromatin remodeling factors (remodelers), therefore providing specific epigenetic information. However, the in vivo nucleosome distribution pattern in plants and how plant remodelers control the pattern formation are not yet clear. Here we use the Micrococcal Nuclease digestion followed by deep sequencing (MNase-seq) assay to show the genome-wide nucleosome pattern in plants and the role of the Arabidopsis thaliana Imitation Switch (AtISWI) subfamily remodelers in the pattern formation. Our data revealed three patterns in wild-type plants: 1) Promoters have a relative low nucleosome density compared with gene bodies; 2) Nucleosome density is negatively associated with gene expression levels; 3) The evenly and periodically spaced nucleosomes in gene bodies are positively associated with gene expression levels. Double mutations in the AtISWI genes CHROMATIN REMODELING 11 (CHR11) and CHR17 resulted in loss of the evenly-spaced-nucleosome pattern in gene bodies, but did not affect nucleosome density, suggesting that the primary role of AtISWI is to slide nucleosomes in gene bodies for promotion of transcription. The overall design of the experiment: (1) Nuclear extraction from Col-0 and chr11-1 chr17-1. (2) MNase treatment. (3) DNA purification. (4) Library construction. (5) Deep sequencing. (6) Data analysis.
2014-03-30 | E-GEOD-50242 | biostudies-arrayexpress
Project description:The goal of the current study was to identify differentially-expressed genes upon CgSNF2 deletion, as well as, upon macrophage internalization in C. glabrata wild-type (wt) and Cgsnf2Δ strains. For this study, RNA samples were collected from RPMI-grown and macrophage-internalized cells of C. glabrata wild-type and Cgsnf2Δ strains at 2 h and 10 h post-infection. Comparative transcriptome analysis shows the differential regulation of 1419 genes in C. glabrata wild-type cells upon macrophage internalization, whereas the CgSNF2 deletion leads to altered regulation of 935 genes in C. glabrata wild-type cells.
2024-04-16 | GSE234670 | GEO
Project description:Chromatin has a highly organized structure with the repeating nucleosome subunits. The position of nucleosomes on the chromatin is dynamically regulated by ATP-dependent chromatin remodeling factors (remodelers), therefore providing specific epigenetic information. However, the in vivo nucleosome distribution pattern in plants and how plant remodelers control the pattern formation are not yet clear. Here we use the Micrococcal Nuclease digestion followed by deep sequencing (MNase-seq) assay to show the genome-wide nucleosome pattern in plants and the role of the Arabidopsis thaliana Imitation Switch (AtISWI) subfamily remodelers in the pattern formation. Our data revealed three patterns in wild-type plants: 1) Promoters have a relative low nucleosome density compared with gene bodies; 2) Nucleosome density is negatively associated with gene expression levels; 3) The evenly and periodically spaced nucleosomes in gene bodies are positively associated with gene expression levels. Double mutations in the AtISWI genes CHROMATIN REMODELING 11 (CHR11) and CHR17 resulted in loss of the evenly-spaced-nucleosome pattern in gene bodies, but did not affect nucleosome density, suggesting that the primary role of AtISWI is to slide nucleosomes in gene bodies for promotion of transcription.
2014-03-30 | GSE50242 | GEO
Project description:The structural complexity of nucleosomes underlies their functional versatility. Here we report a new type of complexity – nucleosome fragility, manifested as high sensitivity to micrococcal nuclease, in contrast to the common presumption that nucleosomes are similar in resistance to MNase digestion. Using differential MNase digestion of chromatin and high-throughput sequencing, we have identified a special group of nucleosomes termed fragile nucleosomes throughout the yeast genome, nearly one thousand of which are at previously determined “nucleosome free” loci. Nucleosome fragility is broadly implicated in multiple chromatin processes, including transcription, translocation and replication, in correspondence to specific physiological states of cells. In the environmental-stress-response genes, the presence of fragile nucleosomes prior to the occurrence of environmental changes suggests that nucleosome fragility poises genes for swift up-regulation in response to the environmental changes. We propose that nucleosome fragility underscores distinct functional statuses of the chromatin and provides a new dimension for portraying the landscape of genome organization. Comparing nucleosome occupancy under different MNase digestion levels and growth conditions.
2011-01-24 | E-GEOD-26412 | biostudies-arrayexpress
Project description:The classic view of nucleosome organization at active promoters is that two well-positioned nucleosomes flank a nucleosome-depleted region (NDR). However, this view has been recently challenged by contradictory reports as to whether a distinct set of wider (≳150 bp) NDRs instead contain unusually unstable Micrococcal Nuclease-sensitive “fragile” particles, thought to be nucleosomal because of their size. To determine the composition of fragile particles we introduce CUT&RUN.ChIP, in which targeted nuclease cleavage and release is followed by chromatin immunoprecipitation. We find that fragile particles represent the occupancy and action of the RSC nucleosome remodeler acting on dynamically unwrapped nucleosomal intermediates. We also find that general regulatory factors (GRFs) bind to partially unwrapped nucleosomal intermediates at NDRs. We propose that RSC-engagement and its action cause nucleosomes to unravel, and subsequent binding of GRFs constitute a dynamic cycle of nucleosome deposition and clearance at the subset of wide Pol II promoter NDRs.
2018-12-22 | GSE116853 | GEO
Project description:The structural complexity of nucleosomes underlies their functional versatility. Here we report a new type of complexity – nucleosome fragility, manifested as high sensitivity to micrococcal nuclease, in contrast to the common presumption that nucleosomes are similar in resistance to MNase digestion. Using differential MNase digestion of chromatin and high-throughput sequencing, we have identified a special group of nucleosomes termed fragile nucleosomes throughout the yeast genome, nearly one thousand of which are at previously determined “nucleosome free” loci. Nucleosome fragility is broadly implicated in multiple chromatin processes, including transcription, translocation and replication, in correspondence to specific physiological states of cells. In the environmental-stress-response genes, the presence of fragile nucleosomes prior to the occurrence of environmental changes suggests that nucleosome fragility poises genes for swift up-regulation in response to the environmental changes. We propose that nucleosome fragility underscores distinct functional statuses of the chromatin and provides a new dimension for portraying the landscape of genome organization.
2011-01-24 | GSE26412 | GEO
Project description:The eukaryotic nuclear genome is organized into the fundamental units of chromatin, nucleosomes. The positions and biochemical states of nucleosomes on DNA can regulate protein-DNA interactions, and in turn influence DNA-templated events. Despite the increasing number of genome-wide maps of nucleosome position, how global changes in nucleosome position relate to changes in gene expression is poorly understood. Using micrococcal nuclease (MNase) to map nucleosome positions, we show that in the maize genome, nucleosome occupancy signals are remarkably uniform between different tissues, whereas particular genomic regions are highly susceptible to variation. We demonstrate that much of this variation is associated with the degree to which chromatin is digested with MNase. Using high-density DNA microarrays, we exploited this digestion-linked variation to identify protein footprints in the maize genome that are hypersensitive to MNase digestion, a method we term Differential Nuclease-Sensitivity profiling (DNS-chip). Hypersensitive footprints were enriched at the 5’ and 3’ ends of genes, associated with gene-expression levels, and significantly overlapped with conserved noncoding sequences and the binding sites of the homeobox transcription-factor Knotted1, suggesting a functional role in genome regulation. We also found that the tissue-specific regulation of gene expression was linked to tissue-specific hypersensitive footprints in gene promoters. These results demonstrate the value of DNS-chip for revealing biochemical features of nucleosome organization that correlate with gene expression levels and colocalize with functional DNA elements. This approach to chromatin profiling should be broadly applicable to other species and should shed light on how chromatin organization might influence protein-DNA interactions and genome regulation.
2014-08-06 | GSE60090 | GEO