Global gene expression analysis of H4T80A mutants vs WT H4 in Saccharomyces cerevisiae
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB27986 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Global RNA-seq gene expression analysis of H4T80A mutants vs WT H4 in Saccharomyces cerevisiae.
2018-09-05 | E-MTAB-7090 | biostudies-arrayexpress
Project description:The structural integrity of the nucleosome is central to regulation of DNA metabolism and transcription. We describe a library of 486 systematic histone H3 and H4 substitution and deletion mutants in Saccharomyces cerevisiae that probe the contribution of each residue to nucleosome function and can be episomal or genomically integrated. We tagged each mutant histone gene with unique molecular barcodes, facilitating identification of mutant pools through barcode amplification, labeling, and microarray hybridization. We probed fitness contributions of each residue to chemical perturbagens of chromosome integrity and transcription, mapping global patterns of chemical sensitivities and requirements for three forms of transcriptional silencing onto the nucleosome surface. Lethal mutants were surprisingly rare and of distinct types; one set of mutations mapped precisely to the DNA interaction surface. The barcode microarrays were useful for scoring complex phenotypes such as competitive fitness in a chemostat, proficiency of DNA repair, and synthetic genetic interactions. Keywords: genetic modification These nine datasets characterize a microarray platform repurposed for profiling a barcoded comprehensive library of synthetic histone mutants. The first two datasets establish the wide dynamic range and high sensitivity and specificity of data from this platform. The other seven datasets demonstrate the usefulness of this technology for scoring subtle and complex phenotypes of the histone H3 and H4 alleles in this library.
2008-09-18 | E-GEOD-10860 | biostudies-arrayexpress
Project description:The structural integrity of the nucleosome is central to regulation of DNA metabolism and transcription. We describe a library of 486 systematic histone H3 and H4 substitution and deletion mutants in Saccharomyces cerevisiae that probe the contribution of each residue to nucleosome function and can be episomal or genomically integrated. We tagged each mutant histone gene with unique molecular barcodes, facilitating identification of mutant pools through barcode amplification, labeling, and microarray hybridization. We probed fitness contributions of each residue to chemical perturbagens of chromosome integrity and transcription, mapping global patterns of chemical sensitivities and requirements for three forms of transcriptional silencing onto the nucleosome surface. Lethal mutants were surprisingly rare and of distinct types; one set of mutations mapped precisely to the DNA interaction surface. The barcode microarrays were useful for scoring complex phenotypes such as competitive fitness in a chemostat, proficiency of DNA repair, and synthetic genetic interactions. Keywords: genetic modification
2008-09-19 | GSE10860 | GEO
Project description:Investigation of whole genome gene expression level changes in three S. cerevisiae Y55 mutants, compared to the wild-type strain. The UV-induced mutations enable the mutant strains to ferment high-gravity maltose faster than the WT. The mutants analyzed in this study are further described in Baerends, R.J.S., J.L. Qiu, L. Gautier, and A. Brandt. A high-throughput system for screening of fast-fermenting Saccharomyces cerevisiae strains. Manuscript in preparation.
2013-10-25 | GSE25015 | GEO
Project description:Chromatin integrates extracellular signals to regulate gene expression and, therefore, tightly controls development. Mutations in histone genes, including H3.3 and H4, were recently identified in children with developmental disorders characterized by intellectual disability and dysmorphic facial features1–7. However, the mechanistic and functional roles of these de novo, heterozygous germline mutations remain largely unknown. Here, we focus on the histone H4 lysine 91 to arginine (H4K91R) or glutamine (H4K91Q) mutations located within the highly conserved core histone fold domain. Our findings demonstrate that H4K91 mutants form aberrant nuclear puncta in mouse embryonic stem cells (mESCs), as well as in differentiated neural cells in vitro and in vivo. Genome-wide analyses revealed that H4K91 mutants accumulate ectopically at H3.3 and H3K9me3-enriched heterochromatin regions. Mechanistically, H4K91 mutants demonstrated enhanced binding to histone H3 variant H3.3, and ablation of H3.3 or the H3.3-specific chaperone DAXX diminished the formation of H4 mutant puncta and enrichment at heterochromatin regions. Additionally, H4 mutant expression increased chromatin accessibility in mammalian cells. Phenotypically, H4 mutant mice exhibit reduced brain size and altered cortical neuron layers, reminiscent of microcephaly phenotypes observed in patients. Consistent with the altered brain development in vivo, the expression of H4 mutants alter developmental gene expression and accelerate pro-neural differentiation in cell culture models. Together, these studies reveal multiple concurrent pathogenic mechanisms of H4 mutants found in developmental disorders and further our understanding of how histone mutants regulate cell fate during development.
2023-10-19 | GSE231566 | GEO
Project description:Chromatin integrates extracellular signals to regulate gene expression and, therefore, tightly controls development. Mutations in histone genes, including H3.3 and H4, were recently identified in children with developmental disorders characterized by intellectual disability and dysmorphic facial features1–7. However, the mechanistic and functional roles of these de novo, heterozygous germline mutations remain largely unknown. Here, we focus on the histone H4 lysine 91 to arginine (H4K91R) or glutamine (H4K91Q) mutations located within the highly conserved core histone fold domain. Our findings demonstrate that H4K91 mutants form aberrant nuclear puncta in mouse embryonic stem cells (mESCs), as well as in differentiated neural cells in vitro and in vivo. Genome-wide analyses revealed that H4K91 mutants accumulate ectopically at H3.3 and H3K9me3-enriched heterochromatin regions. Mechanistically, H4K91 mutants demonstrated enhanced binding to histone H3 variant H3.3, and ablation of H3.3 or the H3.3-specific chaperone DAXX diminished the formation of H4 mutant puncta and enrichment at heterochromatin regions. Additionally, H4 mutant expression increased chromatin accessibility in mammalian cells. Phenotypically, H4 mutant mice exhibit reduced brain size and altered cortical neuron layers, reminiscent of microcephaly phenotypes observed in patients. Consistent with the altered brain development in vivo, the expression of H4 mutants alter developmental gene expression and accelerate pro-neural differentiation in cell culture models. Together, these studies reveal multiple concurrent pathogenic mechanisms of H4 mutants found in developmental disorders and further our understanding of how histone mutants regulate cell fate during development.
2023-10-19 | GSE231558 | GEO
Project description:RNA sequencing of Saccharomyces cerevisiae wild type and alanyl-tRNA synthetase mutants grown at 30 degrees and challenged at 37 degrees
2021-06-23 | GSE178694 | GEO
Project description:Global gene expression analysis of H4T80A mutants vs WT H4 in Saccharomyces cerevisiae
2018-09-17 | E-MTAB-7090 | ExpressionAtlas
Project description:rs09-10_fwa - wt vs mutants 09. Impact of loss of DNA methylation and small interference RNAs (siRNAs) in gene expression. Determination of the genes misregulated upon ectopic expression of the FWA imprinted gene. Mutants impaired for the DNA methylation maintenance pathway and RNA interference machinery were compared to mutants simultaneously impaired for both. Impact of FWA and SDC ectopic expression.
2011-04-01 | GSE26844 | GEO
Project description:Next-generation proteomics of Saccharomyces cerevisiae mutants for defining their response to lanthanides.
2022-08-12 | PXD025030 | Pride