Saccharomyces cerevisiae
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA343079 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Post-translational modifications (PTMs) of proteins, such as acetylation or phosphorylation, represent a huge untapped source of targets of great biological and therapeutic potential, but their validation can only be indirect. PTMs cannot be selectively hit by the powerful nucleic-acid based interference approaches. Antibodies represent a class of molecules that could be exploited to selectively target PTMs. However, currently it is not possible to systematically derive antibodies that selectively bind PTMs of a native protein and work intracellularly to achieve a native PTM-selective interference. We developed the Post-translational Intracellular Silencing Antibody technology (P.I.S.A.), a new method for the selection of intrabodies targeting the native PTM version of proteins and their use for PTM targeting in cells. We used PISA to select an intrabody against acetylated-K9-H3 Histone (ScFv-58F). Microarray study is aimed at the investigation of ScFv-58F-specific changes in gene expression in yeast, in comparison to yeast expressing a control intrabody (ScFv-112A, anti-acetyl-Integrase, selected with PISA), and to a wild type yeast.
2016-11-14 | GSE86954 | GEO
Project description:ChIP-chip assays to determine the occupancy of acetylated histone H3 K56 in wildtype, isw1, chd1, isw1 chd1 and ISW1[K227R] yeast.
2012-07-25 | GSE36405 | GEO
Project description:ChIP-chip assays to determine the occupancy of acetylated histone H3 K56 in wildtype, isw1, chd1, isw1 chd1 and ISW1[K227R] yeast. Two color experiment. ChIP/Input. K56ac data normalized to histone H3 and plotted as mutant over wildtype. Biological replicates=3. Please note that H3 data for YMS123-125 & YMS127 is part of the AcH4 file.
2012-07-24 | E-GEOD-36405 | biostudies-arrayexpress
Project description:Whole genome ChIP-chip study using human liver cell line HepG2 and anti-Histone H3 acetyl K9/14 (06-599); USF1 antibody (H-86, sc-8983); USF2 antibody (C-20, sc-862) and normal rabbit IgG (12-370). Three completely independent biological replicates were performed for each antibody, obtaining the corresponding input as total genomic DNA reference. Hybridizations were performed using Affymetrix GeneChip Human Tiling 2.0R Array set (7 arrays set).
2007-11-30 | E-TABM-314 | biostudies-arrayexpress
Project description:Histone H3 lysine 4 tri-methylation (H3K4me3) is a hallmark of transcription initiation, but how H3K4me3 is demethylated during gene repression is poorly understood. Jhd2, a JmjC domain protein, was recently identified as the major H3K4me3 histone demethylase (HDM) in S. cerevisiae. While JHD2 is required for removal of methylation upon gene repression, deletion of JHD2 does not result in increased levels of H3K4me3 in bulk histones, indicating that this HDM is unable to demethylate histones during steady state conditions. In this study, we showed that this was due to the negative regulation of Jhd2 activity by histone H3 lysine 14 acetylation, which co-localizes with H3K4me3 across the yeast genome. We demonstrated that loss of the histone H3-specific acetyltransferases (HATs) resulted in genome-wide-depletion of H3K4me3, and this was not due to a transcription defect. Moreover, H3K4me3 levels were reestablished in HAT mutants following loss of JHD2, which suggested that H3-specific HATs and Jhd2 served opposing functions in regulating H3K4me3 levels. We revealed the molecular basis for this suppression by demonstrating that histone H3K14 acetylation negatively regulated Jhd2 demethylase activity on an acetylated peptide in vitro. These results revealed the existence of a general mechanism for removal of H3K4me3 following gene repression. Examination of H3K4me3 in WT, ada2sas3, ada2sas3jhd2, and jhd2 strains.
2012-11-05 | E-GEOD-41424 | biostudies-arrayexpress
Project description:Normal cell type specific histone H3 acetylation of miRNA genes. HMEC and HMF represent two distinct differentiated cell type present in mammary gland each with a distinct phenotype, a distinct epigenotype as well as distinct miRNA expression pattern. The aim of the study was to determine how epigenetic modifications including histone H3 acetylation affect miRNA expression. Two cell types HMEC vs. HMF. Biological replicates: 3 pairs of HMEC-HMF of 3 distinct genotypes. Immunoprecipitation using anti-acetylated histone H3 antibody (06-599, Millipore).
2011-04-05 | E-GEOD-28375 | biostudies-arrayexpress
Project description:Histone acetylation is a major epigenetic control mechanism that is tightly linked to the promotion of gene expression. Histone acetylation levels are balanced through the opposing activities of histone acetyltransferases (HATs) and histone deacetylases (HDACs). Arabidopsis HDAC genes (AtHDACs) compose a large gene family, and distinct phenotypes among AtHDAC mutants reflect the functional specificity of individual AtHDACs. However, the mechanisms underlying this functional diversity are largely unknown. Here, we show that POWERDRESS (PWR), a positive regulator of floral stem cell maintenance, interacts with HDA9 and promotes histone H3 deacetylation possibly by facilitating HDA9 function at target chromatin. The PWR SANT2 domain, which is homologous to that of subunits in animal HDAC complexes, showed specific binding affinity to acetylated histone H3. Three lysine residues (K9, K14 and K27) of H3 retained hyperacetylation status in both pwr and hda9 mutants. Genome wide H3K9 and H3K14 acetylation levels were generally elevated, and a large portion of acetylated targets overlapped between the pwr and hda9 mutants. Comparative analysis revealed a correlation between gene expression and histone H3 acetylation status in the pwr and hda9 mutants. In addition, PWR and HDA9 modulated the AGAMOUS-LIKE 19 (AGL19)-mediated flowering time pathway through histone H3 deacetylation. Finally, PWR was shown to physically interact with HDA9. We therefore propose that PWR acts as a subunit in a complex with HDA9 to negatively regulate the acetylation of specific lysine residues of histone H3 at genomic targets.
2017-01-25 | GSE89769 | GEO
Project description:Histone acetylation is a major epigenetic control mechanism that is tightly linked to the promotion of gene expression. Histone acetylation levels are balanced through the opposing activities of histone acetyltransferases (HATs) and histone deacetylases (HDACs). Arabidopsis HDAC genes (AtHDACs) compose a large gene family, and distinct phenotypes among AtHDAC mutants reflect the functional specificity of individual AtHDACs. However, the mechanisms underlying this functional diversity are largely unknown. Here, we show that POWERDRESS (PWR), a positive regulator of floral stem cell maintenance, interacts with HDA9 and promotes histone H3 deacetylation possibly by facilitating HDA9 function at target chromatin. The PWR SANT2 domain, which is homologous to that of subunits in animal HDAC complexes, showed specific binding affinity to acetylated histone H3. Three lysine residues (K9, K14 and K27) of H3 retained hyperacetylation status in both pwr and hda9 mutants. Genome wide H3K9 and H3K14 acetylation levels were generally elevated, and a large portion of acetylated targets overlapped between the pwr and hda9 mutants. Comparative analysis revealed a correlation between gene expression and histone H3 acetylation status in the pwr and hda9 mutants. In addition, PWR and HDA9 modulated the AGAMOUS-LIKE 19 (AGL19)-mediated flowering time pathway through histone H3 deacetylation. Finally, PWR was shown to physically interact with HDA9. We therefore propose that PWR acts as a subunit in a complex with HDA9 to negatively regulate the acetylation of specific lysine residues of histone H3 at genomic targets.
2017-01-25 | GSE89768 | GEO
Project description:Histone H3 lysine 4 tri-methylation (H3K4me3) is a hallmark of transcription initiation, but how H3K4me3 is demethylated during gene repression is poorly understood. Jhd2, a JmjC domain protein, was recently identified as the major H3K4me3 histone demethylase (HDM) in S. cerevisiae. While JHD2 is required for removal of methylation upon gene repression, deletion of JHD2 does not result in increased levels of H3K4me3 in bulk histones, indicating that this HDM is unable to demethylate histones during steady state conditions. In this study, we showed that this was due to the negative regulation of Jhd2 activity by histone H3 lysine 14 acetylation, which co-localizes with H3K4me3 across the yeast genome. We demonstrated that loss of the histone H3-specific acetyltransferases (HATs) resulted in genome-wide-depletion of H3K4me3, and this was not due to a transcription defect. Moreover, H3K4me3 levels were reestablished in HAT mutants following loss of JHD2, which suggested that H3-specific HATs and Jhd2 served opposing functions in regulating H3K4me3 levels. We revealed the molecular basis for this suppression by demonstrating that histone H3K14 acetylation negatively regulated Jhd2 demethylase activity on an acetylated peptide in vitro. These results revealed the existence of a general mechanism for removal of H3K4me3 following gene repression.
2012-11-05 | GSE41424 | GEO
Project description:Lysine 56 acetylation in the helical core of histone H3 opens yeast chromatin and enables histone gene transcription, DNA replication, DNA repair, and prevents epigenetic silencing. While K56Ac is globally abundant in yeast and flies its presence has been uncertain in mammals. We show here using mass spectrometry and genome wide analyses that K56Ac is present in human embryonic stem cells (hESCs) overlapping strongly at active and inactive promoters with the binding of the key regulators of pluripotency NANOG, SOX2 and OCT4. This includes also the canonical histone gene promoters and those for the hESC-specific microRNAs. K56Ac then relocates to developmental genes upon cellular differentiation. Thus K56Ac state more accurately reflects the epigenetic differences between hESCs and somatic cells than other active histone marks such as H3 K4 tri-methylation and K9 acetylation. These results suggest that K56Ac is involved in the human core transcriptional network of pluripotency. Genome wide location analysis ChIP-chip was performed in two human embryonic stem cell lines (HSF1 and HSF6) and two somatic cell lines (ARPE and BJ), for each of the following histone modifications: H3 K56Ac, H3 K9Ac, H3 K4me3 and H3 K27me3.
2009-02-09 | E-GEOD-14749 | biostudies-arrayexpress