Identify the PTMs of H3 amino acid residues
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo Sapiens
SUBMITTER: 
Gang Zhao
PROVIDER: PXD056572 | iProX | Mon Sep 30 00:00:00 BST 2024
REPOSITORIES: iProX
Similar Datasets
Project description:To investigate how histone post-translational modifications (PTMs) change during the cell cycle, we profiled histone H3 and histone H4 in breast cancer and normal breast cell lines arrested in G1/S or G2/M phases.
2019-09-09 | PXD013288 | Pride
Project description:Here we examined whether histones H3 and H4 produced using native chemical ligation reaction affect protein binding to di-nucleosomes. To test this we performed a set of affinity purification pull-downs using di-nucleosomes containing the following histones H3 and H4: 1. unmodified ligated histone H3 and recombinant wild type histone H4 (unmod. H3), 2. recombinant wild type histone H3 and ligated unmodified histone H4 (unmod. H4) 3. ligated unmodified histones H3 and H4 (unmod. H3&H4). 4. recombinant wild type histones H3 and H4 (WT) Each pull-down was performed in three replicates. Co-purified proteins were quantified using label-free MS. Note that ligated histones H3 and H4 contain T32C or I29C single amino acid substitutions, respectively, that are introduced by the native chemical ligation procedure. In addition, ligated histone H4 is N-terminally acetylated to mimic its naturally blocked N-terminus.
2023-12-12 | PXD042390 | Pride
Project description:Here we examined whether histones H3 and H4 produced using native chemical ligation reaction affect protein binding to di-nucleosomes. To test this we performed a set of affinity purification pull-downs using di-nucleosomes containing the following histones H3 and H4: 1. ligated unmodified histone H3 and recombinant wild type histone H4 (unmod. H3), 2. recombinant wild type histone H3 and ligated unmodified histone H4 (unmod. H4) 3. ligated unmodified histones H3 and H4 (unmod. H3&H4). 4. recombinant wild type histones H3 and H4 (WT) Each pull-down was performed in three replicates. Co-purified proteins were quantified using label-free MS. Note that ligated histones H3 and H4 contain T32C or I29C single amino acid substitutions, respectively, that are introduced by the native chemical ligation procedure. In addition, ligated histone H4 is N-terminally acetylated to mimic its naturally blocked N-terminus.
2023-12-10 | PXD042630 | Pride
Project description:Cells have the ability to sense, respond and adapt to environmental fluctuations. Stress causes a massive reorganization of the transcriptional program. Many examples of histone post-translational modifications (PTMs) have been associated with transcriptional activation or repression under steady-state growth conditions. Comparatively less is known about the role of histone PTMs in the cellular adaptive response to stress. Here, we performed high-throughput genetic screenings that provide a novel global map of the histone residues required for transcriptional reprogramming in response to heat and osmotic stress. Of note, we observed that the histone residues needed depend on the type of gene and/or stress, thereby suggesting a “personalized”, rather than general, subset of histone requirements for each chromatin context. In addition, we identified a number of new residues that unexpectedly serve to regulate transcription. As a proof of concept, we characterized the function of the histone residues H4-S47 and H4-T30 in response to osmotic and heat stress, respectively. Our results uncover novel roles for the kinases Cla4 and Ste20, yeast homologs of the mammalian PAK2 family, which phosphorylate H4-S47 and for the kinase Ste11 that targets H4-T30. This study provides new insights into the role of histone residues in transcriptional regulation under stress conditions.
2020-05-27 | PXD017134 | Pride
Project description:We report genome-wide distribution of newly discovered O-GlcNAcylated H4 at threonine 71 (H4T71Gc) in mouse embryonic stem cells (mESCs, J1 line) cultured in 25 mM glucose (mESCs-25mMG) or 1 mM glucose (mESCs-1mMG) condition, human embryonic stem cells (hESCs, H9) and human induced-pluripotent stem cells (hiPSCs, 201B7). We found that H4T71Gc preferentially localize to gene regions, especially those with relatively high expression levels. Interestingly, the localized gene region of H4T71Gc changes in response to changes in extracellular glucose concentration. This study using ChIP-seq analysis provides genomic distribution of novel histone O-GlcNAcylation in mouse and human pluripotent stem cells.
2024-06-09 | GSE153008 | GEO
Project description:Nucleosome structure directly influences gene transcription. However, the function of each histone residue remains largely unknown. Here we profiled gene expression changes upon the mutation of individual residues of histone H3 and H4. Histone residues grouped by expression change similarity displayed overall structural relevance. This regulatory functional map of the core histones led to novel findings. First, the residues specific to each histone family tend to be more influential than those commonly found among different histones. Second, unlike histone acetylations, H3K4 trimethylation does not appear to be prerequisite for gene activation. Third, H3Q5 has been newly identified for its putative interactions with many chromatin regulators for transcription control. Lastly, the nucleosome lateral surface seems to play a key role through interactions with the surrounding DNA. Remarkably, we discovered a novel role for H3K56 in chromatin dynamics. The deletion of this residue, but not the alteration of acetylation states, caused a genome-wide decrease in nucleosome mobility and stabilized nucleosome positioning near transcription start and end sites. Occupying the DNA entry/exit site, H3K56 is thought to modulate nucleosome sliding along DNA. Taken together, genomics approaches such as microarray and deep sequencing prove valuable for mapping the function of histone residues. Microarray analysis was performed for 123 histone mutants and four wild-types as two reaplications of H3 and H4 of Saccharomyces ceravisiae.
2012-12-05 | E-GEOD-29059 | biostudies-arrayexpress
Project description:We have performed a comprehensive analysis of the involvement of histone H3 and H4 residues in the regulation of chronological lifespan in yeast. Residues where substitution resulted in the most pronounced lifespan extension are all on the exposed face of the nucleosome, with the exception of H3E50, which is present on the lateral surface, between two DNA gyres. Other residues that had a more modest effect on lifespan extension were concentrated at the extremities of the H3-H4 dimer, suggesting a role in stabilizing the dimer in its nucleosome frame. Residues implicated in a reduced lifespan were buried in the histone handshake motif, suggesting that these mutations destabilize the octamer structure. All residues exposed on the disk and that caused lifespan extension are known to interact with Sir3. We find that substitution of H4K16 and H4H18 cause Sir3 to redistribute from telomeres and silent mating loci to secondary positions, often enriched for Rap1 or Abf1 binding sites, whereas H3E50 does not. The redistributed Sir3 cause transcriptional repression at most of the new loci, including of genes where null mutants were previously shown to extend chronological lifespan. The transcriptomic profiles of H4K16 and H4H18 mutant strains are very similar, and compatible with a DNA replication stress response. This is distinct from the transcriptomic profile of H3E50, which matches strong induction of oxidative phosphorylation. We propose that different clusters of H3 and H4 residues are involved in either binding to non-histone proteins, or in destabilizing the association of the nucleosome DNA, or disrupting binding of a H3-H4 dimer in the nucleosome, or disturbing the structural stability of the octamer, each category impacting on chronological lifespan through a different path.
2019-11-09 | GSE140160 | GEO
Project description:Structural mapping of regulatory function of histone H3 and H4 residues
| PRJNA140247 | ENA
Project description:We have performed a comprehensive analysis of the involvement of histone H3 and H4 residues in the regulation of chronological lifespan in yeast. Residues where substitution resulted in the most pronounced lifespan extension are all on the exposed face of the nucleosome, with the exception of H3E50, which is present on the lateral surface, between two DNA gyres. Other residues that had a more modest effect on lifespan extension were concentrated at the extremities of the H3-H4 dimer, suggesting a role in stabilizing the dimer in its nucleosome frame. Residues implicated in a reduced lifespan were buried in the histone handshake motif, suggesting that these mutations destabilize the octamer structure. All residues exposed on the disk and that caused lifespan extension are known to interact with Sir3. We find that substitution of H4K16 and H4H18 cause Sir3 to redistribute from telomeres and silent mating loci to secondary positions, often enriched for Rap1 or Abf1 binding sites, whereas H3E50 does not. The redistributed Sir3 cause transcriptional repression at most of the new loci, including of genes where null mutants were previously shown to extend chronological lifespan. The transcriptomic profiles of H4K16 and H4H18 mutant strains are very similar, and compatible with a DNA replication stress response. This is distinct from the transcriptomic profile of H3E50, which matches strong induction of oxidative phosphorylation. We propose that different clusters of H3 and H4 residues are involved in either binding to non-histone proteins, or in destabilizing the association of the nucleosome DNA, or disrupting binding of a H3-H4 dimer in the nucleosome, or disturbing the structural stability of the octamer, each category impacting on chronological lifespan through a different path.
2019-12-13 | GSE141973 | GEO
Project description:We have performed a comprehensive analysis of the involvement of histone H3 and H4 residues in the regulation of chronological lifespan in yeast. Residues where substitution resulted in the most pronounced lifespan extension are all on the exposed face of the nucleosome, with the exception of H3E50, which is present on the lateral surface, between two DNA gyres. Other residues that had a more modest effect on lifespan extension were concentrated at the extremities of the H3-H4 dimer, suggesting a role in stabilizing the dimer in its nucleosome frame. Residues implicated in a reduced lifespan were buried in the histone handshake motif, suggesting that these mutations destabilize the octamer structure. All residues exposed on the disk and that caused lifespan extension are known to interact with Sir3. We find that substitution of H4K16 and H4H18 cause Sir3 to redistribute from telomeres and silent mating loci to secondary positions, often enriched for Rap1 or Abf1 binding sites, whereas H3E50 does not. The redistributed Sir3 cause transcriptional repression at most of the new loci, including of genes where null mutants were previously shown to extend chronological lifespan. The transcriptomic profiles of H4K16 and H4H18 mutant strains are very similar, and compatible with a DNA replication stress response. This is distinct from the transcriptomic profile of H3E50, which matches strong induction of oxidative phosphorylation. We propose that different clusters of H3 and H4 residues are involved in either binding to non-histone proteins, or in destabilizing the association of the nucleosome DNA, or disrupting binding of a H3-H4 dimer in the nucleosome, or disturbing the structural stability of the octamer, each category impacting on chronological lifespan through a different path.
2019-12-03 | GSE141306 | GEO