Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: GSE66866
PROVIDER: PRJNA278142 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:A nucleosome turnover map reveals that the stability of histone H4 Lys20 methylation depend on histone recycling in transcribed chromatin [ChIP]
| PRJNA255375 | ENA
Project description:Nucleosome composition actively contribute to the chromatin structure and accessibility. To preserve chromatin state during replication, transcription and DNA repair, cells have evolved mechanisms to evict or recycle histones, generating a landscape of differentially aged nucleosomes. To map the stability of nucleosomes, we have adapted the recombination induced tag exchange (RITE) method to Schizosaccharomyces pombe histone H3. The RITE method allows us to study replication-independent protein turnover both through the occurrence of, in our case, new histone H3 and the disappearance or preservation of old histone H3. We contrast the RITE system to nucleosome turnover measured by chromatin incorporation of an epitope-tagged H3 under an inducible promoter. We confirm previous findings that stable nucleosomes are found at heterochromatin, but also at coding regions of actively transcribed genes. Genome-wide comparisons with several chromatin marks showed that high turnover nucleosomes correlate with H2A.Z, acetylated H4 and H3K4me2. The histones with high turnover are primarily found at the nucleosomes on the 5´and/or 3´ edges of the transcribed unit. In addition, in this study we have determined genome-wide maps of all three methylation marks at H4K20. All methylation of H4K20 appeared in low turnover nucleosomes and particularly in euchromatic regions. H4K20me1 marks stable nucleosomes at loci proximal to nucleosome depleted regions (NDR) and H4K20me2/3 were found further inside of transcribed units, especially at coding regions of long genes expressed at low levels. Further, this transcription-dependent accumulation of histone methylations was dependent on the histone chaperone complex FACT (Facilitates Chromatin Transcription), as predicited from its role in recycling nucleosomes during transcription.
2015-03-13 | GSE66865 | GEO
Project description:Nucleosome composition actively contribute to the chromatin structure and accessibility. To preserve chromatin state during replication, transcription and DNA repair, cells have evolved mechanisms to evict or recycle histones, generating a landscape of differentially aged nucleosomes. To map the stability of nucleosomes, we have adapted the recombination induced tag exchange (RITE) method to Schizosaccharomyces pombe histone H3. The RITE method allows us to study replication-independent protein turnover both through the occurrence of, in our case, new histone H3 and the disappearance or preservation of old histone H3. We contrast the RITE system to nucleosome turnover measured by chromatin incorporation of an epitope-tagged H3 under an inducible promoter. We confirm previous findings that stable nucleosomes are found at heterochromatin, but also at coding regions of actively transcribed genes. Genome-wide comparisons with several chromatin marks showed that high turnover nucleosomes correlate with H2A.Z, acetylated H4 and H3K4me2. The histones with high turnover are primarily found at the nucleosomes on the 5´and/or 3´ edges of the transcribed unit. In addition, in this study we have determined genome-wide maps of all three methylation marks at H4K20. All methylation of H4K20 appeared in low turnover nucleosomes and particularly in euchromatic regions. H4K20me1 marks stable nucleosomes at loci proximal to nucleosome depleted regions (NDR) and H4K20me2/3 were found further inside of transcribed units, especially at coding regions of long genes expressed at low levels. Further, this transcription-dependent accumulation of histone methylations was dependent on the histone chaperone complex FACT (Facilitates Chromatin Transcription), as predicited from its role in recycling nucleosomes during transcription.
2015-03-06 | GSE59461 | GEO
Project description:A striking unusual genome architecture characterizes the two related human parasitic pathogens Plasmodium falciparum and Toxoplasma gondii. A major fraction of the bulk parasite genome is packaged as transcriptionally permissive euchromatin with few loci embedded in silenced heterochromatin. Primary chromatin shapers include histone modifications at the nucleosome lateral surface close to the DNA but their mode of action remains unclear. We identify versatile modifications at Lys31 within the globular domain of histone H4 as key determinants of genome organization and expression in Apicomplexa. H4K31 acetylation promotes a relaxed chromatin state at the promoter of active genes through nucleosome disassembly in both parasites. In contrast, monomethylated H4K31 is enriched in the core body of Toxoplasma active genes but inversely correlates with transcription while being astonishingly enriched at transcriptionally inactive pericentromeric heterochromatin in Plasmodium. This is the first evidence for a methylated residue of H4 associating with transcriptional regulation likely by reducing histone turnover hence slowing RNA polymerase progression across transcribed loci.
2017-06-17 | GSE98806 | GEO
Project description:Goal of this project was the identification of chromatin interacting proteins whose binding is differentially regulated by di-methylation of lysine 20 on histone H4 (H4K20me2). To achieve this unodified and H4K20me2-modified histone H4 were generated by native chemical ligation and assembled into recombinant di-nucleosomes. The di-nucleosomes were immobilized on streptavidin-coated beads via the biotinylated di-nucleosomal DNA and used for nucleosome affinity purifications to identify proteins regulated by H4K20me2 from SILAC-labelled HeLaS3 nuclear extracts (Arg10 and Lys8). SILAC affinity purifications were carried out in "forward" (heavy extract on modified nucleosome and light extract on unmodified nucleosome) and "reverse" (light extract on modified nucleosome and heavy extract on unmodified nucleosome) label-swap experiments and protein abundances were quantified by MaxQuant.
2019-02-27 | PXD009281 | Pride
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: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:Compared to the initiation and elongation stages of transcription, the role of chromatin in transcription termination is poorly understood. Through a yeast genetic screen, we identified histone H3 and H4 substitutions that cause transcription to read through the terminator of a small noncoding gene. The substitutions map to the nucleosome DNA entry-exit site, a region that controls nucleosome stability and certain histone modifications. Genome-wide studies on the strongest mutants revealed evidence of transcription read-through of noncoding and coding genes and reduced nucleosome occupancy. Replacement of the native sequence downstream of a gene with a “superbinder” sequence that increases nucleosome occupancy in vivo increased termination efficiency and suppressed the effect of a DNA entry-exit site substitution at this locus. Our results highlight the importance of the DNA entry-exit site in maintaining the integrity of the transcriptome and suggest that nucleosomes can facilitate termination by serving as a barrier to RNA polymerase.
2020-08-10 | GSE147389 | GEO
Project description:Hda1C directly binds to actively transcribed regions likely via the interaction with elongating RNA PolII and/or with nascent RNA transcripts. The Arb2 domain of Hda1 is also critical for its binding to chromatin. Interestingly, Hda1C specifically deacetylates histone H4 but not H3 at active genes to suppress nucleosome instability and partially inhibit elongation. In contrast, Hda1C mainly deacetylates histone H3 at inactive genes to delay gene induction.
2019-07-22 | GSE121762 | GEO
Project description:Hda1C directly binds to actively transcribed regions likely via the interaction with elongating RNA PolII and/or with nascent RNA transcripts. The Arb2 domain of Hda1 is also critical for its binding to chromatin. Interestingly, Hda1C specifically deacetylates histone H4 but not H3 at active genes to suppress nucleosome instability and partially inhibit elongation. In contrast, Hda1C mainly deacetylates histone H3 at inactive genes to delay gene induction.
2019-07-22 | GSE121761 | GEO