Ontology highlight
ABSTRACT:
PROVIDER: PRJNA480011 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7478790.fastq.gz | Fastqsanger.gz | |||
| SRR7478791.fastq.gz | Fastqsanger.gz | |||
| SRR7478792.fastq.gz | Fastqsanger.gz | |||
| SRR7478793.fastq.gz | Fastqsanger.gz | |||
| SRR7478794.fastq.gz | Fastqsanger.gz |
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Project description:Newly discovered histone lysine acylations increase the functional diversity of nucleosomes well beyond acetylation. Here, we focus on histone butyrylation in the context of sperm cell differentiation. Specifically, we investigate the butyrylation of histone H4 lysine 5 and 8 at gene promoters, where acetylation guides the binding of Brdt, a bromodomain-and-extra-terminal protein, thereby mediating stage-specific gene expression programs. Genome-wide mapping data show that highly active Brdt-bound gene promoters systematically harbour competing histone acetylation and butyrylation marks at H4 K5 and K8. Histone butyrylation, despite acting as a direct stimulator of transcription, competes with acetylation, especially at H4 K5, to prevent Brdt binding. The observed in vivo H4 K5K8 acetylation butyrylation state at active promoters is reproduced in vitro where p300 indistinctly acetylates and butyrylates H4 K5 and K8. Altogether, highly active gene promoter regions are characterized by alternating H4 acetylation and butyrylation sustaining direct gene activation and a dynamic bromodomain binding.
2016-07-13 | GSE77277 | GEO
Project description:Chromatin compartments reorganize dramatically during cell cycle transitions, shifting from a compartmentalized interphase to a condensed mitotic configuration in which large-scale compartment signals are attenuated. While histone modifications are linked to compartment identity, their contribution to compartment organization remains unclear. Using meiotic (mouse spermatogenesis) and mitotic (mouse neuronal progenitor cell, mNPC) models, we mapped histone landscapes alongside compartment dynamics. We found that histone H4 lysine 16 acetylation (H4K16ac) strongly tracked compartment reorganization, remaining enriched in A compartments during compartmentalization but redistributing upon chromatin compaction. In spermatogenesis, H4K16ac loss on the X chromosome coincided with condensation and H3K9me3 spreading. Machine learning highlighted H4K16ac as a stronger predictor of compartment transitions than H3K27ac. Acute degradation of MOF, the principal H4K16ac acetyltransferase, disrupted both the spatial distribution and global abundance of H4K16ac and progressively impaired compartmentalization in mNPCs. These results position H4K16ac as a histone modification selectively coupled to chromatin compartment transitions.
2026-05-27 | GSE304211 | GEO
Project description:Chromatin compartments reorganize dramatically during cell cycle transitions, shifting from a compartmentalized interphase to a condensed mitotic configuration in which large-scale compartment signals are attenuated. While histone modifications are linked to compartment identity, their contribution to compartment organization remains unclear. Using meiotic (mouse spermatogenesis) and mitotic (mouse neuronal progenitor cell, mNPC) models, we mapped histone landscapes alongside compartment dynamics. We found that histone H4 lysine 16 acetylation (H4K16ac) strongly tracked compartment reorganization, remaining enriched in A compartments during compartmentalization but redistributing upon chromatin compaction. In spermatogenesis, H4K16ac loss on the X chromosome coincided with condensation and H3K9me3 spreading. Machine learning highlighted H4K16ac as a stronger predictor of compartment transitions than H3K27ac. Acute degradation of MOF, the principal H4K16ac acetyltransferase, disrupted both the spatial distribution and global abundance of H4K16ac and progressively impaired compartmentalization in mNPCs. These results position H4K16ac as a histone modification selectively coupled to chromatin compartment transitions.
2026-05-27 | GSE299092 | GEO
Project description:Chromatin compartments reorganize dramatically during cell cycle transitions, shifting from a compartmentalized interphase to a condensed mitotic configuration in which large-scale compartment signals are attenuated. While histone modifications are linked to compartment identity, their contribution to compartment organization remains unclear. Using meiotic (mouse spermatogenesis) and mitotic (mouse neuronal progenitor cell, mNPC) models, we mapped histone landscapes alongside compartment dynamics. We found that histone H4 lysine 16 acetylation (H4K16ac) strongly tracked compartment reorganization, remaining enriched in A compartments during compartmentalization but redistributing upon chromatin compaction. In spermatogenesis, H4K16ac loss on the X chromosome coincided with condensation and H3K9me3 spreading. Machine learning highlighted H4K16ac as a stronger predictor of compartment transitions than H3K27ac. Acute degradation of MOF, the principal H4K16ac acetyltransferase, disrupted both the spatial distribution and global abundance of H4K16ac and progressively impaired compartmentalization in mNPCs. These results position H4K16ac as a histone modification selectively coupled to chromatin compartment transitions.
2026-05-27 | GSE299090 | GEO
Project description:Chromatin compartments reorganize dramatically during cell cycle transitions, shifting from a compartmentalized interphase to a condensed mitotic configuration in which large-scale compartment signals are attenuated. While histone modifications are linked to compartment identity, their contribution to compartment organization remains unclear. Using meiotic (mouse spermatogenesis) and mitotic (mouse neuronal progenitor cell, mNPC) models, we mapped histone landscapes alongside compartment dynamics. We found that histone H4 lysine 16 acetylation (H4K16ac) strongly tracked compartment reorganization, remaining enriched in A compartments during compartmentalization but redistributing upon chromatin compaction. In spermatogenesis, H4K16ac loss on the X chromosome coincided with condensation and H3K9me3 spreading. Machine learning highlighted H4K16ac as a stronger predictor of compartment transitions than H3K27ac. Acute degradation of MOF, the principal H4K16ac acetyltransferase, disrupted both the spatial distribution and global abundance of H4K16ac and progressively impaired compartmentalization in mNPCs. These results position H4K16ac as a histone modification selectively coupled to chromatin compartment transitions.
2026-05-27 | GSE332824 | GEO
Project description:The Mediator complex transmits activation signals from DNA bound transcription factors to the core transcription machinery. Genome wide localization studies have demonstrated that Mediator occupancy not only correlates with high levels of transcription, but that the complex also is present at transcriptionally silenced locations. We provide evidence that Mediator localization is guided by an interaction with histone tails, and that this interaction is regulated by their post-translational modifications. A quantitative, high-density genetic interaction map revealed links between Mediator components and factors affecting chromatin structure, especially histone deacetylases. Peptide binding assays demonstrated that pure wild type Mediator forms stable complexes with the tails of Histone H3 and H4. These binding assays also showed Mediator – histone H4 peptide interactions are specifically inhibited by acetylation of the histone H4 lysine 16, a residue critical in transcriptional silencing. Finally, these findings were validated by tiling array analysis, that revealed a broad correlation between Mediator and nucleosome occupancy in vivo, but a negative correlation between Mediator and nucleosomes acetylated at histone H4 lysine 16. Our studies show that chromatin structure and the acetylation state of histones are intimately connected to Mediator localization. Med8-TAP strain ChIPed with IgG beads vs. Input in Saccharomyces cerevisiae
2011-11-22 | E-GEOD-28613 | biostudies-arrayexpress
Project description:Chromatin compartments reorganize dramatically during cell cycle transitions, shifting from a compartmentalized interphase organization to a condensed mitotic configuration in which large-scale compartment signals are attenuated. While histone modifications are linked to compartment identity, their causal contribution to compartment organization remained unclear. Using meiotic (mouse spermatogenesis) and mitotic (mouse neuronal progenitor cells, mNPCs) models, we mapped histone landscapes alongside compartment dynamics. We found that histone H4 lysine 16 acetylation (H4K16ac) strongly tracked compartment reorganization, remaining enriched in A compartments during compartmentalization but redistributing upon chromatin compaction. In spermatogenesis, H4K16ac loss on the X chromosome coincided with condensation and H3K9me3 spreading. Machine learning highlighted H4K16ac as a stronger predictor of compartment transitions than H3K27ac. To probe causality, we acutely degraded MOF, the principal H4K16ac acetyltransferase, which disrupted both the spatial distribution and global abundance of H4K16ac and progressively impaired compartmentalization in mNPCs. Together, these results position H4K16ac as a selectively coupled and influential histone modification of chromatin compartment transitions.
2026-05-27 | GSE332823 | GEO
Project description:The Mediator complex transmits activation signals from DNA bound transcription factors to the core transcription machinery. Genome wide localization studies have demonstrated that Mediator occupancy not only correlates with high levels of transcription, but that the complex also is present at transcriptionally silenced locations. We provide evidence that Mediator localization is guided by an interaction with histone tails, and that this interaction is regulated by their post-translational modifications. A quantitative, high-density genetic interaction map revealed links between Mediator components and factors affecting chromatin structure, especially histone deacetylases. Peptide binding assays demonstrated that pure wild type Mediator forms stable complexes with the tails of Histone H3 and H4. These binding assays also showed Mediator – histone H4 peptide interactions are specifically inhibited by acetylation of the histone H4 lysine 16, a residue critical in transcriptional silencing. Finally, these findings were validated by tiling array analysis, that revealed a broad correlation between Mediator and nucleosome occupancy in vivo, but a negative correlation between Mediator and nucleosomes acetylated at histone H4 lysine 16. Our studies show that chromatin structure and the acetylation state of histones are intimately connected to Mediator localization.
2011-11-22 | GSE28613 | GEO
Project description:Intergenerationally maintained Histone H4 lysine 16 acetylation is instructive for future gene activation
| PRJNA535511 | ENA
Project description:The histone acetyltransferase Sas2 is part of the SAS-I complex and acetylates lysine 16 of histone H4 (H4 K16Ac) in the genome of Saccharomyces cerevisiae. Sas2-mediated H4 K16Ac is strongest over the coding region of genes with low expression. However, it is unclear how Sas2-mediated acetylation is incorporated into chromatin. Our previous work has shown physical interactions of SAS with the histone chaperones CAF-I and Asf1, suggesting a link between SAS-I mediated acetylation and chromatin assembly. Here, we find that Sas2-dependent H4 K16Ac in bulk histones requires passage of the cells through the S-phase of the cell cycle, and the rate of increase in H4 K16Ac depends on both CAF-I and Asf1, whereas steady-state levels and genome-wide distribution of H4 K16Ac shows only mild changes in their absence. Furthermore, H4 K16Ac is deposited in chromatin at genes upon repression, and this deposition requires the histone chaperone Spt6, but not CAF-I, Asf1, HIR or Rtt106. Altogether, our data indicate that Spt6 controls H4 K16Ac levels by incorporating K16-unacetylated H4 in strongly transcribed genes. Upon repression, Spt6 association is decreased, resulting in less deposition of K16-unacetylated and therefore in a concomitant increase of H4 K16Ac that is recycled during transcription.
2015-09-14 | E-MTAB-2638 | biostudies-arrayexpress