Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA151369 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR400537.fastq.gz | Fastqsanger.gz | |||
| SRR400538.fastq.gz | Fastqsanger.gz | |||
| SRR400539.fastq.gz | Fastqsanger.gz | |||
| SRR400540.fastq.gz | Fastqsanger.gz | |||
| SRR400541.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 8 |
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Project description:Background. The histone variant H3.3 plays key roles in regulating chromatin states and transcription. However, the role of endogenous H3.3 in mammalian cells and during development has been less thoroughly investigated. To address this gap, we report the production and phenotypic analysis of mice and cells with targeted disruption of the H3.3-encoding gene, H3f3b. Results. H3f3b KO mice exhibit a semi-lethal phenotype traceable at least in part to defective cell division and chromosome segregation. H3f3b KO cells have widespread ectopic CENP-A protein localization suggesting one possible mechanism for defective chromosome segregation. KO cells have abnormal karyotypes and cell cycle profiles as well. The transcriptome and euchromatin-related epigenome were moderately affected by loss of H3f3b in MEFs with ontology most notably pointing to changes in chromatin regulatory and histone coding genes. Reduced numbers of H3f3b KO mice survive to maturity and almost all survivors from both sexes are infertile. Conclusions. Taken together, our studies suggest that endogenous mammalian histone H3.3 has important roles in regulating chromatin and chromosome functions that in turn are important for cell division, genome integrity, and development. Examination of H3K9Ac and H3K4me3 in wild-type and H3.3 null MEFs
2013-04-24 | E-GEOD-34546 | biostudies-arrayexpress
Project description:Background. The histone variant H3.3 plays key roles in regulating chromatin states and transcription. However, the role of endogenous H3.3 in mammalian cells and during development has been less thoroughly investigated. To address this gap, we report the production and phenotypic analysis of mice and cells with targeted disruption of the H3.3-encoding gene, H3f3b. Results. H3f3b KO mice exhibit a semi-lethal phenotype traceable at least in part to defective cell division and chromosome segregation. H3f3b KO cells have widespread ectopic CENP-A protein localization suggesting one possible mechanism for defective chromosome segregation. KO cells have abnormal karyotypes and cell cycle profiles as well. The transcriptome and euchromatin-related epigenome were moderately affected by loss of H3f3b in MEFs with ontology most notably pointing to changes in chromatin regulatory and histone coding genes. Reduced numbers of H3f3b KO mice survive to maturity and almost all survivors from both sexes are infertile. Conclusions. Taken together, our studies suggest that endogenous mammalian histone H3.3 has important roles in regulating chromatin and chromosome functions that in turn are important for cell division, genome integrity, and development.
2013-04-24 | GSE34546 | GEO
Project description:The closely related replicative H3 and non-replicative H3.3 variants show specific requirement during development in vertebrates. Whether it involves distinct mode of deposition or unique roles once incorporated into chromatin remains unclear. To disentangle the two aspects, we took advantage of the Xenopus early development combined with chromatin assays. We systematically mutated H3.3 at each four residues that differ from H3.2 and tested their ability to rescue developmental defects due to endogenous H3.3 depletion. Surprisingly, all H3.3 mutated variants functionally complemented endogenous H3.3, regardless of their incorporation pathways, except for one residue, the serine at position 31. The phosphorylation at this unique residue occurs onto chromatin with a peak in late mitosis, and depends on the networks of cell cycle kinases. Notably, while the alanine substitution failed to rescue H3.3 depletion, a phosphomimic residue sufficed. Based on proteomics studies with histone peptides and Xenopus extracts, we find that the phosphomimic histone mutant attracts transcription related factors. Furthermore, we evidence a crosstalk whereby phosphorylation on H3.3S31 favors H3.3K27ac. At gastrulation, we conclude that the critical importance of the H3.3S31 residue is independent of the variant incorporation pathway. It rather reflects a signaling role engaging key binding partners and crosstalks on neighboring amino acids. We discuss how this single evolutionary conserved residue conveys both in interphase and mitosis unique properties for this variant in vertebrates during cell cycle and cell fate commitment.
2020-03-13 | PXD016497 | Pride
Project description:Replication-independent deposition of histone variant H3.3 into chromatin is essential for many biological processes, including development, oogenesis and nuclear reprogramming. Unlike replication-dependent H3.1/2 isoforms, H3.3 is expressed throughout the cell cycle and becomes enriched in postmitotic cells with age. However, lifelong dynamics of H3 variant replacement and the impact of this process on chromatin organization remain largely undefined. To address this, we investigated genome-wide changes in histone H3 variants composition and H3 modification abundances throughout the lifespan in mice using quantitative mass spectrometry (MS) – based middle-down proteomics strategy. Using middle-down MS we demonstrate that H3.3 accumulates in the chromatin of various somatic mouse tissues throughout life, resulting in near complete replacement of H3.1/2 isoforms by the late adulthood. Accumulation of H3.3 is associated with profound changes in the global level of H3 methylation. H3.3-containing chromatin exhibits distinct stable levels of H3R17me2 and H3K36me2, different from those on H3.1/H3.2-containing chromatin, indicating a direct link between H3 variant exchange and histone methylation dynamics with age. In summary, our study provides the first time comprehensive characterization of dynamic changes in the H3 modification landscape during mouse lifespan and links these changes to the age-dependent accumulation of histone variant H3.3.
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Project description:Histone H3.3 maintains genome integrity during mammalian development
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Project description:Endogenous retroviruses (ERVs) have provided an evolutionary advantage in the diversification of transcript regulation and are thought to be involved in the establishment of extraembryonic tissues during development. However, silencing of these elements remains critical for the maintenance of genome stability. Here, we define a new chromatin state that is uniquely characterized by the combination of the histone variant H3.3 and H3K9me3, two chromatin ‘marks’ that have previously been considered to belong to fundamentally opposing chromatin states. H3.3/H3K9me3 heterochromatin is fundamentally distinct from ‘canonical’ H3K9me3 heterochromatin that has been under study for decades and this unique functional interplay of a histone variant and a repressive histone mark is crucial for silencing ERVs in ESCs. Our study solidifies the emerging notion that H3.3 is not a histone variant associated exclusively with “active” chromatin and further suggests that its incorporation at unique heterochromatic regions may be central to its function during development and the maintenance of genome stability. RNA-seq analysis of three embryonic stem cell lines WT, H3.3 KO1, and H3.3 KO2)
2015-05-05 | E-GEOD-59104 | biostudies-arrayexpress
Project description:The acquisition of germination and post-embryonic developmental ability during seed maturation is vital for seed vigor, an important trait for plant propagation and crop production. How seed vigor is established in seeds is still poorly understood. Here, we report the crucial function of Arabidopsis histone variant H3.3 in chromatin structure regulation that endows seeds with post-embryonic developmental potentials. H3.3 is not essential for seed formation, but the loss of H3.3 results in severely impaired germination and post-embryonic development. H3.3 exhibits a seed-specific 5’ gene end distribution, which facilities chromatin opening in seeds. During germination, this H3.3-established chromatin accessibility is essential for proper gene transcriptional regulation. Moreover, H3.3 is constantly loaded at the 3’ gene end and restricts chromatin accessibility to prevent cryptic transcription and protect gene body DNA methylation. Our results suggest a fundamental role of H3.3 in initiating chromatin opening at regulatory regions in seed to license the embryonic to post-embryonic transition.
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Project description:The acquisition of germination and post-embryonic developmental ability during seed maturation is vital for seed vigor, an important trait for plant propagation and crop production. How seed vigor is established in seeds is still poorly understood. Here, we report the crucial function of Arabidopsis histone variant H3.3 in chromatin structure regulation that endows seeds with post-embryonic developmental potentials. H3.3 is not essential for seed formation, but the loss of H3.3 results in severely impaired germination and post-embryonic development. H3.3 exhibits a seed-specific 5’ gene end distribution, which facilities chromatin opening in seeds. During germination, this H3.3-established chromatin accessibility is essential for proper gene transcriptional regulation. Moreover, H3.3 is constantly loaded at the 3’ gene end and restricts chromatin accessibility to prevent cryptic transcription and protect gene body DNA methylation. Our results suggest a fundamental role of H3.3 in initiating chromatin opening at regulatory regions in seed to license the embryonic to post-embryonic transition.
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Project description:The acquisition of germination and post-embryonic developmental ability during seed maturation is vital for seed vigor, an important trait for plant propagation and crop production. How seed vigor is established in seeds is still poorly understood. Here, we report the crucial function of Arabidopsis histone variant H3.3 in chromatin structure regulation that endows seeds with post-embryonic developmental potentials. H3.3 is not essential for seed formation, but the loss of H3.3 results in severely impaired germination and post-embryonic development. H3.3 exhibits a seed-specific 5’ gene end distribution, which facilities chromatin opening in seeds. During germination, this H3.3-established chromatin accessibility is essential for proper gene transcriptional regulation. Moreover, H3.3 is constantly loaded at the 3’ gene end and restricts chromatin accessibility to prevent cryptic transcription and protect gene body DNA methylation. Our results suggest a fundamental role of H3.3 in initiating chromatin opening at regulatory regions in seed to license the embryonic to post-embryonic transition.
2022-12-01 | GSE209638 | GEO
Project description:The acquisition of germination and post-embryonic developmental ability during seed maturation is vital for seed vigor, an important trait for plant propagation and crop production. How seed vigor is established in seeds is still poorly understood. Here, we report the crucial function of Arabidopsis histone variant H3.3 in chromatin structure regulation that endows seeds with post-embryonic developmental potentials. H3.3 is not essential for seed formation, but the loss of H3.3 results in severely impaired germination and post-embryonic development. H3.3 exhibits a seed-specific 5’ gene end distribution, which facilities chromatin opening in seeds. During germination, this H3.3-established chromatin accessibility is essential for proper gene transcriptional regulation. Moreover, H3.3 is constantly loaded at the 3’ gene end and restricts chromatin accessibility to prevent cryptic transcription and protect gene body DNA methylation. Our results suggest a fundamental role of H3.3 in initiating chromatin opening at regulatory regions in seed to license the embryonic to post-embryonic transition.
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