Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA285041 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Retrotransposons are widely spread in the mammalian genome and are usually silenced during development to avoid transposition-inducing mutations. But how they are repressed in embryos shortly before implantation remain to be identified, since the genome at this stage is globally hypomethylated. Here we show a histone chaperon, CAF-1, is responsible for retrotransposon silencing at the morula-blastocyst stages by depositing histone H4 lysine 20 trimethylation (H4K20me3). Knockdown of CAF-1 with a specific siRNA resulted in derepression of LINE-1, SINE-B2 and IAP associated with the decreased H4K20me3 level, and arrested embryonic development at the morula stage. The identical results were obtained with siRNAs against Suv420h1/2, H4K20 methyltransferases. Treatment with reverse transcriptase inhibitors rescued at least a part of these embryos. Thus, CAF-1 ensures the genomic integrity of preimplantation embryos by establishing repressive histone marks in the multiple retrotransposon classes. Comparative gene expression analyses using P150 knockdown (P150KD) embryos at morula stage were performed by microarray. P150KD embryos were produced with the injection of P150 siRNA into 1-cell embryos. As controls, siControl embryos were produced by the injection of control siRNA. These embryos were subjected to gene expression microarray.
2015-11-01 | E-GEOD-69260 | biostudies-arrayexpress
Project description:Retrotransposons are widely spread in the mammalian genome and are usually silenced during development to avoid transposition-inducing mutations. But how they are repressed in embryos shortly before implantation remain to be identified, since the genome at this stage is globally hypomethylated. Here we show a histone chaperon, CAF-1, is responsible for retrotransposon silencing at the morula-blastocyst stages by depositing histone H4 lysine 20 trimethylation (H4K20me3). Knockdown of CAF-1 with a specific siRNA resulted in derepression of LINE-1, SINE-B2 and IAP associated with the decreased H4K20me3 level, and arrested embryonic development at the morula stage. The identical results were obtained with siRNAs against Suv420h1/2, H4K20 methyltransferases. Treatment with reverse transcriptase inhibitors rescued at least a part of these embryos. Thus, CAF-1 ensures the genomic integrity of preimplantation embryos by establishing repressive histone marks in the multiple retrotransposon classes.
2015-11-01 | GSE69260 | GEO
Project description:Histone chaperones and chromatin remodelers control nucleosome dynamics, essential for transcription, replication, and DNA repair. The histone chaperone Anti-Silencing Factor 1 (ASF1) plays a central role in facilitating CAF-1-mediated replication-dependent H3.1 deposition and HIRA-mediated replication-independent H3.3 deposition in yeast and metazoans. Whether ASF1 function is evolutionarily conserved in plants is unknown. Here, we show that Arabidopsis ASF1 proteins display an exclusive preference for the H3.3-depositing HIRA complex. Simultaneous mutation of both Arabidopsis ASF1 genes caused a decrease in chromatin density and ectopic H3.1 occupancy at loci typically enriched with H3.3. Genetic, transcriptomic, and proteomic data indicate that ASF1 proteins strongly prefer the HIRA complex over CAF-1. asf1 mutants also displayed an increase in spurious Pol II transcriptional initiation, and showed defects in the maintenance of gene body CG DNA methylation and in the distribution of histone modifications. Furthermore, ectopic targeting of ASF1 caused excessive histone deposition, less accessible chromatin, and gene silencing. These findings reveal the importance of ASF1-mediated H3.3-H4 deposition via the HIRA pathway for proper epigenetic regulation of the genome.
2022-10-31 | PXD035578 | Pride
Project description:Histone chaperones and chromatin remodelers control nucleosome dynamics, which are essential for transcription, replication, and DNA repair. The histone chaperone Anti-Silencing Factor 1 (ASF1) plays a central role in facilitating CAF-1-mediated replication-dependent H3.1 deposition and HIRA-mediated replication-independent H3.3 deposition in yeast and metazoans. Whether ASF1 function is evolutionarily conserved in plants is unknown. Here, we show that Arabidopsis ASF1 proteins display a preference for the HIRA complex. Simultaneous mutation of both Arabidopsis ASF1 genes caused a decrease in chromatin density and ectopic H3.1 occupancy at loci typically enriched with H3.3. Genetic, transcriptomic, and proteomic data indicate that ASF1 proteins strongly prefers the HIRA complex over CAF-1. asf1 mutants also displayed an increase in spurious Pol II transcriptional initiation and showed defects in the maintenance of gene body CG DNA methylation and in the distribution of histone modifications. Furthermore, ectopic targeting of ASF1 caused excessive histone deposition, less accessible chromatin, and gene silencing. These findings reveal the importance of ASF1-mediated histone deposition for proper epigenetic regulation of the genome.
2022-10-27 | GSE188493 | GEO
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
Project description:Histones are the protein components of the basic unit of chromatin, the core particle of the nucleosome. They play a central role in defining chromatin states associated with distinct cell fates and are classified into replicative and non-replicative/replacement histone variants. While the latter do not exhibit S phase regulation in their expression, the replicative histone variants show a major peak in expression early during S phase to support chromatin assembly during replication of the genome. Their expression is tightly regulated during the cell-cycle both transcriptionally and post-transcriptionally and involves a number of actors. During replication in human cells, two main chaperones ensure the deposition of H3-H4 onto DNA: Chromatin assembly factor 1 (CAF-1) and Anti-silencing factor 1 (ASF1). Interestingly, on the one hand, ASF1 binds the newly synthesized replicative histones H3.1/H3.2-H4 to hand them off to the downstream chaperone, CAF-1, for deposition onto the duplicated DNA strands in a DNA synthesis-coupled (DSC) manner. On the other hand, ASF1 also promotes the recycling of parental histones during replication. In addition, ASF1 binds the non-replicative variant H3.3 and hands it off to the downstream chaperone Histone regulator A (HIRA) for deposition of H3.3 in a DNA synthesis independent (DSI) manner. Finally, in human cells, ASF1 but not CAF-1, also provides a buffering system for histone excess generated in response to stalled replication, indicating yet another role for ASF1 in regulating the flow of replicative histones in higher eukaryotes. However, to date, roles of these chaperones in histone RNA metabolism in mammals had remained unexplored. This is particularly interesting to consider given that in budding yeast, where there are no distinct replicative and non-replicative H3 variants, the single ASF1 ortholog participates in activating transcription of histone genes in S phase and transcriptional repression outside S phase in combination with Hir1, the budding yeast counterpart of HIRA. We thus decided to explore how the key histone chaperones involved in DNA synthesis-coupled chromatin assembly could contribute to the critical regulation of expression of replicative histone genes in human cells during S phase. From total RNA extracted from asynchronous and synchronized human cells, we performed RNA-seq and found that most of the annotated replicative histone genes decreased in expression upon ASF1 depletion by siRNA during S phase compared to the control condition with siRNA againt GFP. However, by 4sU-labeled RNA-seq we detected an increase in newly synthesized replicative histone transcripts. These findings indicate that the decrease in expression of replicative histone genes in ASF1-depleted cells cannot be due to a decrease at the level of transcription. We then inspected closely the sequences at the 3’ end of the replicative histone transcripts in our RNA-seq data and detected a defect of their 3’ processing. Thus, we propose that in mammals ASF1 plays a role in the unique regulation of replicative histone RNA metabolism.
2023-11-29 | E-MTAB-12501 | biostudies-arrayexpress
Project description:The assembly of nucleosomes by histone chaperones is an important component of transcriptional regulation. Here we have assessed the global roles of the S. pombe HIRA histone chaperone complex. Microarray analysis indicates that inactivation of the HIRA complex results in increased expression of at least 4% of fission yeast genes. HIRA-regulated genes overlap with those which are normally repressed in vegetatively growing cells, such as targets of the Clr6 histone deacetylase and silenced genes located in subtelomeric regions. HIRA is also required for silencing of all 13 intact copies of the Tf2 long terminal repeat (LTR) retrotransposon. However, the role of HIRA is not restricted to bona fide promoters, because it also suppresses non-coding transcripts from solo LTR elements and spurious antisense transcripts from cryptic promoters associated with transcribed regions. Furthermore, the HIRA complex is essential in the absence of the quality control provided by nuclear exosome-mediated degradation of illegitimate transcripts. This suggests that HIRA restricts genomic accessibility, and, consistent with this, the chromosomes of cells lacking HIRA are more susceptible to genotoxic agents that cause double strand breaks. Thus the HIRA histone chaperone is required to maintain the protective functions of chromatin.
2009-07-22 | E-MTAB-130 | biostudies-arrayexpress
Project description:Correct localization of the centromeric histone variant CenH3/CENP-A/Cse4 is an important part of faithful chromosome segregation. Mislocalization of CenH3 could lead to ectopic centromere formation and missegregation, and could affect DNA replication and transcription. CENP-A is often overexpressed and mislocalized in cancer genomes, but the underlying mechanisms are not understood. One major regulator of Cse4 deposition is Psh1, an E3 ubiquitin ligase that controls levels of Cse4 to prevent deposition into noncentromeric regions. We present evidence that Chromatin assembly factor-1 (CAF-1), an evolutionarily conserved histone H3/H4 chaperone shown previously to interact with CenH3 in flies and human cells, regulates Cse4 deposition in budding yeast. Yeast CAF-1 (yCAF-1) is a heterotrimeric protein complex consisting of CAC1, CAC2, and CAC3, which interacts with Cse4, and can assemble Cse4 nucleosomes in vitro. yCAF-1 regulates the stability of both soluble and chromatin associated Cse4. Loss of yCAF-1 can rescue growth defects and changes in gene expression associated with Cse4 deposition that occur in the absence of Psh1-mediated proteolysis. Incorporation of Cse4 into promoter nucleosomes at transcriptionally active genes depends on yCAF-1. Overall our findings suggest CAF-1 can act as a CenH3 chaperone, regulating levels and incorporation of CenH3 in chromatin. Furthermore, the misincorporation of CenH3 at promoter regions may have negative consequences for gene expression.
2017-09-01 | GSE98396 | GEO
Project description:Correct localization of the centromeric histone variant CenH3/CENP-A/Cse4 is an important part of faithful chromosome segregation. Mislocalization of CenH3 could lead to ectopic centromere formation and missegregation, and could affect DNA replication and transcription. CENP-A is often overexpressed and mislocalized in cancer genomes, but the underlying mechanisms are not understood. One major regulator of Cse4 deposition is Psh1, an E3 ubiquitin ligase that controls levels of Cse4 to prevent deposition into noncentromeric regions. We present evidence that Chromatin assembly factor-1 (CAF-1), an evolutionarily conserved histone H3/H4 chaperone shown previously to interact with CenH3 in flies and human cells, regulates Cse4 deposition in budding yeast. Yeast CAF-1 (yCAF-1) is a heterotrimeric protein complex consisting of CAC1, CAC2, and CAC3, which interacts with Cse4, and can assemble Cse4 nucleosomes in vitro. yCAF-1 regulates the stability of both soluble and chromatin associated Cse4. Loss of yCAF-1 can rescue growth defects and changes in gene expression associated with Cse4 deposition that occur in the absence of Psh1-mediated proteolysis. Incorporation of Cse4 into promoter nucleosomes at transcriptionally active genes depends on yCAF-1. Overall our findings suggest CAF-1 can act as a CenH3 chaperone, regulating levels and incorporation of CenH3 in chromatin. Furthermore, the misincorporation of CenH3 at promoter regions may have negative consequences for gene expression.
2017-09-01 | GSE98395 | GEO
Project description:The transcriptional repression of alternative lineage genes is critical for cell fate commitment. Mechanisms by which locus-specific gene silencing is initiated and heritably maintained during cell division are not clearly understood. To study the maintenance of silent gene states, we investigated how the Cd4 gene is stably repressed in CD8+ T cells. Through CRISPR and shRNA screening, we identified the histone chaperone CAF-1 as a critical component for Cd4 repression. We found that the large subunit of CAF-1, Chaf1a, requires the N-terminal KER domain to associate with the histone deacetylases HDAC1/2 and the histone demethylase LSD1, enzymes that also participate in Cd4 silencing. When CAF-1 was lacking, Cd4 derepression was markedly enhanced in the absence of the de novo DNA methyltransferase Dnmt3a, but not the maintenance DNA methyltransferase Dnmt1. In contrast to Dnmt1, Dnmt3a deficiency did not significantly alter levels of DNA methylation at the Cd4 locus. Instead, Dnmt3a deficiency sensitized CD8+ T cells to Cd4 derepression mediated by compromised functions of histone modifying factors, including the enzymes associated with CAF-1. Thus, we propose that the heritable silencing of the Cd4 gene in CD8+ T cells exploits cooperative functions among the DNA methyltransferases, CAF-1, and histone modifying enzymes.
2019-03-14 | GSE128245 | GEO