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Transcriptome analysis of Atasf1 mutants in comparison with wild type.

ABSTRACT: ASF1 is a conserved histone chaperone with affinity to histone H3-H4. Arabidopsis thaliana genome encodes two ASF1 homologues, which play redundant roles in S-phase progression and cell proliferation in plant development. Here, in an attempt to obtain the knowledge of ASF1 role in transcriptional regulation, we perform the transcriptome analysis of each asf1 single mutant (Atasf1a and Atasf1b) as well as Atasf1ab double mutant in comparison with wild type (WT).

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE48854 | GEO | 2013/12/31

SECONDARY ACCESSION(S): PRJNA212006

REPOSITORIES: GEO

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Transcriptome analysis of Atasf1 mutants in comparison with wild type.

Project description:ASF1 is a conserved histone chaperone with affinity to histone H3-H4. Arabidopsis thaliana genome encodes two ASF1 homologues, which play redundant roles in S-phase progression and cell proliferation in plant development. Here, in an attempt to obtain the knowledge of ASF1 role in transcriptional regulation, we perform the transcriptome analysis of each asf1 single mutant (Atasf1a and Atasf1b) as well as Atasf1ab double mutant in comparison with wild type (WT). 12-day-old seedlings of wild-type (WT), each single mutants and double mutant grown in normal growth condition were used for RNA extraction and microarray. Duplicate samples were analyzed.

2013-12-31 | E-GEOD-48854 | biostudies-arrayexpress

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Project description:The evolutionarily conserved HIRA/Hir histone chaperone complex and ASF1/Asf1 co-chaperone cooperate for replication-independent chromatin assembly. Here we report the molecular architecture of the Hir complex with Asf1/H3/H4 via single-particle cryo-EM and crosslinking mass spectrometry.

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A link between Sas2-mediated H4 K16 acetylation, chromatin assembly in S-phase by CAF-I and Asf1, and nucleosome assembly by Spt6 during transcription

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.

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DAXX adds a de novo H3.3K9me3 deposition pathway to the histone chaperone network (part 1)

Project description:A multitude of histone chaperones are required to support histones from their biosynthesis until DNA deposition. They cooperate through the formation of histone co-chaperone complexes, but the crosstalk between nucleosome assembly pathways remains enigmatic. Using exploratory interactomics, we define the interplay between histone H3–H4 chaperones in the histone chaperone network. We identify several novel histone dependent complexes and predict the structure of the ASF1 and SPT2 co-chaperone complex, expanding the role of ASF1 in histone dynamics. We show that DAXX provides a unique functionality to the histone chaperone network, recruiting histone methyltransferases to promote H3K9me3 catalysis on new histone H3.3–H4 prior to deposition onto DNA. Hereby, DAXX provides a molecular mechanism for de novo H3K9me3 deposition and heterochromatin assembly. Collectively, our findings provide a framework for understanding how cells orchestrate histone supply and employ targeted deposition of modified histones to underpin specialized chromatin states.

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DAXX adds a de novo H3.3K9me3 deposition pathway to the histone chaperone network (part 2)

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Histone chaperone ASF1 mediates H3.3-H4 deposition in Arabidopsis

Project description:Histone chaperone ASF1 mediates H3.3-H4 deposition in Arabidopsis

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Hi-C analysis of the Sordaria macrospora wild type and developmental mutant delta-asf1 [HiC]

Project description:Chromatin organization of the wild type and delta-asf1 mutant of the filamentous ascomycete Sordaria macrospora was analyzed by Hi-C. The delta-asf1 mutant lacks the conserved histone chaperone ASF1 and is unable to produce sexual fruiting bodies. It was hypothesized that the lack of the histone chaperone ASF1 in the mutant might lead to differences in short- or long-distance interactions of chromatin. Furthermore, it was hypothesized that chromatin organization might change during sexual development in the wild type as a prerequisite for the drastic transcriptome changes during development that were observed in earlier studies.

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ChIP-seq analysis of the Sordaria macrospora wild type and the developmental mutant delta-asf1

Project description:Genome-wide distribtuion of histone H3K56ac (histone H3 acetylated at lysine 56) was analyzed in the wild type and the sterile mutant asf1. The asf1 gene encodes a conserved histone chaperone, and preliminary experimentes indicated changes in histone modifications in the mutant that were analyzed on a genome-wide basis in these experiments.

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ChIP-seq analysis of the Sordaria macrospora wild type and the developmental mutant delta-asf1 [ChIP-seq]

Project description:Genome-wide distribtuion of histone H3 and H3K27me3 (histone H3 tri-methylated at lysine 27) was analyzed in the wild type and the sterile mutant asf1. The asf1 gene encodes a conserved histone chaperone, and preliminary experimentes indicated changes in histone modifications in the mutant that were analyzed on a genome-wide basis in these experiments.

2023-11-20 | GSE216629 | GEO

Histone chaperone ASF1 mediates H3.3-H4 deposition in Arabidopsis

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

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