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Comprehensive analysis of the SWR1 complex reveals the coupling of H2A.Z deposition with nucleosome sliding in Arabidopsis [ChIP-Seq]

ABSTRACT: We identified three classes of previously uncharacterized plant-specific SWR1 components: MBD9, TRA1a/1b and CHR11/17. We found that CHR11/17 were recruited to the SWR1 complex and facilitate the coupling of H2A.Z deposition with nucleosome sliding, thereby co-regulating gene expression, development, and flowering time.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE139459 | GEO | 2019/10/29

REPOSITORIES: GEO

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Comprehensive analysis of the SWR1 complex reveals the coupling of H2A.Z deposition with nucleosome sliding in Arabidopsis [MNase-Seq]

Project description:We identified three classes of previously uncharacterized plant-specific SWR1 components: MBD9, TRA1a/1b and CHR11/17. We found that CHR11/17 were recruited to the SWR1 complex and facilitate the coupling of H2A.Z deposition with nucleosome sliding, thereby co-regulating gene expression, development, and flowering time.

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Comprehensive analysis of the SWR1 complex reveals the coupling of H2A.Z deposition with nucleosome sliding in Arabidopsis [RNA-Seq]

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Project description:Deposition of histone variant H2A.Z by the SWR1 chromatin-remodeling complex is critical for the appropriate expression of many genes in eukaryotes, yet, despite its importance, the composition of the Arabidopsis SWR1 complex has not been thoroughly analyzed. Here we have identified the interacting partners of a conserved Arabidopsis SWR1 subunit, actin-related protein 6 (ARP6). We isolated 9 predicted components, identifying subunits implicated in histone acetylation and interacting partners implicated in chromatin biology. We found that the methyl-CpG-binding domain 9 (MBD9) subunit functioned synergistically with ARP6 to control flowering time. MBD9, in combination with ARP6, was involved in the SWR1-mediated incorporation of the majority of H2A.Z. MBD6 was further required for deposition of H2A.Z at a distinct subset of loci. MBD9 was preferentially bound to nucleosome-depleted regions at the 5’ of genes containing high levels of activating histone marks. Our data suggests a model for MBD9 in recruiting the SWR1 complex to open chromatin of actively transcribing genes.

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Comprehensive analysis of the SWR1 complex reveals the coupling of H2A.Z deposition with nucleosome sliding in Arabidopsis

Project description:Comprehensive analysis of the SWR1 complex reveals the coupling of H2A.Z deposition with nucleosome sliding in Arabidopsis

| PRJNA579912 | ENA

Methyl-CpG-binding domain 9 (MBD9) is required for H2A.Z incorporation into chromatin at a subset of H2A.Z-enriched regions in the Arabidopsis genome

Project description:The SWR1 chromatin remodeling complex, which deposits the histone variant H2A.Z into nucleosomes, has been characterized in yeast and animals but had not been purified from plants. We used the conserved SWR1 subunit ACTIN RELATED PROTEIN 6 (ARP6) as bait in tandem affinity purification experiments to isolate associated proteins from Arabidopsis thaliana. We identified all 11 subunits found in yeast SWR1 and the homologous mammalian SRCAP complexes, demonstrating that this complex is conserved in plants. We also identified several additional proteins not previously associated with SWR1, including Methyl-CpG-BINDING DOMAIN 9 (MBD9). Since mbd9 mutant plants were phenotypically similar to arp6 mutants, we further explored a potential role for MBD9 in H2A.Z deposition. We found that MBD9 is required for proper H2A.Z incorporation at thousands of discrete sites, which represent a subset of the regions normally enriched with H2A.Z. Genetic analyses showed that arp6;mbd9 double mutants have far more severe phenotypes than either single mutant. In conjunction with the finding that MBD9 does not appear to be a core subunit of the Arabidopsis SWR1 complex, this suggests that MBD9 also has important roles beyond H2A.Z deposition. Our data establish the SWR1 complex as being conserved across eukaryotes and also provide new insights into the mechanisms that target H2A.Z to chromatin.

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Comprehensive analysis of the SWR1 complex reveals the coupling of H2A.Z deposition with nucleosome sliding in Arabidopsis [ChIP-Seq]

Project description:Comprehensive analysis of the SWR1 complex reveals the coupling of H2A.Z deposition with nucleosome sliding in Arabidopsis [ChIP-Seq]

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