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Arabidopsis SWR1-associated protein methyl-CpG-binding domain 9 is required for histone H2A.Z deposition.

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE123263 | GEO | 2019/06/21

REPOSITORIES: GEO

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Arabidopsis SWR1-associated protein methyl-CpG-binding domain 9 is required for histone H2A.Z deposition.

Project description:Deposition of the histone variant H2A.Z by the SWI2/SNF2-Related 1 chromatin remodeling complex (SWR1-C) is important for gene regulation in eukaryotes, but the composition of the Arabidopsis SWR1-C has not been thoroughly characterized. Here, we aim to identify interacting partners of a conserved Arabidopsis SWR1 subunit ACTIN-RELATED PROTEIN 6 (ARP6). We isolate nine predicted components and identify additional interactors implicated in histone acetylation and chromatin biology. One of the interacting partners, methyl-CpG-binding domain 9 (MBD9), also strongly interacts with the Imitation SWItch (ISWI) chromatin remodeling complex. MBD9 is required for deposition of H2A.Z at a distinct subset of ARP6-dependent loci. MBD9 is preferentially bound to nucleosome-depleted regions at the 5' ends of genes containing high levels of activating histone marks. These data suggest that MBD9 is a SWR1-C interacting protein required for H2A.Z deposition at a subset of actively transcribing genes.

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Arabidopsis SWR1-associated protein methyl-CpG-binding domain 9 is required for histone H2A.Z deposition. [ChIPSeq_MBD9]

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.

2019-06-21 | GSE123261 | GEO

Arabidopsis SWR1-associated protein methyl-CpG-binding domain 9 is required for histone H2A.Z deposition. [ChIPSeq_H3Ac]

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Arabidopsis SWR1-associated protein methyl-CpG-binding domain 9 is required for histone H2A.Z deposition. [ChIPSeq_H2AZ]

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Arabidopsis SWR1-associated protein methyl-CpG-binding domain 9 is required for histone H2A.Z deposition. [RNA-Seq]

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Arabidopsis SWR1-associated protein methyl-CpG-binding domain 9 is required for histone H2A.Z deposition. [ATAC-Seq]

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Arabidopsis SWR1-associated protein methyl-CpG-binding domain 9 is required for histone H2A.Z deposition.

Project description:Arabidopsis SWR1-associated protein methyl-CpG-binding domain 9 is required for histone H2A.Z deposition.

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