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

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

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE139465 | 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 [ChIP-Seq]

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A plant-specific SWR1 chromatin-remodeling complex couples histone H2A.Z deposition with nucleosome sliding.

Project description:Deposition of H2A.Z in chromatin is known to be mediated by a conserved SWR1 chromatin-remodeling complex in eukaryotes. However, little is known about whether and how the SWR1 complex cooperates with other chromatin regulators. Using immunoprecipitation followed by mass spectrometry, we found all known components of the Arabidopsis thaliana SWR1 complex and additionally identified the following three classes of previously uncharacterized plant-specific SWR1 components: MBD9, a methyl-CpG-binding domain-containing protein; CHR11 and CHR17 (CHR11/17), ISWI chromatin remodelers responsible for nucleosome sliding; and TRA1a and TRA1b, accessory subunits of the conserved NuA4 histone acetyltransferase complex. MBD9 directly interacts with CHR11/17 and the SWR1 catalytic subunit PIE1, and is responsible for the association of CHR11/17 with the SWR1 complex. MBD9, TRA1a, and TRA1b function as canonical components of the SWR1 complex to mediate H2A.Z deposition. CHR11/17 are not only responsible for nucleosome sliding but also involved in H2A.Z deposition. These results indicate that the association of the SWR1 complex with CHR11/17 may 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

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

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

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

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

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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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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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