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

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

PROVIDER: PRJNA579918 | ENA |

REPOSITORIES: ENA

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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.

2019-10-29 | GSE139460 | GEO

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

2019-10-29 | GSE139458 | GEO

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

2019-10-29 | GSE139459 | GEO

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

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]

| PRJNA579920 | ENA

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]

| PRJNA579919 | ENA

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.

| S-EPMC7110101 | biostudies-literature

Stepwise histone replacement by SWR1 requires dual activation with histone H2A.Z and canonical nucleosome

Project description:Histone variant H2A.Z-containing nucleosomes are incorporated at most eukaryotic promoters. This incorporation is mediated by the conserved SWR1 complex, which replaces histone H2A in canonical nucleosomes with H2A.Z in an ATP-dependent manner. Here, we show that promoter-proximal nucleosomes are highly heterogeneous for H2A.Z in Saccharomyces cerevisiae, with substantial representation of nucleosomes containing one, two, or no H2A.Z molecules. SWR1-catalyzed H2A.Z replacement in vitro occurs in a stepwise and unidirectional fashion, one H2A.Z-H2B dimer at a time, producing heterotypic nucleosomes as intermediates and homotypic H2A.Z nucleosomes as end products. The ATPase activity of SWR1 is specifically stimulated by H2A-containing nucleosomes without ensuing histone H2A eviction. Remarkably, further addition of free H2A.Z-H2B dimer leads to hyperstimulation of ATPase activity, eviction of nucleosomal H2A-H2B and deposition of H2A.Z-H2B. These results suggest that the combination of H2A-containing nucleosome and free H2A.Z-H2B dimer acting as both effector and substrate for SWR1 governs the specificity and outcome of the replacement reaction. Total nucleosomes from MNase-treated nuclear extracts were fractionated by sequential immunoprecipitation into homotypic H2A/H2A (AA), heterotypic H2A/H2A.Z (AZ), and homotypic H2A.Z/H2A.Z (ZZ) nucleosomes.

2010-10-12 | E-GEOD-24618 | biostudies-arrayexpress

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

Project description:This SuperSeries is composed of the SubSeries listed below.

2019-10-29 | GSE139465 | GEO

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

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 | GSE123260 | GEO

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