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

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

PROVIDER: PRJNA579920 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10354434_1.fastq.gz	Fastqsanger.gz
	SRR10354434_2.fastq.gz	Fastqsanger.gz
	SRR10354435_1.fastq.gz	Fastqsanger.gz
	SRR10354435_2.fastq.gz	Fastqsanger.gz
	SRR10354436_1.fastq.gz	Fastqsanger.gz

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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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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

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 [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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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.

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

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Nucleosome free DNA- and acetyl histone-binding components recruit SWR1 to yeast promoters for H2A.Z replacement

Project description:The histone variant H2A.Z is a genome-wide signature of nucleosomes proximal to eukaryotic regulatory DNA. While the multi-subunit SWR1 chromatin remodeling complex is known to catalyze ATP-dependent deposition of H2A.Z, the mechanism of recruitment to S. cerevisiae promoters has been unclear. A sensitive assay for competitive binding of di-nucleosome substrates revealed that SWR1 preferentially binds long nucleosome-free DNA adjoining core particles, allowing discrimination of gene promoters over gene bodies. We traced the critical DNA binding component of SWR1 to the conserved Swc2/YL1 subunit, whose activity is required for both SWR1 binding and H2A.Z incorporation in vivo. Histone acetylation by NuA4 enhances SWR1 binding, but the interaction with nucleosome-free DNA is the major determinant. ‘Hierarchical cooperation’ between high affinity DNA- and low affinity histone modification-binding factors may reconcile the large disparity in affinities for chromatin substrates, and unify classical control by DNA-binding factors with post-translational histone modifications and ATP-dependent nucleosome mobility. Swr1 TAP IF of various mutants

2013-09-16 | E-GEOD-49183 | biostudies-arrayexpress

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

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