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AtINO80 represses photomorphogenesis by modulating nucleosome density and H2A.Z incorporation in light-related genes (RNA-seq)

ABSTRACT: AtINO80 represses photomorphogenesis by modulating nucleosome density and H2A.Z incorporation in light-related genes (RNA-seq)

PROVIDER: PRJNA631216 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11734452_1.fastq.gz	Fastqsanger.gz
	SRR11734452_2.fastq.gz	Fastqsanger.gz
	SRR11734453_1.fastq.gz	Fastqsanger.gz
	SRR11734453_2.fastq.gz	Fastqsanger.gz
	SRR11734454_1.fastq.gz	Fastqsanger.gz

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AtINO80 represses photomorphogenesis by modulating nucleosome density and H2A.Z incorporation in light-related genes (ChIP-seq)

2020-11-30 | GSE149841 | GEO

AtINO80 represses photomorphogenesis by modulating nucleosome density and H2A.Z incorporation in light-related genes (ChIP-seq)

Project description:AtINO80 represses photomorphogenesis by modulating nucleosome density and H2A.Z incorporation in light-related genes (ChIP-seq)

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AtINO80 represses photomorphogenesis by modulating nucleosome density and H2A.Z incorporation in light-related genes.

Project description:Photomorphogenesis is a critical developmental process bridging light-regulated transcriptional reprogramming with morphological changes in organisms. Strikingly, the chromatin-based transcriptional control of photomorphogenesis remains poorly understood. Here, we show that the Arabidopsis (Arabidopsis thaliana) ortholog of ATP-dependent chromatin-remodeling factor AtINO80 represses plant photomorphogenesis. Loss of AtINO80 inhibited hypocotyl cell elongation and caused anthocyanin accumulation. Both light-induced genes and dark-induced genes were affected in the atino80 mutant. Genome-wide occupancy of the H2A.Z histone variant and levels of histone H3 were reduced in atino80 In particular, AtINO80 bound the gene body of ELONGATED HYPOCOTYL 5 (HY5), resulting in lower chromatin incorporations of H2A.Z and H3 at HY5 in atino80 Genetic analysis revealed that AtINO80 acts in a phytochrome B- and HY5-dependent manner in the regulation of photomorphogenesis. Together, our study elucidates a mechanism wherein AtINO80 modulates nucleosome density and H2A.Z incorporation and represses the transcription of light-related genes, such as HY5, to fine tune plant photomorphogenesis.

| S-EPMC7777152 | biostudies-literature

AtINO80 represses photomorphogenesis by modulating nucleosome density and H2A.Z incorporation in light-related genes (RNA-seq)

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

2020-11-30 | GSE150116 | GEO

RNAseq for atino80 mutant at dark condition

2020-11-30 | GSE150114 | GEO

RNAseq for atino80 mutant in long-day condition

2020-11-30 | GSE150109 | GEO

Project description:The Chromatin-remodeling factor AtINO80 mediates photomorphogenesis by modulating H2A.Z incorporation(ChIPseq)

| PRJNA553626 | ENA

Project description:The Chromatin-remodeling factor AtINO80 mediates photomorphogenesis by modulating H2A.Z incorporation(RNASeq)

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The Histone Variant H2A.Z C-terminal Domain Has Locus- Specific Differential Effects on H2A.Z Occupancy and Nucleosome Localization

Project description:The incorporation of histone variant H2A.Z, a conserved H2A variant, into nucleosomes creates specialized chromatin domains that regulate DNA-templated processes, including transcription. H2A.Z-containing nucleosomes may poise gene regulatory regions for transcription, but mechanistic details are lacking. In Saccharomyces cerevisiae, the diverging H2A.Z C-terminus is thought to provide the H2A.Z exclusive functions. To elucidate the roles of this H2A.Z C-terminus genome wide, we made use of derivatives where the C-terminus was replaced with the corresponding region of H2A (ZA protein), or the H2A region plus a transcriptional activating peptide, with the idea of regenerating the H2A.Z-dependent regulation globally. An assessment of the genome-wide distribution of these H2A.Z derivatives shows that the H2A.Z C-terminal region is crucial for both maintaining the occupation level of H2A.Z and the proper positioning of the targeted nucleosomes. Interestingly, the specific contribution on incorporation efficiency vs nucleosome positioning varies enormously, depending on loci analyzed. For the ZA protein, positioning changes most importantly near origins of replication and snoRNA gene promoters, while incorporation is affected on all other sites. Furthermore, the role of H2A.Z in global transcription regulation also depends on its C-terminal region. Remarkably however, the latter mostly involves genes without a H2A.Z nucleosome in the promoter.

2022-08-18 | GSE156492 | GEO

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