Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA121461 | ENA |
REPOSITORIES: ENA
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Project description:In eukaryotes, DNA wraps around histones to form nucleosomes, which are compacted into chromatin. DNA-templated processes, including transcription, require chromatin disassembly and reassembly mediated by histone chaperones. Additionally, distinct histone variants can replace core histones to regulate chromatin structure and function. Although replacement of H2A with the evolutionarily conserved H2A.Z via the SWR1 histone chaperone complex has been extensively studied, in plants little is known about how a reduction of H2A.Z levels can be achieved. Here, we show that NRP proteins cause a decrease of H2A.Z-containing nucleosomes in Arabidopsis under standard growing conditions. nrp1-1 nrp2-2 double mutants show an over-accumulation of H2A.Z genome-wide, especially at heterochromatic regions normally H2A.Z-depleted in wild-type plants. Our work suggests that NRP proteins regulate gene expression by counteracting SWR1, thereby preventing excessive accumulation of H2A.Z.
2020-05-18 | PXD019248 | Pride
Project description:Post-translational histone modifications and the dynamics of histone variant H2A.Z are key mechanisms underlying the floral transition. In yeast, SWR1-C and NuA4-C mediate the deposition of H2A.Z and the acetylation of histone H4, H2A and H2A.Z respectively. Yaf9 is a subunit shared by both chromatin remodeling complexes. The significance of the two Arabidopsis YAF9 homologs, YAF9A and YAF9B, is unknown. We performed a transcriptomic analysis of wild-type and yaf9a yaf9b double mutant seedlings in order to reveal target genes whose transcription is regulated by YAF9 proteins.
2019-02-06 | GSE126020 | GEO
Project description:Genome-wide analysis of transcription, H2A.Z, nucleosomes and HSF1 dynamics in response to temperature increase in Arabidopsis thaliana [RNA-seq I]
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Project description:Genome-wide analysis of transcription, H2A.Z, nucleosomes and HSF1 dynamics in response to temperature increase in Arabidopsis thaliana [RNA-Seq II]
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Project description:Genome-wide analysis of transcription, H2A.Z, nucleosomes and HSF1 dynamics in response to temperature increase in Arabidopsis thaliana [RNA-Seq III]
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Project description:The histone variant H2A.Z is important for transcriptional regulation across eukaryotes, where it can alternately promote or repress transcription. Actively transcribed genes show H2A.Z enrichment in nucleosomes immediately downstream of the transcription start site (TSS), while silent genes show H2A.Z enrichment across the gene body. In plants, previous work shows that silent genes responsive to temperature and light lose gene body H2A.Z upon activation, but whether H2A.Z loss is generally required for transcription is not clear. We profiled H2A.Z and components of its deposition complex, SWR1, before and after treating Arabidopsis thaliana with the hormone abscisic acid (ABA). Our results show that transcribed genes with TSS-enriched H2A.Z have high SWR1 binding, indicating continuous replacement of H2A.Z, while silent genes with gene body H2A.Z show lower SWR1 binding. Surprisingly, upon ABA treatment, thousands of previously silent genes activate, correlating with recruitment of SWR1 and retention of gene body H2A.Z enrichment. We also found that the SWR1-interacting protein MBD9 is not required for SWR1 recruitment to activated genes. These results provide new insights into the relationship between H2A.Z and transcription and the mechanics of H2A.Z targeting to chromatin.
2025-06-01 | GSE269827 | GEO
Project description:Genome-wide analysis of transcription, H2A.Z, nucleosomes and HSF1 dynamics in response to temperature increase in Arabidopsis thaliana [ChIP-seq & Mnase-seq]
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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.
2010-10-12 | GSE24618 | GEO
Project description:Chromatin structure and function is regulated by reader proteins recognizing histone modifications and/or histone variants. We recently identified PWWP2A, which tightly binds to H2A.Z-containing nucleosomes and is involved in mitotic progression and cranial-facial development. Here, using in vitro assays we show that distinct domains of PWWP2A moreover mediate binding to free linker DNA as well as H3K36me3 nucleosomes. In vivo, PWWP2A strongly recognizes H2A.Z-containing regulatory regions and weakly H3K36me3-containing gene bodies. Additionally, PWWP2A bind to an MTA1-specific core NuRD (M1HR) complex solely consisting of MTA1, HDAC1 and RBBP4/7, excluding CHD and MBD proteins. Depletion of PWWP2A leads to an increase of acetylation levels on H3K27 as well as H2A.Z, presumably by impaired chromatin recruitment of M1HR. Thus, this study identifies PWWP2A as an ever more complex chromatin binding protein serving as adapter for M1HR to H2A.Z-containing chromatin, thereby promoting changes in histone acetylation levels and likely fine-tuning the transcriptional balance.
2018-08-27 | PXD010424 | Pride
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