Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA401700 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5996680.fastq.gz | Fastqsanger.gz | |||
| SRR5996690.fastq.gz | Fastqsanger.gz | |||
| SRR5996700_1.fastq.gz | Fastqsanger.gz | |||
| SRR5996700_2.fastq.gz | Fastqsanger.gz | |||
| SRR5996710_1.fastq.gz | Fastqsanger.gz |
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Project description:ChIP-seq was performed using anti-H3, anti-H3K27me3, and anti-H2A.Z antibodies in three-week-old WT, pkl-1, clf-28, and pie1-5 shoots using paired-end sequencing. Strand-specific RNA-seq was performed on RNA extracted from the same biological samples.
2018-07-31 | GSE103361 | GEO
Project description:H3K27me3 is a histone modification associated with transcriptional repression that plays a pivotal role in differentiation and development in plants and animals. H2A.Z, a histone variant of H2A, is often colocalized with H3K27me3 in Arabidopsis. Previous genome-wide studies have raised the possibility that H2A.Z contributes to H3K27me3 homeostasis in plants. To examine the contribution of H2A.Z to H3K27me3, we utilized hta9 hta11, a plant line which is defective in two of three genes that code for H2A.Z and has been previously characterized as an H2A.Z-depletion mutant. Surprisingly, ChIP-seq analysis of H2A.Z enrichment revealed that hta9 hta11 plants exhibit a nearly indistinguishable genic H2A.Z enrichment pattern relative to wild type with few genes that are enriched or depleted for H2A.Z. Mass spectrometry measurement of histone protein abundance in hta9 hta11 plants in conjunction with our ChIP-seq analysis indicates that the chromatin of hta9 hta11 plants exhibits altered relative abundance of H2A.Z variants rather than a global depletion of H2A.Z. In contrast, ChIP-seq analysis of H3K27me3 reveals that hta9 hta11 plants exhibit a robust global reduction in H3K27me3 enrichment, and numerous genes are identified that exhibit altered levels for H3K27me3. In addition, hta9 hta11 plants exhibit differential expression of thermoresponsive genes that have previously been shown to be dependent on H2A.Z. Our combined analyses indicate that specific H2A.Z isoforms play distinct roles in chromatin composition and gene expression in Arabidopsis, particularly with regards to H3K27me3 homeostasis.
2026-08-03 | PXD058289 | Pride
Project description:H3K27me3 is a histone modification associated with transcriptional repression that plays a pivotal role in differentiation and development in plants and animals. H2A.Z, a histone variant of H2A, is often colocalized with H3K27me3 in Arabidopsis. Previous genome-wide studies have raised the possibility that H2A.Z contributes to H3K27me3 homeostasis in plants. To examine the contribution of H2A.Z to H3K27me3, we utilized hta9 hta11, a plant line which is defective in two of three genes that code for H2A.Z and has been previously characterized as an H2A.Z-depletion mutant. Surprisingly, ChIP-seq analysis of H2A.Z enrichment revealed that hta9 hta11 plants exhibit a nearly indistinguishable genic H2A.Z enrichment pattern relative to wild type with few genes that are enriched or depleted for H2A.Z. Mass spectrometry measurement of histone protein abundance in hta9 hta11 plants in conjunction with our ChIP-seq analysis indicates that the chromatin of hta9 hta11 plants exhibits altered relative abundance of H2A.Z variants rather than a global depletion of H2A.Z. In contrast, ChIP-seq analysis of H3K27me3 reveals that hta9 hta11 plants exhibit a robust global reduction in H3K27me3 enrichment, and numerous genes are identified that exhibit altered levels for H3K27me3. In addition, hta9 hta11 plants exhibit differential expression of thermoresponsive genes that have previously been shown to be dependent on H2A.Z. Our combined analyses indicate that specific H2A.Z isoforms play distinct roles in chromatin composition and gene expression in Arabidopsis, particularly with regards to H3K27me3 homeostasis.
2026-08-03 | PXD058581 | panorama
Project description:H3K27me3 is a histone modification associated with transcriptional repression that plays a pivotal role in differentiation and development in plants and animals. H2A.Z, a histone variant of H2A, is often colocalized with H3K27me3 in Arabidopsis. Previous genome-wide studies have raised the possibility that H2A.Z contributes to H3K27me3 homeostasis in plants. To examine the contribution of H2A.Z to H3K27me3, we made use of hta9 hta11, a plant line which is defective in two of three genes that code for H2A.Z and which has been previously characterized as an H2A.Z-depletion mutant. Surprisingly, ChIP-seq analysis of H2A.Z enrichment revealed that hta9 hta11 plants exhibit a nearly indistinguishable genic H2A.Z enrichment pattern relative to wild type with few genes that are differentially enriched for H2A.Z. Mass spectrometry measurement of histone abundance in hta9 hta11 plants in conjunction with our ChIP-seq analysis indicates that the chromatin of hta9 hta11 plants exhibits altered relative abundance of H2A.Z variants rather than a global depletion of H2A.Z. In contrast, ChIP-seq analysis of H3K27me3 reveals that hta9 hta11 plants exhibit a robustly global reduction in H3K27me3 enrichment, and numerous genes are identified that exhibit altered levels for H3K27me3. In addition, hta9 hta11 plants exhibit differential expression of thermoresponsive genes that have previously been shown to be dependent on H2A.Z. Our combined analyses indicate that specific H2A.Z isoforms play distinct roles in chromatin composition and gene expression in Arabidopsis, particularly with regards to H3K27me3 homeostasis.
2026-08-04 | GSE282948 | GEO
Project description:H3K27me3 is a histone modification associated with transcriptional repression that plays a pivotal role in differentiation and development in plants and animals. H2A.Z, a histone variant of H2A, is often colocalized with H3K27me3 in Arabidopsis. Previous genome-wide studies have raised the possibility that H2A.Z contributes to H3K27me3 homeostasis in plants. To examine the contribution of H2A.Z to H3K27me3, we made use of hta9 hta11, a plant line which is defective in two of three genes that code for H2A.Z and which has been previously characterized as an H2A.Z-depletion mutant. Surprisingly, ChIP-seq analysis of H2A.Z enrichment revealed that hta9 hta11 plants exhibit a nearly indistinguishable genic H2A.Z enrichment pattern relative to wild type with few genes that are differentially enriched for H2A.Z. Mass spectrometry measurement of histone abundance in hta9 hta11 plants in conjunction with our ChIP-seq analysis indicates that the chromatin of hta9 hta11 plants exhibits altered relative abundance of H2A.Z variants rather than a global depletion of H2A.Z. In contrast, ChIP-seq analysis of H3K27me3 reveals that hta9 hta11 plants exhibit a robustly global reduction in H3K27me3 enrichment, and numerous genes are identified that exhibit altered levels for H3K27me3. In addition, hta9 hta11 plants exhibit differential expression of thermoresponsive genes that have previously been shown to be dependent on H2A.Z. Our combined analyses indicate that specific H2A.Z isoforms play distinct roles in chromatin composition and gene expression in Arabidopsis, particularly with regards to H3K27me3 homeostasis.
2026-08-04 | GSE282947 | GEO
Project description:The Polycomb Group (PcG) proteins form two protein complexes, PcG Repressive Complex 1 (PRC1) and PRC2, which are key epigenetic regulators in eukaryotes. PRC2 represses gene expression by catalyzing the trimethylation of histone H3 lysine 27 (H3K27me3). In Arabidopsis (Arabidopsis thaliana), CURLY LEAF (CLF) and SWINGER (SWN) are two major H3K27 methyltransferases and core components of PRC2, playing essential roles in plant growth and development. Despite their importance, genome-wide binding profiles of CLF and SWN have not been determined and compared yet. In this study, we generated transgenic lines expressing GFP-tagged CLF/SWN under their respective native promoters and used them for ChIP-seq analyses to profile the genome-wide distributions of CLF and SWN in Arabidopsis seedlings. We also profiled and compared the global H3K27me3 levels in wild-type (WT) and PcG mutants (clf, swn, and clf swn). Our data show that CLF and SWN bind to almost the same set of genes, except that SWN has a few hundred more targets. Two short DNA sequences, the GAGA-like and Telo-box-like motifs, were found enriched in the CLF and SWN binding regions. The H3K27me3 levels in clf, but not in swn, were markedly reduced compared with WT; and the mark was undetectable in the clf swn double mutant. Further, we profiled the transcriptomes in clf, swn, and clf swn, and compared with that in WT. Thus this work provides a useful resource for the plant epigenetics community for dissecting the functions of PRC2 in plant growth and development.
2019-01-28 | GSE108960 | GEO
Project description:Nucleation and spreading of H3K27me3 are critical steps for the initiation and maintenance, respectively, of mitotically inheritable Polycomb-mediated repressive chromatin states in cell identity memory, in both animals and plants. Although a semiconservative read-and-write mechanism is proposed to play a key role in H3K27me3 propagation, the specific determinant and underlying mechanism by which the Polycomb Repressive Complex 2 (PRC2) accesses unmodified nucleosomes for propagating H3K27me3 remain enigmatic. Using Arabidopsis thaliana as a model, we show that the chromatin remodeling activity of PICKLE (PKL) has a specialized role in H3K27me3 spreading to safeguard cell identity during differentiation. PKL specifically binds to H3K27me3 spreading regions but not nucleation sites of Polycomb target genes and physically interacts with the MSI1 subunit of PRC2. Loss of PKL abolishes the occupancy of the PRC2 catalytic subunit CLF in spreading regions and leads to aberrant differentiation. Nucleosome condensing endowed by the ATPase function of PKL ensures that unmodified nucleosomes are accessible to PRC2 catalytic activity. Our findings highlight that PKL-dependent nucleosome compaction is critical for PRC2-mediated H3K27me3 read-and-write functions in H3K27me3 spreading, thus revealing a mechanism by which repressive chromatin domains are established and propagated.
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Project description:Nucleation and spreading of H3K27me3 are critical steps for the initiation and maintenance, respectively, of mitotically inheritable Polycomb-mediated repressive chromatin states in cell identity memory, in both animals and plants. Although a semiconservative read-and-write mechanism is proposed to play a key role in H3K27me3 propagation, the specific determinant and underlying mechanism by which the Polycomb Repressive Complex 2 (PRC2) accesses unmodified nucleosomes for propagating H3K27me3 remain enigmatic. Using Arabidopsis thaliana as a model, we show that the chromatin remodeling activity of PICKLE (PKL) has a specialized role in H3K27me3 spreading to safeguard cell identity during differentiation. PKL specifically binds to H3K27me3 spreading regions but not nucleation sites of Polycomb target genes and physically interacts with the MSI1 subunit of PRC2. Loss of PKL abolishes the occupancy of the PRC2 catalytic subunit CLF in spreading regions and leads to aberrant differentiation. Nucleosome condensing endowed by the ATPase function of PKL ensures that unmodified nucleosomes are accessible to PRC2 catalytic activity. Our findings highlight that PKL-dependent nucleosome compaction is critical for PRC2-mediated H3K27me3 read-and-write functions in H3K27me3 spreading, thus revealing a mechanism by which repressive chromatin domains are established and propagated.
2024-10-02 | GSE267571 | GEO
Project description:CURLY LEAF (CLF), the major histone methyltransferase of Polycomb Repressive Complex 2 (PRC2), modifies trimethylation of histone H3 lysine 27 (H3K27me3) and mediates dynamical chromatin repression in Arabidopsis. Here we profiled Arabidopsis transcriptomes obtained from roots, leaves, flowers and siliques of Col-0 and clf-28 plants using RNA-seq. Our analysis uncovered 3835 transcription units were up-regulated in clf-28. Compared with H3K27me3 ChIP-CHIP data, we found at least 42% of them were associated with H3K27me3.
2015-02-01 | GSE43983 | GEO
Project description:LHP1, CLF binding sites and their role in H3K27me3 spreading in Arabidopsis thaliana
| PRJNA308073 | ENA