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: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: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 | GSE267567 | 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: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:The Polycomb repressive complex 2 (PRC2) is an essential epigenetic regulator that deposits repressive H3K27me3 for transcriptional gene silencing in eukaryotes. The PRC2-mediated gene silencing process occurs in two steps: the initial H3K27me3 deposition at the nucleation region, and the subsequent spreading of H3K27me3 over the entire gene. Lack of H3K27me3 spreading gives rise to a metastable state that could lead to loss of silencing. H3K27me3 spreading is thus a key step critical for the establishment of stable long-term Polycomb silencing in both animals and plants.Here, we uncover that Arabidopsis thaliana PICKLE (PKL), a member of the conserved Chromodomain Helicase DNA-binding (CHD) family of chromatin remodeling ATPase13, is dispensable for the nucleation but especially required for the efficient spreading of H3K27me3 at thousands of Polycomb target genes. PKL localizes to the spreading regions in a non-DNA-sequence-specific manner through its SANT-SILDE domain. PKL then upregulates the chromatin density by its CHROMODOMAIN and ATPase domain , enabling the H3K27me3 methyltransferase CURLY LEAF (CLF) to deposit H3K27me3 on nucleosomes in the spreading regions to facilitate the H3K27me3 spreading.
2024-10-02 | GSE201375 | GEO
Project description:The Polycomb repressive complex 2 (PRC2) is an essential epigenetic regulator that deposits repressive H3K27me3 for transcriptional gene silencing in eukaryotes. The PRC2-mediated gene silencing process occurs in two steps: the initial H3K27me3 deposition at the nucleation region, and the subsequent spreading of H3K27me3 over the entire gene. Lack of H3K27me3 spreading gives rise to a metastable state that could lead to loss of silencing. H3K27me3 spreading is thus a key step critical for the establishment of stable long-term Polycomb silencing in both animals and plants.Here, we uncover that Arabidopsis thaliana PICKLE (PKL), a member of the conserved Chromodomain Helicase DNA-binding (CHD) family of chromatin remodeling ATPase13, is dispensable for the nucleation but especially required for the efficient spreading of H3K27me3 at thousands of Polycomb target genes. PKL localizes to the spreading regions in a non-DNA-sequence-specific manner through its SANT-SILDE domain. PKL then upregulates the chromatin density by its CHROMODOMAIN and ATPase domain , enabling the H3K27me3 methyltransferase CURLY LEAF (CLF) to deposit H3K27me3 on nucleosomes in the spreading regions to facilitate the H3K27me3 spreading.
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Project description:LHP1, CLF binding sites and their role in H3K27me3 spreading in Arabidopsis thaliana
| PRJNA308073 | ENA
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 used strand specific RNA-sequencing to profile Arabidopsis transcriptomes obtained from roots, shoots, flowers and siliques of Col-0 and clf-28 plants. Our analysis identified a large number of CLF-regulatedd transcripts in Arabidopsis.
2016-03-28 | GSE61545 | GEO
Project description:Histone modifications are essential for chromatin activity and play an important role in many biological processes. Trimethylation of histone H3K27 (H3K27me3) is a repressive modification established by Polycomb repressive complex 2 (PRC2). Although the presence of the histone H3 serine 28 phosphorylation (H3S28ph) modification at adjacent amino acid residues has both positive and negative effects on Polycomb silencing in mammals, little is known about the effect of H3S28ph on H3K27me3-mediated gene silencing in plants. In this study, we show that mutating H3S28A in Arabidopsis causes a dominant-negative effect that leads to an early-flowering phenotype by promoting the expression of flowering-promoting genes independently of abnormal cell division. While H3S28ph levels decreased due to the H3S28A mutation, H3K27me3 levels at the same loci did not increase. Moreover, we observed decreased H3K27me3 levels at some known PRC2 target genes in H3.3S28A transgenic lines, rather than the expected enhanced H3K27me3-mediated silencing. In line with the reduced H3K27me3 levels, the expression of the PRC2 catalytic subunits CLF and SWN decreased. Taken together, these data demonstrate that H3.3S28 is required for PRC2-dependent H3K27me3-mediated silencing in Arabidopsis, suggesting that H3S28 has a non-canonical function in H3K27me3-mediated gene silencing.
2022-09-01 | GSE197502 | GEO