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Upregulation of transcripts in the absence of prc2 repressory complex-Dissecting the role of the polycomb repressor

ABSTRACT: rs09-08_fie - upregulation of transcripts in the absence of prc2 repressory complex - Role of PRC2 repressory complex for differentiation pathways in Arabidopsis thaliana? - Comparison of transcriptome between two biological replicates of fie mutants in comparison with two biological replicates of Col WT. Keywords: gene knock out

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE19851 | GEO | 2010/12/01

SECONDARY ACCESSION(S): PRJNA122123

REPOSITORIES: GEO

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upregulation of transcripts in the absence of prc2 repressory complex-Dissecting the role of the polycomb repressor

Project description:rs09-08_fie - upregulation of transcripts in the absence of prc2 repressory complex - Role of PRC2 repressory complex for differentiation pathways in Arabidopsis thaliana? - Comparison of transcriptome between two biological replicates of fie mutants in comparison with two biological replicates of Col WT. Keywords: gene knock out 6 dye-swap - CATMA arrays

2010-12-01 | E-GEOD-19851 | biostudies-arrayexpress

Arabidopsis Polycomb Repressive Complex 2 binding sites contain putative GAGA factor binding motifs within coding regions of genes

Project description:Background. Polycomb Repressive Complex 2 (PRC2) is an essential regulator of gene expression that maintains genes in a repressed state by marking chromatin with trimethylated Histone H3 lysine 27 (H3K27me3). In Arabidopsis, loss of PRC2 function leads to pleiotropic effects on growth and development thought to be due to ectopic expression of seed and embryo-specific genes. While there is some understanding of the mechanisms by which specific genes are targeted by PRC2 in animal systems, it is still not clear how PRC2 is recruited to specific regions of plant genomes.Results. We used ChIP-seq to determine the genome-wide distribution of hemagglutinin (HA)-tagged FERTLIZATION INDEPENDENT ENDOSPERM (FIE-HA), the Extra Sex Combs homolog protein present in all Arabidopsis PRC2 complexes. We found that the FIE-HA binding sites co-locate with a subset of the H3K27me3 sites in the genome and the associated genes were more likely to be de-repressed in mutants of PRC2 components. The FIE-HA binding sites are enriched for three sequence motifs including a putative GAGA factor binding site that is also found in Drosophila Polycomb Response Elements (PREs).Conclusions. Our results suggest that PRC2 binding sites in plant genomes share some sequence features with Drosophila PREs. However, RNA was extracted from intermediate phenotype siFIE plants, clf-7 swn-28 and Col using Qiagen Plant RNeasy mini kit. For each sample, three pools of 10-12 plants were used. The siFIE plants were analysed for FIE mRNA by RT-qPCR; the maximum level of FIE mRNA was found to be 10% of wildtype.

2013-09-01 | E-GEOD-48857 | biostudies-arrayexpress

Genome wide analysis of the chromatin state and gene expression in Wild-type, tor-es mutant, and fie mutants

Project description:Using Western blot, we found the level of H3K27me3, but not H3K4me3, H3K9me2 and H3K36me3, was specifically reduced in the tor-es mutant. To gain a genome-wide view of the effects of TOR activity on H3K27me3 distribution, we performed quantitative chromatin immunoprecipitation with an exogenous reference genome (ChIP-Rx) followed by deep-sequencing. We find a global reduction of H3K27me3 occupancy in tor-es, whereas the H3K9me2 level was largely unaffected. These results suggest that TOR may be a specific and direct regulator of global deposition of H3K27me3. To investigate the function of TOR phosphorylation of FIE, we complemented the heterozygous fie/+ plants with GFP-FIE or the phosphorylation site mutant (SSTS/AAAA) under the control of the FIE promoter. To provide a parallel comparison with SSTS/AAAA/fie, we generated estradiol-inducible fie-amiR-es transgenic lines, that eliminated FIE protein. Quantitative ChIP-seq analyses revealed greatly reduced H3K27me3 levels across the genome in SSTS/AAAA and fie-amiR-es mutants. And transcriptome profiling by RNA-Seq was conducted to globally identify thousands of genes coordinately dysregulated in the shoots of SSTS/AAAA and fie-amiR-es plants. Furthermore, gene Ontology analysis of 986 TOR-FIE-PRC2 target genes revealed significant enrichment for transcription factors/regulators controlling a broad spectrum of developmental programs.

2022-06-20 | GSE161807 | GEO

Arabidopsis Polycomb Repressive Complex 2 binding sites contain putative GAGA factor binding motifs within coding regions of genes

2013-09-01 | GSE48857 | GEO

Physical and functional screening of Polycomb Repressor Complex 2 highlights novel regulators of histone H3 lysine 27 methylation status

Project description:Polycomb Repressor Complex 2 (PRC2) is a multi-protein epigenetic regulator complex that plays critical roles in early development and tissue differentiation. The complex catalyzes the methylation of histone H3 lysine 27 (H3K27). The tri-methyl state (H3K27me3) is well studied as an agent of gene repression, but more recently distinct roles for the mono- and di-methyl states have been discovered. In order to more fully understand how PRC2-associated factors might influence H3K27 status, we screened for physical associations of PRC2 subunits. Knockdown of these factors was used to produce functional interaction maps focused on H3K27 methylation, including proteins that have positive and negative effects on the levels each histone mark.

2018-04-05 | PXD005381 | Pride

complex i-Analysis of complex I mutants

Project description:rs12-03_complex-i - complex i - Can we identify differences between mutants affecte din different subunits of complex I - direct comparison between col-0 (wild type) and 4 mutants, each mutants having different levels of residual complex I. Three biological replicates were processed

2014-09-10 | GSE60533 | GEO

quinolinate-Deregulation of NAD biosynthesis

Project description:rs09-02_quinolinate - quinolinate - Study of the impact of an inductible increase in the NAD concentration in arabidopsis - Comparison between the mutant or the control after a quinolinate treatment Keywords: treated vs untreated comparison,wt vs mutant comparison

2010-07-01 | GSE19084 | GEO

Polycomb Repressor Complex 2 and REST-associated histone deacetylases are independent pathways toward a mature neuronal phenotype.

Project description:These experiments were designed to test the hypothesis that REST and Polycomb Repressor Complex 2 function cooperatively in undifferentiated ESCs. Our results showed that a majority of REST-bound genomic regions were not associated with H3K27me3 enrichment and loss of H3K27me3 enrichment was not a general observation in REST -/- ESCs. These results support the conclusion that REST and PRC2 function independently in ESCs and similarly contribute to maintaing a transcriptionally poised state through antagonism of H3K4me3. Examination of REST-bound regions in undifferentiated mouse embryonic stem cells (ESC), and a comparison of H3K27me3 distribution between WT and REST-/- ESCs.

2014-09-30 | E-GEOD-48320 | biostudies-arrayexpress

RNA-seq characterization of downstream effects of upregulating SMN2 via down-regulating PRC2 or blocking the PRC2:SMN-AS1 interaction with a mixmer oligonucleotide

Project description:To determine how targeting the disruption of PRC2:SMN-AS1 interactions might affect PRC2 targets globally, we performed RNA-sequencing after transfection of a PRC2:SMN-AS1 targeting mixmer oligo, RN-0005, an antisense gapmer oligonucleotide targeting SUZ12, a subunit of the PRC2 complex, or mock in SMA fibroblasts. Via RT-qPCR, treatment with either the mixmer oligo or the SUZ12 gapmer for 2 and 3 days results in significant increases of SMN mRNA levels compared to transfection control samples. We sequenced total RNA from 12 GM09677 fibroblast samples split into two day or three day treatments (6 samples each). Within each set of six samples, there were 2 mock control replicates, 2 mixmer replicates, and 2 SUZ12kd-gapmer replicates. By controlling for time and looking at the two treatments versus mock samples, we identified the genes that change when knocking down PRC2 systemically with a gapmer versus more specifically blocking PRC2 activity with a mixmer oligo targeting the SMN2-AS1 lncRNA.

2017-03-06 | GSE83549 | GEO

An ErbB2/c-Src axis drives mammary tumorigenesis through metabolically directed translational regulation of Polycomb Repressor Complex 2 [array]

Project description:Perturbations in histone modifications alter transcription and promote carcinogenesis. Breast cancers frequently overexpress the histone methyltransferase EZH2, the catalytic subunit of Polycomb Repressor Complex 2 (PRC2). However, the mechanisms driving EZH2 overexpression are obscure and elucidating the role of PRC2 in breast cancer, which is highly heterogeneous, is challenging given its context-dependent oncogenic and tumor suppressive functions. Here, using genetically engineered mouse, PDX and cell line models, we show that the tyrosine kinase c-Src links energy sufficiency with PRC2 subunit overexpression via control of mRNA translation. In breast cancers initiated by the oncogene ErbB2, c-Src stimulates mitochondrial ATP production to suppress energy stress and permit sustained activation of the mammalian/mechanistic target of rapamycin complex 1 (mTORC1), which increases the translation of mRNAs encoding the PRC2 subunits Ezh2 and Suz12. We show that Ezh2 overexpression and activity are pivotal in ErbB2-mediated mammary tumorigenesis. These results reveal the hitherto unknown c-Src/mTORC1/PRC2 axis, which is essential for ErbB2-driven carcinogenesis.

2018-01-31 | GSE93892 | GEO

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