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Polycomb mutant seedlings

ABSTRACT: We have identified a histone methyltransferase gene CURLY LEAF (CLF), which is required to repress a floral homeotic gene AGAMOUS (AG). CLF acts redundantly with a related gene SWINGER (SWN), so that clf swn double mutants have extreme, near lethal phenotypes in which expression of many target genes is disrupted. To understand better when and where these genes act, we propose to use a system for generating mosaic plants in which marked sectors of cells are created that gain or lose CLF (or other Pc-G) gene function in SWN+ and swn- mutant backgrounds. This will allow us to address questions such as whether the Pc-G genes are needed throughout development to silence their targets, whether they are needed once cell division has ceased, whether they can silence their targets once the targets have been activated, and whether genes that are epigenetically silenced by CLF are impervious to activating factors.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE20256 | GEO | 2010/04/20

SECONDARY ACCESSION(S): PRJNA124217

REPOSITORIES: GEO

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Polycomb mutant seedlings

Project description:We have identified a histone methyltransferase gene CURLY LEAF (CLF), which is required to repress a floral homeotic gene AGAMOUS (AG). CLF acts redundantly with a related gene SWINGER (SWN), so that clf swn double mutants have extreme, near lethal phenotypes in which expression of many target genes is disrupted. To understand better when and where these genes act, we propose to use a system for generating mosaic plants in which marked sectors of cells are created that gain or lose CLF (or other Pc-G) gene function in SWN+ and swn- mutant backgrounds. This will allow us to address questions such as whether the Pc-G genes are needed throughout development to silence their targets, whether they are needed once cell division has ceased, whether they can silence their targets once the targets have been activated, and whether genes that are epigenetically silenced by CLF are impervious to activating factors. Aim is to compare gene expression in wild-type and polycomb mutant seedlings. Comparison of bulked seedlings of four genotypes: wild-type (Columbia), clf-28, swn-7, clf-28 swn-7 double mutant. 8 samples were used in this experiment, 2 of each genotype. Tissue grown in tissue culture.

2010-04-28 | E-GEOD-20256 | biostudies-arrayexpress

Genome-wide occupancy of histone H3K27 methyltransferases CURLY LEAF and SWINGER in Arabidopsis seedlings

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

The Transcriptional Repressors VAL1 and VAL2 Recruit PRC2 for Genome-wide Polycomb Silencing in Arabidopsis

Project description:The Polycomb repressive complex 2 (PRC2) catalyzes histone H3 Lys27 trimethylation (H3K27me3) to repress gene transcription in multicellular eukaryotes. Despite its importance in gene silencing and cellular differentiation, how PRC2 is recruited to target loci is still not fully understood. Here, we report genome-wide evidence for the recruitment of PRC2 by the transcriptional repressors VIVIPAROUS1/ABI3-LIKE1 (VAL1) and VAL2 in Arabidopsis thaliana. We show that the val1 val2 double mutant possesses somatic embryonic phenotypes and a transcriptome strikingly similar to those of the swn clf double mutant, which lacks the PRC2 catalytic subunits SWINGER (SWN) and CURLY LEAF (CLF). We further show that VAL1 and VAL2 physically interact with SWN and CLF in vivo. Genome-wide binding profiling demonstrated that they colocalize with SWN and CLF at PRC2 target loci. Loss of VAL1 and VAL2 significantly reduces SWN and CLF enrichment at PRC2 target loci and leads to a genome-wide redistribution of H3K27me3 that strongly affects transcription. Finally, we provide evidence that the VAL1/VAL2–RY regulatory system is largely independent of the TRB–Telobox and BPC1–GA/AZF1–Telobox modules for Polycomb silencing in plants. Taken together, our work demonstrates an extensive genome-wide interaction between VAL1/2 and PRC2 and provides mechanistic insights into the establishment of Polycomb silencing in plants.

2020-11-06 | GSE145387 | GEO

Arabidopsis thaliana treatments to trigger somatic embryo formation under RNAseq

Project description:Arabidopsis clf/swn mutant is able to form somatic embryos under the proper treatment conditions. In order to get more information about the process, we compared the expression profiles of wt and clf/swn in absence of treatment, Injury, Auxin, and Auxin+Injury treatments

2017-01-10 | GSE81166 | GEO

Arabidopsis thaliana

Project description:H3K27 tri-methyltransferases CLF and SWN redundantly buffer ABA-induced senescence

| PRJNA384645 | ENA

VAL1 and 2 recruit SWN to targets

Project description:VAL1 and 2 recruit SWN to targets

2020-11-06 | GSE159499 | GEO

VAL1 and 2 recruit SWN to targets

Project description:VAL1 and 2 recruit SWN to targets

| PRJNA669062 | ENA

Transcription profiling of human PC-3 prostate cancer cells expressing shTCEB1 leading to TCEB1 silencing

Project description:Lentivirus mediated RNAi was used to silence TCEB1 expression in PC-3 prostate cancer cell line. Whole human genome microarray was used to study changes in gene expression induced by the silencing.

2008-10-31 | E-MEXP-1627 | biostudies-arrayexpress

H2A monoubiquitination in Arabidopsis is generally independent of LHP1 and PRC2 activity [RNA-seq]

Project description:BACKGROUND: Polycomb group complexes PRC1 and PRC2 repress gene expression at the chromatin level in eukaryotes. The classic recruitment model of Polycomb group complexes in which PRC2-mediated H3K27 trimethylation recruits PRC1 for H2A monoubiquitination was recently challenged by data showing that PRC1 activity can also recruit PRC2. However, the prevalence of these two mechanisms is unknown, especially in plants as H2AK121ub marks were examined at only a handful of Polycomb group targets. RESULTS: By using genome-wide analyses, we show that H2AK121ub marks are surprisingly widespread in Arabidopsis thaliana, often co-localizing with H3K27me3 but also occupying a set of transcriptionally active genes devoid of H3K27me3. Furthermore, by profiling H2AK121ub and H3K27me3 marks in atbmi1a/b/c, clf/swn, and lhp1 mutants we found that PRC2 activity is not required for H2AK121ub marking at most genes. In contrast, loss of AtBMI1 function impacts the incorporation of H3K27me3 marks at most Polycomb group targets. CONCLUSIONS: Our findings show the relationship between H2AK121ub and H3K27me3 marks across the A. thaliana genome and unveil that ubiquitination by PRC1 is largely independent of PRC2 activity in plants, while the inverse is true for H3K27 trimethylation.

2017-03-21 | GSE89356 | GEO

H2A monoubiquitination in Arabidopsis is generally independent of LHP1 and PRC2 activity [ChIP-seq]

2017-03-21 | GSE89357 | GEO

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