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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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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. 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.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Nottingham Arabidopsis Stock Centre (NASC)

PROVIDER: E-GEOD-20256 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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.

2010-04-20 | GSE20256 | GEO

Identification of CLF-regulated transcripts using strand-specific RNA-sequencing in Arabidopsis

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. Transcriptome profiling in roots, shoots, inflorescences and siliques of WT and clf-28 plants with 3 biological replicates.

2016-03-28 | E-GEOD-61545 | biostudies-arrayexpress

Genome-wide analysis reveals CLF-regulated transcripts in Arabidopsis

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 (As described under GEO ID: GSE38612) and clf-28 plants using RNA-seq. Our analysis uncovered 3835 transcription units were up-regulated in clf-28. Compared with ChIP-CHIP data, we found at least 42% of them were associated with H3K27me3. Transcriptom profiling in roots, leaves, flowers and siliques of clf-28 plants.

2015-02-01 | E-GEOD-43983 | biostudies-arrayexpress

Gene expression in clf and lhp1

Project description:Transcriptome changes in leaves of PcG protein mutants clf and lhp1. Fully expanded rosette leaf 6 was collected from 10 35-d-old plants grown in short day photoperiods.

2013-08-22 | E-MTAB-1412 | 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 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

Wide-type, brm, clf, and brm clf mutant seedlings

Project description:Wide-type, brm, clf, and brm clf mutant seedlings

| PRJNA232492 | ENA

Micro-array analysis of gene expression in the Arabidopsis chr11-1 chr17-1 mutant

Project description:Chromatin remodeling factors of the Imitation Switch (ISWI) family play important roles in epigenetic regulations of gene expression in yeast and animals, whereas their function in plants remains elusive. Here we report characterization of the Arabidopsis ISWI genes CHR11 and CHR17. Double mutant chr11 chr17 displayed a dramatically reduced plant size with early flowering. In addition, epidermis of the double mutant leaves showed cell characteristics seen only in floral organs. These phenotypes resemble, at least partially, those of the Polycomb mutants curly leaf (clf) and like heterochromatin protein1 (lhp1). Microarray analysis revealed that a number of targets of the Polycomb pathway were derepressed in chr11 chr17 leaves. Furthermore, triple mutants combining chr11 chr17 with clf-29 or lhp1-6 both greatly enhanced clf-29 and lhp1-6 phenotypes, respectively. All these results strongly suggest that the ISWI family genes in Arabidopsis may function in gene silencing via the Polycomb pathway

2010-06-11 | GSE22159 | GEO

The Enzyme-Like Domain of Arabidopsis Nuclear Beta-Amylases is Critical During DNA Sequence Recognition and Transcriptional Activation

Project description:Plant BZR1-BAM transcription factors contain a M-NM-2-amylase (BAM)-like domain, characteristic of proteins involved in starch breakdown. The enzyme-derived domains appear to be non-catalytic, but determine the function of the Arabidopsis thaliana BZR1-BAMs (BAM7 and BAM8) during transcriptional initiation. Microarray experiments with plants overexpressing different mutant versions of the proteins show that only functional BZR1-BAM variants deregulate gene expression and cause leaf developmental abnormalities. Transcriptional changes caused by overexpression of the BZR1 domain alone indicate that the BAM domain increases selectivity for the preferred cis-regulatory element BBRE (BZR1-BAM Responsive Element). In this study, we used the ATH1 GeneChip microarray to investigate transcript abundance in different Arabidopsis thaliana genotypes. Arabidopsis thaliana (accession Columbia) were grown in a nutrient-rich, medium-grade, peat-based compost in Percival AR95 growth chambers (CLF Plant Climatics) at a constant temperature of 20M-BM-0C, 70% humidity and a 12-h light period with constant, uniform light intensity of 150 M-NM-<molM-bM-^@M-"m-2M-bM-^@M-"s-1. Three-week-old plants were harvested 4 h after onset of the light period and immediately frozen in liquid nitrogen. Fourteen individual plants were pooled per replicate.

2014-06-10 | E-GEOD-58370 | biostudies-arrayexpress

Micro-array analysis of gene expression in the Arabidopsis chr11-1 chr17-1 mutant

2010-06-23 | E-GEOD-22159 | biostudies-arrayexpress

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