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

ABSTRACT: 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.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE145387 | GEO | 2020/11/06

REPOSITORIES: GEO

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

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2019-01-28 | GSE108960 | GEO

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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

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2010-04-20 | GSE20256 | GEO

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2022-09-01 | GSE197502 | GEO

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2022-10-13 | PXD036548 | Pride

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

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

VAL1 and 2 recruit SWN to targets

Project description:VAL1 and 2 recruit SWN to targets

2020-11-06 | GSE159499 | GEO

VAL1 acts as an assembly platform co-ordinating co-transcriptional repression and chromatin regulation at Arabidopsis FLC

Project description:Polycomb (PcG) silencing is crucial for development, but how targets are specified remains incompletely understood. The cold-induced Polycomb Repressive Complex 2 (PRC2) silencing of Arabidopsis thaliana FLOWERING LOCUS C (FLC) provides an excellent system to elucidate PcG regulation. Association of the DNA binding protein VAL1 to the PcG nucleationregion at FLC is an important step. VAL1 interacts with APOPTOSIS AND SPLICING ASSOCIATED PROTEIN (ASAP) complex and PRC1. Here, we show that ASAP and PRC1 are necessary for co-transcriptional repression and chromatin regulation during FLC silencing. ASAP mutants affect FLC transcription in warm conditions, but the rate of FLC silencing in the cold is unaffected. PRC1-mediated H2Aub accumulates at FLC nucleation region during cold, but unlike the PRC2-delivered H3K27me3 does not spread across the locus. H2Aub thus marks the transition to epigenetic silencing, while H3K27me3 is necessary for long-term epigenetic memory. Overall, our work highlights the importance of VAL1 as an assembly platform co-ordinating the co-transcriptional repression and chromatin regulation necessary for the epigenetic silencing of FLC.

2022-08-15 | PXD036057 | iProX

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