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Arabidopsis Flower and Embryo Developmental Genes are Repressed in Seedlings by Different Combinations of Polycomb Group Proteins in Association with Distinct Sets of Cis-regulatory Elements

ABSTRACT: Polycomb Group Proteins (PcGs) is critical in defining the epigenetic blueprint for animal and plant development. In plants, loss of different PcGs display both common and unique phenotypic defects, yet little is known about how these are established. Here, based on quantitative comparison of epigenomics data from mutants of key PcG components in Arabidopsis seedlings, we found that the PcG partners of CURLY LEAF (CLF), one of the major plant H3K27 trimethyltransferases, determines its selectivity in repressing gene loci involved in distinct developmental programs. The non-redundant role of CLF in determining flower development is specifically associated with HETEROCHROMATIN PROTEIN1 (LHP1). This context dependent effect of CLF corresponds well with tissue-biased target gene expression, and importantly, to differential co-occupancy of transcription factors, such as MADS box and B3-domain transcription factors. These results provide valuable insight as to the dynamic interplay between different PcGs and their collaborative control of plant development.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE67322 | GEO | 2016/01/19

SECONDARY ACCESSION(S): PRJNA279505

REPOSITORIES: GEO

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Arabidopsis Flower and Embryo Developmental Genes are Repressed in Seedlings by Different Combinations of Polycomb Group Proteins in Association with Distinct Sets of Cis-regulatory Elements

Project description:Polycomb Group Proteins (PcGs) is critical in defining the epigeneticÂ blueprintÂ for animal and plant development. In plants, loss of different PcGs display both common and unique phenotypic defects, yet little is known about how these are established. Here, based on quantitative comparison of epigenomics data from mutants of key PcG components in Arabidopsis seedlings, we found that the PcG partners of CURLY LEAF (CLF), one of the major plant H3K27 trimethyltransferases, determines its selectivity in repressing gene loci involved in distinct developmental programs. The non-redundant role of CLF in determining flower development is specifically associated with HETEROCHROMATIN PROTEIN1 (LHP1). This context dependent effect of CLF corresponds well with tissue-biased target gene expression, and importantly, to differential co-occupancy of transcription factors, such as MADS box and B3-domain transcription factors. These results provide valuable insight as to the dynamic interplay between different PcGs and their collaborative control of plant development. To compare the effect of different PcGs on epigenetic structure from the genome-wide scale, we used chromatin immunoprecipitation followed by high-throughtput sequencing (ChIP-seq) to characterize the genome-wide binding profile of H3K27me3 in Col, clf-29, tfl2-2, atbmi1a/b and atring1a/b ; To investigate the functional consequence of the distinct H3K27me3 profile controlled by different combinations of PcGs, we characterized the transcriptome change in PcG mutants, including Col, clf-29, tfl2-2, lhp1-6, atbmi1a/b, atring1a/b, and clf29swn21.

2016-01-19 | E-GEOD-67322 | biostudies-arrayexpress

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

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

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

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

The Arabidopsis Polycomb Repressive Complex 1 (PRC1) components AtBMI1A, B and C impact gene networks throughout all stages of plant development

Project description:PcG regulation in Arabidopsis is required to maintain cell differentiation and to allow developmental phase transitions. This is achieved by the activity of three PRC2s and the participation of a yet poorly defined PRC1. Previous results showed that apparent PRC1 components perform discrete roles during plant development, suggesting the existence of PRC1 variants; however, it is not clear in how many processes these components participate. We show that AtBMI1 proteins are required to promote all developmental phase transitions and to control cell proliferation during organ growth and development, expanding their proposed range of action. While AtBMI1 function during germination is closely linked to B3 domain transcription factors VAL1/2 possibly in combination with GT-box binding factors, other AtBMI1 regulatory networks require participation of different factor combinations. Conversely, EMF1 and LHP1 bind many H3K27me3 positive genes upregulated in atbmi1a/b/c mutants; however, loss of their function affects expression of a different subset, suggesting that even if EMF1, LHP1 and AtBMI1 exist in a common PRC1 variant, their role in repression depends on the functional context.

2016-11-10 | GSE83568 | GEO

Expression data from Col, brm-1, clf-29 and brm-1 clf-29 14-d-old seedlings

Project description:To understand how actions of the chromatin-remodeler BRAHMA (BRM) and Polycomb Group (PcG) proteins are coordinated during plant development, we performed a genome-wide profiling of trimethylated histone H3 lysine 27 (H3K27me3) in brm mutant seedlings by chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq). Increased H3K27me3 deposition at several hundred genes was observed in brm mutants and this increase was partially supressed upon removal of the CURLING LEAF (CLF) H3K27me3 methyltransferase. ChIP experiments demonstrated that BRM directly binds to a subset of genes and prevents the inappropriate association of PcG proteins at some of the loci. Together, these results indicate a crucial role of BRM in restricting the inappropriate activity of PcG protein complexes during plant development.

2015-03-09 | GSE53621 | 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

RNA-seq of Arabidopsis thalianal Col-0 wild type and clf-29 lhp1-4 mutant root

Project description:RNA-seq was performed in order to identify qualitative variation of transcripts in clf-29 lhp1-4 compared to WT, including SNPS, indels, splicing fidelity

2022-09-19 | E-MTAB-11263 | biostudies-arrayexpress

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

2016-03-28 | GSE61545 | GEO

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