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

ABSTRACT: 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.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE61545 | GEO | 2016/03/28

SECONDARY ACCESSION(S): PRJNA261433

REPOSITORIES: GEO

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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

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 and clf-28 plants using RNA-seq. Our analysis uncovered 3835 transcription units were up-regulated in clf-28. Compared with H3K27me3 ChIP-CHIP data, we found at least 42% of them were associated with H3K27me3.

2015-02-01 | GSE43983 | GEO

Identification of CLF-regulated transcripts in embryos at the mature-green stage by 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. Our previous results suggested that CLF may play regulatory roles on seed size and lipid biosynthesis in embryos at the mature-green stages. Here we used strand specific RNA-sequencing to profile Arabidopsis transcriptomes obtained from isolated embryos at the mature-green stage of Col-0 and clf-28 plants. Our analysis identified a large number of CLF-regulatedd transcripts in developmenting embryos in Arabidopsis. Issolated embryos of WT and clf-28 with 2 biological replicates

2016-03-28 | E-GEOD-68080 | biostudies-arrayexpress

Identification of CLF-regulated transcripts in embryos at the mature-green stage by 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. Our previous results suggested that CLF may play regulatory roles on seed size and lipid biosynthesis in embryos at the mature-green stages. Here we used strand specific RNA-sequencing to profile Arabidopsis transcriptomes obtained from isolated embryos at the mature-green stage of Col-0 and clf-28 plants. Our analysis identified a large number of CLF-regulatedd transcripts in developmenting embryos in Arabidopsis.

2016-03-28 | GSE68080 | GEO

Increased long-distance interactions related to heterotic expression in Arabidopsis hybrids (clf)

Project description:In plants, the genomic structure of hybrids changed compared with their parents. However, the effects of genomic structure changes on heterotic expression in hybrids remain elusive. By comparing interspecific hybrids between Col×C24 and their backcross C24×Col in Arabidopsis with Hi-C analysis, we found that the three-dimensional (3D) chromatin organization had more long-distance interactions relative to parents. The compartment strength related to the increased A-B compartment interactions decreased in hybrids. In the boundaries of topologically associated domains (TADs) like regions in hybrids, the values of Interchromosomal Fraction of Interactions (ICF) and Distal-to-Local [log2] (DLR) were higher than or close to the highest value of their parents. While in the hybrids of CURLY LEAF (clf) mutants, which affects the long-distance interactions, the heterosis phenotype disappeared and the ICF and DLR in hybrids were lower than their parents. In addition, compared with the clf mutant, the differential expressed genes located in TAD boundaries and loop regions in the wild type changed more obviously. In the long-distance interaction and the loop region between WT and clf, there were obvious differences in the functional enrichment for DEGs. The genes with cell cycle and mitotic related process were specifically enriched in clf. By analyzing ChIP-seq data, we found that the enrichment of H3K27me3 were higher in the hybrids in WT, which may lead to more long-distance interactions. Our findings may therefore propose a new epigenetic explanation of the heterotic expression in Arabidopsis hybrids and provide new insights into crop breeding and yield increasing.

2024-03-24 | GSE222132 | GEO

Genome-wide profiling of trimethylated histone H3 lysine 27 (H3K27me3) in wide-type, brm, clf, and brm clf mutant seedlings

Project description:By using ChIP-seq, we found that loss of BRM activity in developing seedlings leads to ectopic and increased H3K27me3 deposition at several hundred genes, indicating the critical role of BRM in preventing the inappropriate deposition of this histone mark. Removal of CLF in brm mutant could partcially suppress the increased H3K27me3. Examination of H3K27me3 in 14-day-old wt, brm, clf, and brm clf seedlings. Two biological replicates for each one.

2015-03-09 | E-GEOD-53620 | 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

CLF Pulldown

Project description:CLF binding sites Keywords: ChIP-chip

2009-01-01 | GSE7065 | GEO

Analysis of the contributions of PKL, CLF, and PIE1 to gene expression, H2A.Z levels, and H3K27me3 levels in Arabidopsis

Project description:ChIP-seq was performed using anti-H3, anti-H3K27me3, and anti-H2A.Z antibodies in three-week-old WT, pkl-1, clf-28, and pie1-5 shoots using paired-end sequencing. Strand-specific RNA-seq was performed on RNA extracted from the same biological samples.

2018-07-31 | GSE103361 | GEO

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