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Series GSE108960 Query DataSets for GSE108960
Status Public on Jan 28, 2019
Title Genome-wide occupancy of histone H3K27 methyltransferases CURLY LEAF and SWINGER in Arabidopsis seedlings
Organism Arabidopsis thaliana
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary 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.
 
Overall design Examination of CLF and SWN genome-wide bindings, and the distribution of H3K27me3 in WT, clf, swn, and clf swn seedlings.
 
Contributor(s) Shu J, Cui Y
Citation(s) 31245749
Shu, J, Chen, C, Thapa, RK, et al. Genome-wide occupancy of histone H3K27 methyltransferases CURLY LEAF and SWINGER in Arabidopsis seedlings. Plant Direct. 2019; 3: 1-14.
Submission date Jan 09, 2018
Last update date Jul 02, 2019
Contact name YUHAI CUI
E-mail(s) yuhai.cui@agr.gc.ca
Phone 519-953-6622
Organization name Agriculture and Agri-Food Canada
Department London Research and Development Centre
Street address 1391 Sandford Street
City London
State/province ON
ZIP/Postal code N5V 4T3
Country Canada
 
Platforms (3)
GPL13222 Illumina HiSeq 2000 (Arabidopsis thaliana)
GPL17639 Illumina HiSeq 2500 (Arabidopsis thaliana)
GPL21785 Illumina HiSeq 4000 (Arabidopsis thaliana)
Samples (29)
GSM2916533 CLF-GFP Rep1
GSM2916534 CLF-GFP Rep2
GSM2916535 SWN-GFP Rep1
Relations
BioProject PRJNA429247
SRA SRP128550

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE108960_RAW.tar 306.7 Mb (http)(custom) TAR (of BIGWIG, WIG)
GSE108960_wt_vs_clf-29_swn-4.tabular.txt.gz 1.1 Mb (ftp)(http) TXT
GSE108960_wt_vs_clf.txt.gz 1.7 Mb (ftp)(http) TXT
GSE108960_wt_vs_mutants.tabular.txt.gz 6.7 Mb (ftp)(http) TXT
GSE108960_wt_vs_swn.txt.gz 1.7 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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