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Series GSE155502 Query DataSets for GSE155502
Status Public on Apr 29, 2021
Title Polycomb-dependent differential chromatin compartmentalization determines gene co-regulation in Arabidopsis
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
Summary Previous studies in animals have shown that polycomb targets marked with H3K27me3 can establish interactions between them, forming a repressive chromatin hub (Lanzuolo et al., 2007; Cheutin and Cavalli, 2014). In plants few studies suggested that H3K27me3 may act directly or indirectly to regulate the interactivity of polycomb marked genes. However, several aspects of the molecular function of the H3K27me3 histone modification on the 3D chromatin architecture remained obscure. To decipher the impact of H3K27me3 levels on loop formation, we combined genetics, 3D epigenomics and transcriptomic approaches. By using the ref6 mutant, defective for a histone demethylase, that displays ectopic accumulation of H3K27me3, we demonstrated that H3K27me3 is important to trigger chromatin loop formation. Reciprocally, using clf mutant, a histone methyltransferase mutant that displays a strong reduction of H3K27me3 we found that a reduction of the H3K27me3 leads to the decrease of interactions inside the polycomb repressive domain. Surprisingly, we observed that regions losing H3K27me3 in clf establish new interactions with regions marked with the H3K9ac active histone modification, showing that a reduction in H3K27me3 levels induces a global reconfiguration of chromatin architecture. Altogether our results demonstrate that the 3D organization of the genome is tightly linked to histone modifications that trigger the formation of chromatin domains associated with gene co-regulation, thereby allowing proper plant development and in which H3K27me3 is a key regulator of chromatin topology at global and local scales.
 
Overall design H3K27me3 histone modification on the 3D chromatin architecture in Arabidopsis
 
Contributor(s) Huang Y, Sicar S, Latrasse D, Benhamed M
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Submission date Jul 31, 2020
Last update date May 02, 2021
Contact name Sanchari Sircar
E-mail(s) sancharisircar24@gmail.com
Organization name IPS2
Lab Chromosome Dynamics
Street address Batiment 630 Rue Noetzlin
City Orsay
ZIP/Postal code 75015
Country France
 
Platforms (1)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
Samples (36)
GSM4705366 HiChIP-K27-Root-rep1
GSM4705367 HiChIP-K27-Shoot-rep1
GSM4705368 HiChIP-K27-Root-rep2
Relations
BioProject PRJNA649954
SRA SRP274603

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
GSE155502_RAW.tar 8.6 Gb (http)(custom) TAR (of BIGWIG, BW, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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