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Series GSE103924 Query DataSets for GSE103924
Status Public on Sep 12, 2018
Title Topoisomerase VI participates to a chromatin barrier-like function that prevents heterochromatin spreading in euchromatic islands (HTS)
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary The plant Topoisomerase VI complex has been implicated in a wide array of biological processes but little is known about its precise molecular role. In this study, we provide evidence that Topo VI acts as a chromatin barrier between chromatin territories by interacting with methionine adenosyltransferases (MAT), which produce the universal donor of methyl groups S-adenosyl-methionine (SAM). We first show that pericentromeric transposable elements (TEs) are awakened whereas euchromatic island genes (EIGs) within heterochromatin are downregulated in mutants of the Topo VI complex. Consistent with this, the level of repressive H3K9me2 marks increases at EIGs loci while it decreases at TEs in a hypomorphic Topo VI mutant. We demonstrate that the Topo VI complex can interact with the SAM synthase MAT3 and drives it to TEs. A deficiency of Topo VI induces relocation of MAT3 from TEs to EIGs islands, leading to the levelling of the H3K9me2 mark and hence heterochromatin spreading.
Overall design The transcriptome analysis of the caa39 mutant comprises three biological replicates for mutant and WT genotypes. The ChiPseq analysis of H3K9me2 includes a comparison of a pool of two biological replicates for caa39 and wt. This was done in duplicate for H3K27me3. In addition, an input chromatin control comprising a pool of two biological replicates was used for both genotypes. In total, we analyzed 6 RNAseq samples, and 6 ChIP samples and 2 input chromatin samples.
Contributor(s) Méteignier L, Lecampion C, Vriet C, Térèse M, Rougée M, Breuer C, Soubigou-Taconnat L, Sugimoto K, Barneche F, Laloi C
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Submission date Sep 15, 2017
Last update date Jul 25, 2021
Contact name Christophe Laloi
Phone +334 91 82 95 64
Organization name Aix-Marseille Université
Department Biology
Street address 163 avenue de Luminy
City Marseille
State/province France
ZIP/Postal code 13009
Country France
Platforms (3)
GPL13222 Illumina HiSeq 2000 (Arabidopsis thaliana)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
GPL23157 HiSeq X Ten (Arabidopsis thaliana)
Samples (28)
GSM2786261 WTCol0-0-1
GSM2786262 WTCol0-0-2
GSM2786263 WTCol0-0-3
This SubSeries is part of SuperSeries:
GSE129249 Topoisomerase VI participates to a chromatin barrier-like function that prevents heterochromatin spreading in euchromatic islands
BioProject PRJNA407573
SRA SRP117759

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
GSE103924_RAW.tar 1021.0 Mb (http)(custom) TAR (of BIGWIG, BW)
GSE103924_RNAseq_caa39_Vs_WT.xlsx 2.9 Mb (ftp)(http) XLSX
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Processed data are available on Series record
Processed data provided as supplementary file
Raw data are available in SRA

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