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| Status |
Public on Aug 05, 2024 |
| Title |
THE EPIGENOME PLAYS A MAJOR ROLE IN TOMATO 3D CHROMATIN ORGANIZATION [RNA-seq] |
| Organism |
Solanum lycopersicum |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Understanding the 3D genome organization in the nucleus is becoming increasingly crucial given its involvement in many processes from transcription to the integrity of the nucleus itself, which play a role in every stage of an organism's life. Beyond the linear genome defined by its nucleotide sequence, this organization is also governed by its epigenome, but how the latter controls the 3D architecture of the nucleus is poorly understood. To decipher the epigenome influence on the formation of all levels of the nuclear organization, we studied tomato mutants defective for DDM1, a chromatin remodeler determining for the constitutive heterochromatin establishment. We observed that the ddm1 mutant exhibited weakened compartmentalization with lower insulation, more inter-compartment contacts and an increase in long-range contacts. This disorganization is accompanied by a reconfiguration of the epigenome, ultimately resulting in a reprogramming of its transcriptome. By integrating all our data, we have shown that this redistribution of the epigenome is linked to the global disorganization of the nucleus notably via new interactions mediated by H3K27me3, and is also related to new interactions between genes and/or TEs which display the same epigenetic characteristics. Altogether, our results strongly suggest that epigenetic features drive the formation of distinct compartments by playing a segregating role between active and inactive chromatin, becoming an essential characteristic for the identity of genes and TEs in terms of genome organization.
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| Overall design |
To assess the effect of the epigenome reconfiguration on transcriptome reprogramming, we performed RNA-seq analyses in WT and mutant. Then, we performed DESeq2 analysis and found differentially expressed genes in ddm1.
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| Contributor(s) |
He X, Lopes CD, Bistrain LI, Bouché N, Latrasse D, Raynaud C, Benhamed M |
| Citation(s) |
39149894 |
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| Submission date |
Sep 24, 2023 |
| Last update date |
Oct 10, 2024 |
| Contact name |
Xiaoning HE |
| E-mail(s) |
[email protected]
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| Organization name |
IPS2
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| Street address |
630 Rue Noetzlin
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| City |
Gif-sur-Yvette |
| ZIP/Postal code |
91190 |
| Country |
France |
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| Platforms (1) |
| GPL21762 |
Illumina NextSeq 500 (Solanum lycopersicum) |
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| Samples (4)
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| This SubSeries is part of SuperSeries: |
| GSE243911 |
THE EPIGENOME PLAYS A MAJOR ROLE IN TOMATO 3D CHROMATIN ORGANIZATION |
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| Relations |
| BioProject |
PRJNA1020556 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE243910_count_read.txt.gz |
704.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
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