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HSFA1a controls plant heat stress response through its action on the 3D chromatin reorganization of enhancer-promoter interactions.

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Solanum lycopersicum

PROVIDER: GSE206365 | GEO | 2023/01/03

REPOSITORIES: GEO

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HSFA1a controls plant heat stress response through its action on the 3D chromatin reorganization of enhancer-promoter interactions [HiChIP]

Project description:We investigated the role of HSFA1a, a master regulator of heat stress response, in this reorganization through promotion of the formation of promoter/enhancer chromatin loops. To validate the presence of transcription factories we performed a HiChIP experiment, which is a sensitive and efficient method to analyze protein-centric chromosome conformation, using an anti-RNA polymerase II antibody.

2023-01-03 | GSE206361 | GEO

HSFA1a controls plant heat stress response through its action on the 3D chromatin reorganization of enhancer-promoter interactions [DAP-seq]

2023-01-03 | GSE206359 | GEO

HSFA1a controls plant heat stress response through its action on the 3D chromatin reorganization of enhancer-promoter interactions [Hi-C]

Project description:We investigated the role of HSFA1a, a master regulator of heat stress response, in this reorganization through promotion of the formation of promoter/enhancer chromatin loops. To map the three-dimensional chromatin interactions we performed in situ Hi-C, a genome-wide method that detects DNA-DNA physical interactions.

2023-01-03 | GSE206360 | GEO

HSFA1a controls plant heat stress response through its action on the 3D chromatin reorganization of enhancer-promoter interactions [ChIP-seq]

Project description:To investigate the HSFA1a, a master regulator of heat stress response, plays a key role in this reorganization by promoting the formation of promoter/enhancer chromatin loops. To determine if a typical chromatin signature could differentiate distal and proximal REs, we performed ChIP-seq experiments and analyzed the levels of four histone covalent modifications that are permissive for transcription: H3K4me3, H3K9ac, H3K18ac and H3K27ac at 0, 1 and 6 hours after heat stress on both proximal and distal REs specifically active at 1 hour after HS. In addition, To assess if RNAPII could also by recruited at distal active enhancers in plants, we performed an RNAPII ChIP-seq on plant subjected to 0, 1 and 6 hours of heat stress and analyzed its accumulation on distal REs specifically active at 1 hour after HS. Moreover, we did ChIP-seq of H3K27me1 associated constitutive heterochromatin at normal condition.

2023-01-03 | GSE206358 | GEO

HSFA1a controls plant heat stress response through its action on the 3D chromatin reorganization of enhancer-promoter interactions [ATAC-seq]

Project description:We investigated the role of HSFA1a, a master regulator of heat stress response, in this reorganization through promotion of the formation of promoter/enhancer chromatin loops. We performed ATAC-seq experiments which provide accessible chromatin sites that can be used to identify putative regulatory elements coming in physical contact with promoters when they are actived.

2023-01-03 | GSE206355 | GEO

HSFA1a controls plant heat stress response through its action on the 3D chromatin reorganization of enhancer-promoter interactions [RNA-seq 2]

Project description:We investigated the role of HSFA1a, a master regulator of heat stress response, in this reorganization through promotion of the formation of promoter/enhancer chromatin loops. We performed gene expression profiling analysis using data obtained from RNA-seq of 4 weeks old tomato (Solanum lycopersicum cv. Moneymaker background ) plants (wild type and RNAi knock-down lines) which were treated at 45°C for 0h, 1h and 6h.

2023-01-03 | GSE206363 | GEO

HSFA1a controls plant heat stress response through its action on the 3D chromatin reorganization of enhancer-promoter interactions [RNA-seq 1]

Project description:We investigated the role of HSFA1a, a master regulator of heat stress response, in this reorganization through promotion of the formation of promoter/enhancer chromatin loops. To confirm that the temperature and timing used for the heat stress are relevant, we generated RNA-seq data and analyzed changes in gene expression induced by the heat stress treatment.

2023-01-03 | GSE206362 | GEO

HSFA1a controls plant heat stress response through its action on the 3D chromatin reorganization of enhancer-promoter interactions [Capture Hi-C]

Project description:We investigated the role of HSFA1a, a master regulator of heat stress response, in this reorganization through promotion of the formation of promoter/enhancer chromatin loops. To determine whether distal REs come into contact with promoters, instead of using a classical Hi-C, we further combined Hi-C with a capture enrichment step. We generated a biotinylated RNA bait library specifically targeting 212,735 promoter regions and performed a capture Hi-C after 0h, 1h and 6h after stress.

2023-01-03 | GSE206356 | GEO

HSFA1a modulates plant heat stress responses and alters the 3D chromatin organization of enhancer-promoter interactions.

Project description:The complex and dynamic three-dimensional organization of chromatin within the nucleus makes understanding the control of gene expression challenging, but also opens up possible ways to epigenetically modulate gene expression. Because plants are sessile, they evolved sophisticated ways to rapidly modulate gene expression in response to environmental stress, that are thought to be coordinated by changes in chromatin conformation to mediate specific cellular and physiological responses. However, to what extent and how stress induces dynamic changes in chromatin reorganization remains poorly understood. Here, we comprehensively investigated genome-wide chromatin changes associated with transcriptional reprogramming response to heat stress in tomato. Our data show that heat stress induces rapid changes in chromatin architecture, leading to the transient formation of promoter-enhancer contacts, likely driving the expression of heat-stress responsive genes. Furthermore, we demonstrate that chromatin spatial reorganization requires HSFA1a, a transcription factor (TF) essential for heat stress tolerance in tomato. In light of our findings, we propose that TFs play a key role in controlling dynamic transcriptional responses through 3D reconfiguration of promoter-enhancer contacts.

| S-EPMC9884265 | biostudies-literature

HSFA1a controls plant heat stress response through its action on the 3D chromatin reorganization of enhancer-promoter interactions.

Project description:HSFA1a controls plant heat stress response through its action on the 3D chromatin reorganization of enhancer-promoter interactions.

| PRJNA850378 | ENA

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