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

ABSTRACT: 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.

ORGANISM(S): Solanum lycopersicum

PROVIDER: GSE206361 | 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 [DAP-seq]

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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.

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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.

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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 [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.

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

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

| PRJNA850381 | ENA

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.

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

| PRJNA850378 | ENA

HiChIP: Efficient and sensitive analysis of protein-directed genome architecture

Project description:Three-dimensional genome structure is central to gene control, but current technologies are often impractical for many biological questions due to cell and read number requirements. Here we present HiChIP, a protein-centric chromatin conformation method. HiChIP improves the fraction of conformation-informative reads by over 10-fold and lowers input requirement greater than 100-fold to 1 million cells. HiChIP of cohesin reveals multi-scale genome architecture with greater signal to noise than in situ Hi-C. Thus, HiChIP will enable insight into the genome’s three-dimensional structure and regulation in once-inaccessible biological systems.

2016-08-31 | GSE80820 | GEO

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