Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

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

PROVIDER: PRJNA850382 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

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 [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 [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 [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 [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 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.

2023-01-03 | GSE206363 | GEO

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

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

| PRJNA850390 | 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

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data