Project description:We established a comprehensive temporal dynamic response profile of a large set of BAC-GFP HepG2 cell lines representing the following components of stress signaling: i) unfolded protein response (UPR) [ATF4, XBP1, BIP and CHOP]; ii) oxidative stress [NRF2, SRXN1, HMOX1]; iii) DNA damage [P53, P21, BTG2, MDM2]; and iv) NF-κB pathway [A20, ICAM1]. Using logic-based ordinary differential equation (Logic-ODE), we modelled the dynamic profiles of the different stress responses and extracted specific descriptors potentially predicting the progressive outcomes. Please see the most updated version on GitHub: https://github.com/saezlab/LogicODE_GFP_SR

2022-08-02 | MODEL2206070001 | BioModels

Hypoxia-induced SETX links replication stress with the unfolded protein response

Project description:Hypoxia-induced SETX links replication stress with the unfolded protein response

| PRJNA661072 | ENA

Toxoplasma gondii

Project description:The Toxoplasma unfolded protein response

| PRJNA187165 | ENA

Effect of IMD-0354 on gene expression in melanoma A375 cells

Project description:The purpose of this RNAseq is to analyse the effect of compound IMD-0354 on gene expression in melanoma A375 cells. RNAseq analysis identified unfolded protein response, cell cycle and DNA damage pathways to be effected by IMD-0354.

2021-02-02 | GSE165899 | GEO

NEAT1 promotes genome stability via m6A methylation-dependent regulation of CHD4

Project description:Long non-coding (lnc)RNA emerge as regulators of genome stability. The nuclear enriched abundant transcript 1 (NEAT1) is overexpressed in many tumours and responsive to genotoxic stress. However, the mechanism that links NEAT1 to DNA damage response (DDR) is unclear. Here, we investigate the expression, modification levels, localization and structure of NEAT1 in response to DNA double-strand breaks (DSBs). DNA damage increases the levels and N6-methyladenosine (m6A) marks on NEAT1, which promotes alterations in NEAT1 structure, accumulation of hyper-methylated NEAT1 at promoter-associated DSBs and DSB foci formation. The depletion of NEAT1 delays DSB signalling and elevates DNA damage. The genome-protective role of NEAT1 is mediated by the RNA methyltransferase 3 (METTL3) and involves the release of the chromodomain helicase DNA binding protein 4 (CHD4) from NEAT1 to fine-tune histone deacetylation, which links NEAT1 to DDR.

2024-09-16 | GSE273351 | GEO

Homo sapiens

Project description:Analysis of transcriptome and translatome regulation in unfolded protein response

| PRJDB15146 | ENA

Homo sapiens

Project description:Endoplasmic reticulum (ER) stress and the unfolded protein response (UPR)

| PRJNA137213 | ENA