RNA-seq of med14-3 and uvh6-3 mutants in heat stress (37°C) and control stress (23°C), with WT controls. RNA-seq of double mutants: med14-3 or uvh6-3 combined with either ddm1-2 or mom1-2 mutants. Bisulfite-seq of WT samples subjected to control or heat stress. Bisulfite-seq of med14-3 and WT samples in control stress.
ABSTRACT: Heterochromatin transcription is functionally important, for instance to establish heterochromatin silencing or condensation, but the factors allowing transcription in a repressive chromatin environment are little known. To gain insight in this process, we triggered heterochromatin transcription using heat stress or mutations for the silencing factors DDM1 or MOM1 and generated mRNA profiles of med14 and uvh6 mutants in these different contexts. We used rosette leaves incubated 24h in dH2O at 23°C for control stress and 37°C for heat stress. Our data and analysis suggest that UVH6/XPD/RAD3 is involved in a heat stress specific transcriptional process where it promotes transcription of most but not all genes. MED14 promotes transcription at a more reduced number of loci during heat stress, and preferentially targets heterochromatic loci. In addition, MED14 is required for heterochromatin transcription without heat stress, but this function is lost when heterochromatin properties are disrupted, suggesting it is specifically involved in transcription of heterochromatic sequences. In addition, bisulfite-seq of med14 mutants indicates that MED14 participates in RNA-directed DNA methylation, suggesting that MED14 is required both for heterochromatin transcription and formation.
Project description:Arabidopsis 5’-3’ exoribonuclease, AtXRN4, a homolog of yeast Xrn1p, functions in degradation of uncapped RNAs after de-capping step. While Xrn1p-dependent on plant XRN4’s targets for degradation is still limited. For understanding biological function of AtXRN4, we tested survivability of atxrn4 mutants under heat stress. Our results showed that atxrn4 mutants increased survival rate under short-term degradation is a main mRNA decay in yeast, knowledge heat stress compared with WT plants. Our microarray and mRNA decay assay showed that loss of AtXRN4 function caused reduction of mRNA degradation of heat shock factor A2 (HSFA2) and ethylene response factor 1 (ERF1). HSFA2 has been known as a key regulator in heat acclimation, was found as a target for AtXRN4 for degradation at non-stress condition. Heat stress applied on atxrn4-3 hsfa2 double mutant severely lacked heat tolerance phenotype of atxrn4 mutant. These results suggest that AtXRN4-mediated mRNA degradation linked to suppress heat acclimation. In the study here, 2 week-old WT and atxrn4-3 mutant plants were exposure to non-stress (22oC) and heat-stress (37oC, 1 h). Custom microarray was applied to acquire expression profile of 32788 Arabidopsis genes. 3 biological repeats of WT (non-stress), WT(heat stress), atxrn4-3 (non-stress) and atxrn4-3 (heat stress) were used for microarray analysis
Project description:Proctor2005 - Actions of chaperones and their
role in ageing
This model is described in the article:
Modelling the actions of
chaperones and their role in ageing.
Proctor CJ, Soti C, Boys RJ,
Gillespie CS, Shanley DP, Wilkinson DJ, Kirkwood TB.
Mech. Ageing Dev. 2005 Jan; 126(1):
Many molecular chaperones are also known as heat shock
proteins because they are synthesised in increased amounts
after brief exposure of cells to elevated temperatures. They
have many cellular functions and are involved in the folding of
nascent proteins, the re-folding of denatured proteins, the
prevention of protein aggregation, and assisting the targeting
of proteins for degradation by the proteasome and lysosomes.
They also have a role in apoptosis and are involved in
modulating signals for immune and inflammatory responses.
Stress-induced transcription of heat shock proteins requires
the activation of heat shock factor (HSF). Under normal
conditions, HSF is bound to heat shock proteins resulting in
feedback repression. During stress, cellular proteins undergo
denaturation and sequester heat shock proteins bound to HSF,
which is then able to become transcriptionally active. The
induction of heat shock proteins is impaired with age and there
is also a decline in chaperone function. Aberrant/damaged
proteins accumulate with age and are implicated in several
important age-related conditions (e.g. Alzheimer's disease,
Parkinson's disease, and cataract). Therefore, the balance
between damaged proteins and available free chaperones may be
greatly disturbed during ageing. We have developed a
mathematical model to describe the heat shock system. The aim
of the model is two-fold: to explore the heat shock system and
its implications in ageing; and to demonstrate how to build a
model of a biological system using our simulation system
(biology of ageing e-science integration and simulation
This model is hosted on
and identified by:
To cite BioModels Database, please use:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
Public Domain Dedication for more information.
Project description:Smith2013 - Regulation of Insulin Signalling by Oxidative Stress
The model describes insulin signalling (in rodent adipocytes), which includes in addition to the core pathway, the transcriptional feedback through the Forkhead box type O (FOXO) transcription factor and interaction with oxidative stress.
This model is described in the article:
Computational modelling of the regulation of Insulin signalling by oxidative stress.
Smith GR, Shanley DP.
BMC Syst Biol. 2013 May 24;7:41.
Existing models of insulin signalling focus on short term dynamics, rather than the longer term dynamics necessary to understand many physiologically relevant behaviours. We have developed a model of insulin signalling in rodent adipocytes that includes both transcriptional feedback through the Forkhead box type O (FOXO) transcription factor, and interaction with oxidative stress, in addition to the core pathway. In the model Reactive Oxygen Species are both generated endogenously and can be applied externally. They regulate signalling though inhibition of phosphatases and induction of the activity of Stress Activated Protein Kinases, which themselves modulate feedbacks to insulin signalling and FOXO.
Insulin and oxidative stress combined produce a lower degree of activation of insulin signalling than insulin alone. Fasting (nutrient withdrawal) and weak oxidative stress upregulate antioxidant defences while stronger oxidative stress leads to a short term activation of insulin signalling but if prolonged can have other effects including degradation of the insulin receptor substrate (IRS1) and FOXO. At high insulin the protective effect of moderate oxidative stress may disappear.
Our model is consistent with a wide range of experimental data, some of which is difficult to explain. Oxidative stress can have effects that are both up- and down-regulatory on insulin signalling. Our model therefore shows the complexity of the interaction between the two pathways and highlights the need for such integrated computational models to give insight into the dysregulation of insulin signalling along with more data at the individual level.A complete SBML model file can be downloaded from BIOMODELS (https://www.ebi.ac.uk/biomodels-main) with unique identifier MODEL1212210000.Other files and scripts are available as additional files with this journal article and can be downloaded from https://github.com/graham1034/Smith2012_insulin_signalling.
This model is hosted on BioModels Database
To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource
for published quantitative kinetic models
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to the public
domain worldwide. Please refer to CC0 Public Domain
for more information.
Project description:Using whole genome bisulfite sequencing to provide single-base resulution of DNA methylation status in rdm16ros1, ros1, nrpd1ros1 mutants and examine the effect of RDM16 on DNA methylation 4 samples examined: C24 wild type with RD29A-LUC transgene, rdm16ros1 double mutant, ros1 mutant, nrpd1ros1 mutant (all in C24 background with RD29A-LUC transgene)
Project description:The yeast protein PBP1 has been implicated in diverse pathways such as polyadenylation, translation, RNA-DNA hybrid formation, stress granule homeostasis, mitochondrial dysfunction, and TORC1 sequestration. Intriguingly, its deletion mitigates the toxicity of human neurodegeneration factors, but the molecular mechanisms of these effects are poorly understood. Here we performed label-free quantitative global proteomics to identify crucial downstream factors, comparing two PBP1 deletion strains (DB and SM) and two cell stress conditions (heat and NaN3). In all four analyses, downregulations of key bioenergetics enzymes (CIT1, SDH1, MLS1), cell wall mannoproteins (HSP150, PST1) and the prion protein RNQ1 as well as upregulations of the leucine biosynthesis enzyme LEU1 and the transcription factor TAF6 were documented. Consistently for both unstressed PBP1-deleted strains, over 2-fold dysregulations were documented for potential PBP1 interactors such as MKT1 or RPL39 and the stress granule component NRP1. Upregulation of the ribosomal biogenesis factor NOP10 was observed as in the mouse mutant. Consistently for both PBP1 deletion strains, heat stress triggered changes of the stress granule component GIS2 and several of its interactors.
Project description:This model is described in detail in [Dudziuk et al.; 2019]. We provide a short description below.
Heat shock proteins (HSP) are a part of cellular machinery maintaining misfolded proteins that appear in excess in stress conditions, including heat shock. One of most important HSP is the stress-inducible chaperone Hsp70. Not all HSP are subject to stress induction. There is a significant amount of constitutively expressed HSP in cellular homeostasis at 37℃. To describe the regulation pathway of heat induction of Hsp70, we expand previously published models from [Szymańska and Żylicz; 2009] and [Rybiński et al.; 2013]. Compared to those models, 1) we propose an improved function for protein misfolding, 2) we introduce temperature dependencies in some of the reactions; cf. [Scheff et al.; 2015], however we use different temperature dependencies, 3) we take into account the constitutive HSP inflow to improve quantitative value of the model.
Project description:Male reproductive tissues are more sensitive to heat stress compared to vegetative tissues, however the basis of this phenomenon is poorly understood. Heat stress transcription factors (Hsfs) regulate the transcriptional changes required for protection and recovery from heat stress. HsfA2 has been characterized as co-activator of HsfA1a in tomato and is considered as one of the major Hsfs accumulating in response to elevated temperatures. The role of HsfA2 in heat stress response of different tissues was examined by exploring the composition and structure of the tissue-specific regulatory networks in transgenic tomato plants with suppressed HsfA2 expression (A2AS). Transcriptome analysis revealed that HsfA2 acts in condition- and tissue-specific manner and that only a subset of heat stress induced genes require HsfA2 for higher expression. Remarkably, although HsfA2 is not essential for thermotolerance in seedlings and flowering plants, it is required for maintenance pollen viability under stress conditions. We show that the activation of Hsf networks is important for the developmentally regulated priming of heat stress response occurring at early stages of anther and pollen development. Thereby, HsfA2 is involved in pollen thermotolerance by directly regulating heat stress responsive genes but also by stimulating the synthesis of molecular chaperones under non-stress conditions. 8 samples
Project description:Mycoplasma gallisepticum proteome reponse under heat stress was studied. Heat stress has been shown previously to induce the most widespread and at the same time the most intense response at transcription level among the panel of several stresses. Here the corresponding proteome response was characterized.
Project description:NF-YC10 is a subunit of the NF-Y transcription factor complex in Arabidopsis thaliana. We identified NF-YC10 as an interactor of the transcription factor DREB2A, which binds to DRE and activate expression of target genes under heat and/or dehydration stress conditions. Transgenic Arabidopsis plants that overexpress NF-YC10 showed stronger expression of DREB2A target genes under heat stress and were more tolerant to heat stress tolerance than the vector control plants. We conducted a transcript profiling by microarray aiming to identify target genes of NF-YC10 under heat stress
Project description:To ensure cell survival and growth during temperature increase, eukaryotic organisms respond with transcriptional activation that results in accumulation of proteins that protect against damage, and facilitate recovery. To define the global cellular adaptation response to heat stress, we performed a systematic genetic screen that yielded 277 yeast genes required for growth at high temperature. Of these, the Rpd3 histone deacetylase complex was enriched. Global gene expression analysis showed that Rpd3 partially regulated gene expression upon heat shock. The Hsf1 and Msn2/4 transcription factors are the main regulators of gene activation in response to heat stress. RPD3-deficient cells had impaired activation of Msn2/4-dependent genes, while activation of genes controlled by Hsf1 was deacetylase independent. Rpd3 bound to heat stress-dependent promoters through the Msn2/4 transcription factors, allowing entry of RNA Pol II and activation of transcription upon stress. Finally, we found that the large, but not the small Rpd3 complex regulated cell adaptation in response to heat stress. Three independent 200 ml cultures of wild-type and rpd3Δ mutant strains were grown to mid-log phase in YPD rich medium at 25ºC (control) or at 39 ºC for 20 min (heat stressed). Results were analyzed comparing thermo-responsive gene expression respect to the control in each individual strain.