Similar Datasets
Project description:Plants respond to environmental challenges via a network of signalling pathways. Early responses prevent damage if the stress persists but delay growth in fluctuating conditions. Optimizing these trade-offs requires tunability of plant responsiveness to environmental signals. We have previously shown that Histone Deacetylation Complex 1 (HDC1), which interacts with multiple proteins in histone deacetylation complexes, regulates the sensitivity of Arabidopsis seedlings to salt and ABA, but the underlying mechanism remained elusive. Here we show that knockout of HDC1 enhances transcriptome re-programming prior to growth arrest of salt-treated seedlings and we identify two genes that mediate the effect of salt stress downstream of HDC1. HDC1 attenuates their transcriptional response via a dual mechanism involving H3K9/14 de-acetylation and H3K27 trimethylation. The latter, but not the former, was dependent on the linker histone H1, which interacts with HDC1 via the conserved RXT3 domain. However, a truncated RXT3-like version of HDC1 was not sufficient to recover H3K27me3 deposition in hdc1 suggesting that H1-aided recruitment H3K27 methylation machinery also requires the full-length HDC1-interacting deacetylases. The apparent paradox of repressive marks on stress-induced genes reveals an 'anti-panic' device that employs HDC1 as epigenetic moderator of stress responsiveness offering a leaver to tune stress sensitivity in plants. To identify potential direct targets of HDC1 we isolated nuclei from control and salt-treated HDC1c and hdc1-1 seedlings and performed chromatin immunoprecipitation (ChIP) with an antibody against acetylated lysines 9 and 14 in histone 3 (anti-H3K9K14Ac).
2024-03-27 | GSE206054 | GEO
Project description:Plants respond to environmental challenges via a network of signalling pathways. Early responses prevent damage if the stress persists but delay growth in fluctuating conditions. Optimizing these trade-offs requires tunability of plant responsiveness to environmental signals. We have previously shown that Histone Deacetylation Complex 1 (HDC1), which interacts with multiple proteins in histone deacetylation complexes, regulates the sensitivity of Arabidopsis seedlings to salt and ABA, but the underlying mechanism remained elusive. Here we show that knockout of HDC1 enhances transcriptome re-programming prior to growth arrest of salt-treated seedlings and we identify two genes that mediate the effect of salt stress downstream of HDC1. HDC1 attenuates their transcriptional response via a dual mechanism involving H3K9/14 de-acetylation and H3K27 trimethylation. The latter, but not the former, was dependent on the linker histone H1, which interacts with HDC1 via the conserved RXT3 domain. However, a truncated RXT3-like version of HDC1 was not sufficient to recover H3K27me3 deposition in hdc1 suggesting that H1-aided recruitment H3K27 methylation machinery also requires the full-length HDC1-interacting deacetylases. The apparent paradox of repressive marks on stress-induced genes reveals an 'anti-panic' device that employs HDC1 as epigenetic moderator of stress responsiveness offering a leaver to tune stress sensitivity in plants. To identify genes underpinning salt tolerance in Arabidopsis thaliana and regulated by Histone Deacetylation Complex 1 (HDC1) we performed RNA-sequencing on HDC1 fully complemented line (HDC1c), hdc1-1 knock-out mutant (hdc1-1) and hdc1-1 mutant expressing the HDC1 domain RXT3 (RXT3). Seedlings were grown for 3 days on control plates and plates supplemented with 100 mM NaCl.
2024-03-27 | GSE205893 | GEO
Project description:Histone Deacetylase Complex 1 moderates stress responsiveness of germinating seeds via a histone-1-dependent process
| PRJNA848863 | ENA
Project description:Histone Deacetylase Complex 1 moderates stress responsiveness of germinating seeds via a histone-1-dependent process [RNA-Seq]
| PRJNA848121 | ENA
Project description:Histone Deacetylase Complex 1 moderates stress responsiveness of germinating seeds via a histone-1-dependent process [ChIP-Seq]
| PRJNA848923 | ENA
Project description:Histone deacetylase (HDAC) inhibitors have shown enormous promise for treating various disease states, presumably due to their ability to modulate acetylation of histone and non-histone proteins. Many of these inhibitors contain functional groups capable of strongly chelating metal ions. We demonstrate that several members of one such class of compounds, the hydroxamate-based HDAC inhibitors, can protect neurons from oxidative stress via an HDAC-independent mechanism. This previously unappreciated antioxidant mechanism involves the in situ formation of hydroxamate-iron complexes that catalyze the decomposition of hydrogen peroxide in a manner reminiscent of catalase. We demonstrate that while many hydroxamate-containing HDAC inhibitors display a propensity for binding iron, only a subset form active catalase mimetics capable of protecting neurons from exogenous H2O2. In addition to their impact on stroke and neurodegenerative disease research, these results highlight the possibility that HDAC-independent factors might play a role in the therapeutic effects of hydroxamate-based HDAC inhibitors.
| S-EPMC4562013 | biostudies-literature
Project description:Early life stress can elicit long-lasting changes in gene expression and behavior. Recent studies on rodents suggest that these lasting effects depend on the genetic background. Whether epigenetic factors also play a role remains to be investigated. Here we exposed the stress-susceptible mouse strain Balb/c and the more resilient strain C57Bl/6 to a powerful early life stress paradigm, infant maternal separation. In Balb/c mice, infant maternal separation led to decreased expression of mRNA encoding the histone deacetylases (HDACs) 1, 3, 7, 8, and 10 in the forebrain neocortex in adulthood, an effect accompanied by increased expression of acetylated histone H4 proteins, especially acetylated H4K12 protein. These changes in HDAC expression and histone modifications were not detected in C57Bl/6 mice exposed to early life stress. Moreover, a reversal of the H4K12 hyperacetylation detected in infant maternally separated Balb/c mice (achieved with chronic adolescent treatment with a low dose of theophylline that only activates HDACs) worsened the abnormal emotional phenotype resulting from this early life stress exposure. In contrast, fluoxetine, a drug with potent antidepressant efficacy in infant maternally separated Balb/c mice, potentiated all histone modifications triggered by early life stress. Moreover, in non-stressed Balb/c mice, co-administration of an HDAC inhibitor and fluoxetine, but not fluoxetine alone, elicited antidepressant effects and also triggered changes in histone H4 expression that were similar to those provoked by fluoxetine treatment of mice exposed to early life stress. These results suggest that Balb/c mice develop epigenetic modifications after early life stress exposure that, in terms of the emotive phenotype, are of adaptive nature, and that enhance the efficacy of antidepressant drugs.
| S-EPMC3225638 | biostudies-literature
Project description:It is well known that all biological systems which undergo oxidative metabolism or oxidative stress generate a small amount of light. Since the origin of excited states producing this light is generally accepted to come from chemical reactions, the term endogenous biological chemiluminescence is appropriate. Apart from biomedicine, this phenomenon has potential applications also in plant biology and agriculture like monitoring the germination rate of seeds. While chemiluminescence capability to monitor germination has been measured on multiple agriculturally relevant plants, the standard model plant Arabidopsis thaliana has not been analyzed for this process so far. To fill in this gap, we demonstrate here on A. thaliana that the intensity of endogenous chemiluminescence increases during the germination stage. We showed that the chemiluminescence intensity increases since the second day of germination, but reaches a plateau on the third day, in contrast to other plants germinating from larger seeds studied so far. We also showed that intensity increases after topical application of hydrogen peroxide in a dose-dependent manner. Further, we demonstrated that the entropy of the chemiluminescence time series is similar to random Poisson signals. Our results support a notion that metabolism and oxidative reactions are underlying processes which generate endogenous biological chemiluminescence. Our findings contribute to novel methods for non-invasive and label-free sensing of oxidative processes in plant biology and agriculture.
| S-EPMC6212569 | biostudies-literature
Project description:Histones are substrates of the SUMO (small ubiquitin-like modifier) conjugation pathway. Several reports suggest histone sumoylation affects transcription negatively, but paradoxically, our genome-wide analysis shows the modification concentrated at many active genes. We find that trans-tail regulation of histone-H2B ubiquitylation and H3K4 di-methylation potentiates subsequent histone sumoylation. Consistent with the known control of the Set3 histone deacetylase complex (HDAC) by H3K4 di-methylation, histone sumoylation directly recruits the Set3 complex to both protein-coding and noncoding RNA (ncRNA) genes via a SUMO-interacting motif in the HDAC Cpr1 subunit. The altered gene expression profile caused by reducing histone sumoylation matches well to the profile in cells lacking Set3. Histone H2B sumoylation and the Set3 HDAC coordinately suppress cryptic ncRNA transcription initiation internal to mRNA genes. Our results reveal an elaborate co-transcriptional histone crosstalk pathway involving the consecutive ubiquitylation, methylation, sumoylation and deacetylation of histones, which maintains transcriptional fidelity by suppressing spurious transcription.
| S-EPMC7708062 | biostudies-literature
Project description:AimsThe pseudo-cereal quinoa has an outstanding nutritional value. Seed germination is unusually fast, and plant tolerance to salt stress exceptionally high. Seemingly all seeds harbor bacterial endophytes. This work examines mitogen-activated protein kinase (MAPK) activities during early development. It evaluates possible contribution of endophytes to rapid germination and plant robustness.MethodsMAPK activities were monitored in water- and NaCl-imbibed seeds over a 4-h-period using an immunoblot-based approach. Cellulolytic and pectinolytic abilities of bacteria were assessed biochemically, and cellular movement, biofilm, elicitor and antimicrobial compound synthesis genes sequenced. GyrA-based, cultivation-independent studies provided first insight into endophyte diversity.ResultsQuinoa seeds and seedlings exhibit remarkably complex and dynamic MAPK activity profiles. Depending on seed origin, variances exist in MAPK patterns and probably also in endophyte assemblages. Mucilage-degrading activities enable endophytes to colonize seed surfaces of a non-host species, chia, without apparent adverse effects.ConclusionsOwing to their motility, cell wall-loosening and elicitor-generating abilities, quinoa endophytes have the potential to drive cell expansion, move across cell walls, generate damage-associated molecular patterns and activate MAPKs in their host. Bacteria may thus facilitate rapid germination and confer a primed state directly upon seed rehydration. Transfer into non-native crops appears both desirable and feasible.
| S-EPMC5798591 | biostudies-literature