Nutrient stress-induced chromatin changes in plants

Secco, David; Whelan, James; Rouached, Hatem; Lister, Ryan

doi:10.1016/j.pbi.2017.04.001

Cited by 57 publications

(37 citation statements)

References 47 publications

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“…Our previous studies also proved that sunflower can grow better under slightly moderate saline conditions, which is contrary to results indicating that sunflower yield decreases with soil salinity [20]. Although salt is usually the dominant factor restricting crop growth in salt-affected regions, other factors such as climate and nutrient status may also impact crop growth [21][22][23], yet experiments cannot consider all these factors due to the associated time and cost.…”

Section: Introductioncontrasting

confidence: 68%

Testing and Improving the WOFOST Model for Sunflower Simulation on Saline Soils of Inner Mongolia, China

Zhu

Zeng

et al. 2018

Agronomy

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Monitoring and improving environmental stress in crops is vital for the sustainable development of agriculture and food security. Traditional experimental methods are costly and time-consuming, yet crop growth models focus mainly only on water and nutrient stresses. In this study, a new World Food Studies (WOFOST) model, WOFOST-ES, was developed by the addition of a general environmental stress factor (ES). To calibrate and validate WOFOST-ES, two-year micro-plot experiments and one-year field experiments with sunflower were conducted in the Hetao Irrigation District, China. The results of the micro-plot experiments indicated that the WOFOST model failed to simulate sunflower growth correctly but that the WOFOST-ES model was highly accurate in simulating both yield (R2 = 0.99, root mean square error (RMSE) = 56 kg/ha) and leaf area index (LAI) (R2 = 0.86, RMSE = 0.44). A statistical method for estimating ESs based on the dominant stress factor (salt at our study site) was also proposed as a supplemental tool for WOFOST-ES, and micro-plot and field experiments conducted in 2013 and 2017 both proved acceptable accuracy of the statistical method when using WOFOST-ES. Comparison between ESs and the water and salt stress factors of Feddes-type stress reduction functions indicated that ESs failed to reveal actual environmental stresses during the sunflower seeding stage but did reflect other environmental stresses in addition to water and salt during the bud, flowering, and maturity stages. Although the present WOFOST-ES model proved to be accurate, stable, and practical, future studies should be performed, focusing on the physical separation of ESs, their mechanistic quantification, and their evaluation at small time steps using more observations.

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Section: Introductioncontrasting

confidence: 68%

Testing and Improving the WOFOST Model for Sunflower Simulation on Saline Soils of Inner Mongolia, China

Zhu

Zeng

et al. 2018

Agronomy

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“…1a) is consistent with the post-transcriptional downregulation of HDC1 (Fig. In recent years, accumulating evidence has suggested that chromatin modification plays important roles in nutrient stresses (Secco et al, 2017). These results suggest that modifications of histone acetylation play roles in Pi deficiency-induced RSA remodeling in Arabidopsis.…”

Section: Researchsupporting

confidence: 81%

Low phosphate represses histone deacetylase complex1 to regulate root system architecture remodeling in Arabidopsis

Wang

et al. 2019

New Phytologist

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The mechanisms involved in the regulation of gene expression in response to phosphate (Pi) deficiency have been extensively studied, but their chromatin-level regulation remains poorly understood.We examined the role of histone acetylation in response to Pi deficiency by using the histone deacetylase complex1 (hdc1) mutant. Genes involved in root system architecture (RSA) remodeling were analyzed by quantitative real-time polymerase chain reaction (qPCR) and chromatin immunoprecipitation qPCR.We demonstrate that histone H3 acetylation increased under Pi deficiency, and the hdc1 mutant was hypersensitive to Pi deficiency, with primary root growth inhibition and increases in root hair number. Concomitantly, Pi deficiency repressed HDC1 protein abundances. Under Pi deficiency, hdc1 accumulated higher concentrations of Fe 3+ in the root tips and had higher expression of genes involved in RSA remodeling, such as ALUMINUM-ACTIVATED MALATE TRANSPORTER1 (ALMT1), LOW PHOSPHATE ROOT1 (LPR1), and LPR2 compared with wild-type plants. Furthermore, Pi deficiency enriched the histone H3 acetylation of ALMT1 and LPR1. Finally, genetic evidence showed that LPR1/2 was epistatic to HDC1 in regulating RSA remodeling.Our results suggest a chromatin-level control of Pi starvation responses in which HDC1-mediated histone H3 deacetylation represses the transcriptional activation of genes involved in RSA remodeling in Arabidopsis.

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“…Blue, orange, and green bars denote mean mCG, mCHG, and mCHH, respectively, at single C resolution. (Seymour et al, 2014;Eichten and Springer, 2015;Secco et al, 2015Secco et al, , 2017. Whether such DNA methylation changes are necessary for transgenerational stress memory is still unclear, with various memory traits not always aligning with changes in the DNA methylome (Ding et al, 2012;Sani et al, 2013;Murgia et al, 2015;Nosalewicz et al, 2016).…”

Section: Discussionmentioning

confidence: 99%

The Arabidopsis DNA Methylome Is Stable under Transgenerational Drought Stress

et al. 2017

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Improving the responsiveness, acclimation, and memory of plants to abiotic stress holds substantive potential for improving agriculture. An unresolved question is the involvement of chromatin marks in the memory of agriculturally relevant stresses. Such potential has spurred numerous investigations yielding both promising and conflicting results. Consequently, it remains unclear to what extent robust stress-induced DNA methylation variation can underpin stress memory. Using a slow-onset water deprivation treatment in Arabidopsis (Arabidopsis thaliana), we investigated the malleability of the DNA methylome to drought stress within a generation and under repeated drought stress over five successive generations. While drought-associated epialleles in the methylome were detected within a generation, they did not correlate with drought-responsive gene expression. Six traits were analyzed for transgenerational stress memory, and the descendants of drought-stressed lineages showed one case of memory in the form of increased seed dormancy, and that persisted one generation removed from stress. With respect to transgenerational drought stress, there were negligible conserved differentially methylated regions in drought-exposed lineages compared with unstressed lineages. Instead, the majority of observed variation was tied to stochastic or preexisting differences in the epigenome occurring at repetitive regions of the Arabidopsis genome. Furthermore, the experience of repeated drought stress was not observed to influence transgenerational epi-allele accumulation. Our findings demonstrate that, while transgenerational memory is observed in one of six traits examined, they are not associated with causative changes in the DNA methylome, which appears relatively impervious to drought stress.

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Nutrient stress-induced chromatin changes in plants

Cited by 57 publications

References 47 publications

Testing and Improving the WOFOST Model for Sunflower Simulation on Saline Soils of Inner Mongolia, China

Testing and Improving the WOFOST Model for Sunflower Simulation on Saline Soils of Inner Mongolia, China

Low phosphate represses histone deacetylase complex1 to regulate root system architecture remodeling in Arabidopsis

The Arabidopsis DNA Methylome Is Stable under Transgenerational Drought Stress

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