Epigenetic regulation of nitrogen and phosphorus responses in plants

Li, Aifu; Hu, Bin; Chu, Chengcai

doi:10.1016/j.jplph.2021.153363

Cited by 17 publications

(5 citation statements)

References 105 publications

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“…One study found that the frequency of chromatin interactions in mutants of the RdDM pathway is increased at RdDM sites, suggesting that RdDM prevents chromatin interactions in some specific regions of wild‐type plants (Rowley et al., 2017). Using methylation data, researchers have reconstructed the division of the A/B compartment (Fortin & Hansen, 2015), and several studies have found that changes in the chromatin state caused by nutrient stress are related to histone modification (Li, Hu, et al., 2021). Nonetheless, to date, there is no evidence that RdDM affects plant growth and development or the response to nutritional stress by affecting chromatin structure (Kim, 2021; Li, Hu, et al., 2021).…”

Section: Introductionmentioning

confidence: 99%

“…Using methylation data, researchers have reconstructed the division of the A/B compartment (Fortin & Hansen, 2015), and several studies have found that changes in the chromatin state caused by nutrient stress are related to histone modification (Li, Hu, et al., 2021). Nonetheless, to date, there is no evidence that RdDM affects plant growth and development or the response to nutritional stress by affecting chromatin structure (Kim, 2021; Li, Hu, et al., 2021).…”

Section: Introductionmentioning

confidence: 99%

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Chromatin remodeling analysis reveals the RdDM pathway responds to low‐phosphorus stress in maize

Luo,

Zhang,

et al. 2023

The Plant Journal

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SUMMARYChromatin in eukaryotes folds into a complex three‐dimensional (3D) structure that is essential for controlling gene expression and cellular function and is dynamically regulated in biological processes. Studies on plant phosphorus signaling have concentrated on single genes and gene interactions. It is critical to expand the existing signaling pathway in terms of its 3D structure. In this study, low‐Pi treatment led to greater chromatin volume. Furthermore, low‐Pi stress increased the insulation score and the number of TAD‐like domains, but the effects on the A/B compartment were not obvious. The methylation levels of target sites (hereafter as RdDM levels) peaked at specific TAD‐like boundaries, whereas RdDM peak levels at conserved TAD‐like boundaries shifted and decreased sharply. The distribution pattern of RdDM sites originating from the Helitron transposons matched that of genome‐wide RdDM sites near TAD‐like boundaries. RdDM pathway genes were upregulated in the middle or early stages and downregulated in the later stages under low‐Pi conditions. The RdDM pathway mutant ddm1a showed increased tolerance to low‐Pi stress, with shortened and thickened roots contributing to higher Pi uptake from the shallow soil layer. ChIP‐seq results revealed that ZmDDM1A could bind to Pi‐ and root development‐related genes. Strong associations were found between interacting genes in significantly different chromatin‐interaction regions and root traits. These findings not only expand the mechanisms by which plants respond to low‐Pi stress through the RdDM pathway but also offer a crucial framework for the analysis of biological issues using 3D genomics.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Chromatin remodeling analysis reveals the RdDM pathway responds to low‐phosphorus stress in maize

Luo,

Zhang,

et al. 2023

The Plant Journal

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“…In the presence of Pi, SYG1/PHO81/XPR1 ( SPX1 ) shows high binding affinity to PHR1 , which inhibits the interaction of PHR1 with its conserved P1BS motif. However, in the absence of Pi, the binding affinity of SPX1 to PHR1 is reduced, allowing the PHR1–P1BS interaction and subsequent induction of transcription to take place ( Liu N. et al, 2018 ; Li et al, 2021 ). For example, in rice ( Oryza sativa ), OsSPX1 and OsSPX2 interact with OsPHR2 and repress the activity of OsPHR2 in a similar way to that in Arabidopsis ( Wang et al, 2014 ; Tyagi et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Integration of small RNA, degradome, and transcriptome sequencing data illustrates the mechanism of low phosphorus adaptation in Camellia oleifera

Chen

Han

et al. 2022

Front. Plant Sci.

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Phosphorus (P) is an indispensable macronutrient for plant growth and development, and it is involved in various cellular biological activities in plants. Camellia oleifera is a unique high-quality woody oil plant that grows in the hills and mountains of southern China. However, the available P content is deficient in southern woodland soil. Until now, few studies focused on the regulatory functions of microRNAs (miRNAs) and their target genes under low inorganic phosphate (Pi) stress. In this study, we integrated small RNA, degradome, and transcriptome sequencing data to investigate the mechanism of low Pi adaptation in C. oleifera. We identified 40,689 unigenes and 386 miRNAs by the deep sequencing technology and divided the miRNAs into four different groups. We found 32 miRNAs which were differentially expressed under low Pi treatment. A total of 414 target genes of 108 miRNAs were verified by degradome sequencing. Gene ontology (GO) functional analysis of target genes found that they were related to the signal response to the stimulus and transporter activity, indicating that they may respond to low Pi stress. The integrated analysis revealed that 31 miRNA–target pairs had negatively correlated expression patterns. A co-expression regulatory network was established based on the profiles of differentially expressed genes. In total, three hub genes (ARF22, WRKY53, and SCL6), which were the targets of differentially expressed miRNAs, were discovered. Our results showed that integrated analyses of the small RNA, degradome, and transcriptome sequencing data provided a valuable basis for investigating low Pi in C. oleifera and offer new perspectives on the mechanism of low Pi tolerance in woody oil plants.

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“…In addition to allelic variation, epigenetic modifications provide a mechanism for short-term adaptation to environmental change and preservation of genetic variation. By increasing genetic plasticity epigenetic modifications may influence many aspects of plant phenology, including flowering time (Basu 2020;Agustí et al 2020;Forestan et al 2020), flower color (Jiang, Zhang & Ma 2020;Sobral, Neylan, Narbona & Dirzo 2021), vegetative growth (Li, Hu & Chu 2021a), kernel color, and vernalization (Bastow et al 2004;Csorba, Questa, Sun & Dean 2014). Epigenetic mechanisms, such as DNA methylation, histone modification, and small RNA-dependent pathways, modify the accessibility of DNA in chromatin and thus modulate gene expression and alter the plant phenotype.…”

Section: Introductionmentioning

confidence: 99%

Temperature-induced methylome changes during asexual reproduction trigger transcriptomic and phenotypic changes inFragaria vesca

Zhang

Fan

Toivainen

et al. 2022

Preprint

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Plants must quickly adapt to a changing environment in order to maintain their fitness. One rapid adaptation mechanism that promotes plasticity is epigenetic memory, which may provide long-lived organisms the precious time needed to adapt to climate change. In this study, we used the perennial plant Fragaria vesca as a model to determine how the methylome and transcriptome adapt to elevated temperatures (28 vs. 18 ˚C) over three asexual generations. Changes in flowering time, stolon number, and petiole length were induced in responses to temperature treatment in one or more ecotypes after three asexual generations in a manner indicative of an epigenetic memory. Induced methylome changes differed between four different ecotypes from Norway, Iceland, Italy, and Spain, but there were also some shared responses. Elevated temperature conditions induced significant phenotypic and methylation changes, particularly in the Norwegian ecotype. Most of the differentially methylated regions (DMRs) were in the CHG context, and most CHG and CHH DMRs were hypermethylated. Notably, the four ecotypes shared only eight CHG DMR peaks. Several differentially methylated genes (DMGs) also showed a change in gene expression. Ecotype-specific methylation and expression patterns were observed for genes related to gibberellin metabolism, flowering time, epigenetics. Furthermore, when repetitive elements (REs) were found near (2 kb) or inside a gene, they showed a negative correlation with gene expression. In conclusion, phenotypic changes induced by elevated temperatures during asexual reproduction were accompanied by changes in DNA methylation patterns. Also, positional influences of REs impacted gene expression, indicating that DNA methylation may be involved in both general and ecotype-specific phenotypic plasticity in F. vesca.

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Epigenetic regulation of nitrogen and phosphorus responses in plants

Cited by 17 publications

References 105 publications

Chromatin remodeling analysis reveals the RdDM pathway responds to low‐phosphorus stress in maize

Chromatin remodeling analysis reveals the RdDM pathway responds to low‐phosphorus stress in maize

Integration of small RNA, degradome, and transcriptome sequencing data illustrates the mechanism of low phosphorus adaptation in Camellia oleifera

Temperature-induced methylome changes during asexual reproduction trigger transcriptomic and phenotypic changes inFragaria vesca

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