Interplay of phytohormones and epigenetic regulation: A recipe for plant development and plasticity

Jiang, Kai; Guo, Haiyang; Zhai, Jixian

doi:10.1111/jipb.13384

Cited by 10 publications

(7 citation statements)

References 231 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…There are abundant causal tests of DNA methylation's effect on plasticity in plants. More than a decade of research interrogating A. thaliana DNA methylation using chemical DNMT inhibitors or epiRILs have demonstrated effects on the plasticity of growth, morphometrics, and flowering time across nitrogen, salinity, and nutrition levels ( Bossdorf et al 2010 ; Boyko et al 2010 ; Zhang et al 2013 ; Jiang et al 2023 ). Similar experiments in non-model plants including angiosperms and bryophytes have detected significant effects of DNA methyltransferase inhibition on plastic responses to intraspecific competition ( Puy et al 2018 ), salinity ( Arya et al 2016 ), transplantation ( Sammarco et al 2022 ), and iron deficiency ( Sun et al 2021 ).…”

Section: Observations At the Organismal Level—causal Tests Of Epigene...mentioning

confidence: 99%

Potential Role of DNA Methylation as a Driver of Plastic Responses to the Environment Across Cells, Organisms, and Populations

Bogan,

2024

Genome Biology and Evolution

View full text Add to dashboard Cite

There is great interest in exploring epigenetic modifications as drivers of adaptive organismal responses to environmental change. Extending this hypothesis to populations, epigenetically driven plasticity could influence phenotypic changes across environments. The canonical model posits that epigenetic modifications alter gene regulation and, subsequently impact phenotypes. We first discuss origins of epigenetic variation in nature, which may arise from genetic variation, spontaneous epimutations, epigenetic drift, or variation in epigenetic capacitors. We then review and synthesize literature addressing three facets of the aforementioned model: (i) causal effects of epigenetic modifications on phenotypic plasticity at the organismal level, (ii) divergence of epigenetic patterns in natural populations distributed across environmental gradients, and (iii) the relationship between environmentally induced epigenetic changes and gene expression at the molecular level. We focus on DNA methylation, the most extensively studied epigenetic modification. We find support for environmentally associated epigenetic structure in populations and selection on stable epigenetic variants, and that inhibition of epigenetic enzymes frequently bears causal effects on plasticity. However, there are pervasive confounding issues in the literature. Effects of chromatin-modifying enzymes on phenotype may be independent of epigenetic marks, alternatively resulting from functions and protein interactions extrinsic of epigenetics. Associations between environmentally induced changes in DNA methylation and expression are strong in plants and mammals but notably absent in invertebrates and non-mammalian vertebrates. Given these challenges, we describe emerging approaches to better investigate how epigenetic modifications affect gene regulation, phenotypic plasticity, and divergence among populations.

show abstract

Section: Observations At the Organismal Level—causal Tests Of Epigene...mentioning

confidence: 99%

Potential Role of DNA Methylation as a Driver of Plastic Responses to the Environment Across Cells, Organisms, and Populations

Bogan,

2024

Genome Biology and Evolution

View full text Add to dashboard Cite

show abstract

“…These key genes in GA biosynthesis and signaling pathway are regulated by epigenetic mechanisms. It has been demonstrated that DELLA protein regulates GA, brassinosteroid and jasmonic acid pathways by histone deacetylation to adjust plant growth and development [ 47 , 48 ]. DELLA displayed a higher expression level in PA-F than that in PA-M at S2, indicating that the DELLA proteins suppress nutritional and reproductive growth [ 23 , 45 ].…”

Section: Discussionmentioning

confidence: 99%

Genome-wide identification and comparative analysis of DNA methyltransferase and demethylase gene families in two ploidy Cyclocarya paliurus and their potential function in heterodichogamy

Wang

et al. 2023

BMC Genomics

View full text Add to dashboard Cite

Background DNA methylation is one of the most abundant epigenetic modifications, which plays important roles in flower development, sex differentiation, and regulation of flowering time. Its pattern is affected by cytosine-5 DNA methyltransferase (C5-MTase) and DNA demethylase (dMTase). At present, there are no reports on C5-MTase and dMTase genes in heterodichogamous Cyclocarya paliurus. Results In this study, 6 CpC5-MTase and 3 CpdMTase genes were identified in diploid (2n = 2 × = 32) C. paliurus, while 20 CpC5-MTase and 13 CpdMTase genes were identified in autotetraploid (2n = 4 × = 64). 80% of identified genes maintained relatively fixed positions on chromosomes during polyploidization. In addition, we found that some DRM subfamily members didn’t contain the UBA domain. The transcript abundance of CpC5-MTase and CpdMTase in male and female flowers of two morphs (protandry and protogyny) from diploidy was analyzed. Results showed that all genes were significantly up-regulated at the stage of floral bud break (S2), but significantly down-regulated at the stage of flower maturation (S4). At S2, some CpC5-MTase genes showed higher expression levels in PG-M than in PG-F, whereas some CpdMTase genes showed higher expression levels in PA-M than in PA-F. In addition, these genes were significantly associated with gibberellin synthesis-related genes (e.g. DELLA and GID1), suggesting that DNA methylation may play a role in the asynchronous floral development process through gibberellin signal. Conclusions These results broaden our understanding of the CpC5-MTase and CpdMTase genes in diploid and autotetraploid C. paliurus, and provide a novel insight into regulatory mechanisms of DNA methylation in heterodichogamy.

show abstract

“…For instance, melatonin enhances thermotolerance in soybean seedlings through balancing redox homeostasis, orchestrating antioxidant defense, and modulating phytohomones and osmolytes biosynthesis ( Imran et al., 2021 ). Meanwhile, phytohormones can reciprocally modulate epigenetic processes and regulate gene expression via other transcriptional regulatory pathways ( Jiang et al., 2023 ). Therefore, untangling the complex crosstalk existing among phytohormones, stress signalling molecules and osmolytes will crucially assist in pinpointing key hub points or nodes for targeted manipulation for metabolic engineering of D/+H tolerance in crops ( Lv et al., 2018 ; Jogawat, 2019 ; Jogawat et al., 2021 ; Saddhe et al., 2021 ; Sun et al., 2021 ; Yaqoob et al., 2022 ).…”

Section: Key Pathways Targeted For Manipulationmentioning

confidence: 99%

“…Therefore, untangling the complex crosstalk existing among phytohormones, stress signalling molecules and osmolytes will crucially assist in pinpointing key hub points or nodes for targeted manipulation for metabolic engineering of D/+H tolerance in crops ( Lv et al., 2018 ; Jogawat, 2019 ; Jogawat et al., 2021 ; Saddhe et al., 2021 ; Sun et al., 2021 ; Yaqoob et al., 2022 ). Additionally, a comprehensive understanding of the common features of plant transcriptional- and epigenetic-regulatory pathways and how cross-regulation among phytohormones acts upon gene expression will be key in identifying hub target genes (such as CPKs and MPKs) for engineering D/+H tolerance ( Waadt et al., 2022 ; Jiang et al., 2023 ; Yin et al., 2023 ). However, it must be highlighted that engineering phytohormone signalling pathways is challenging and delicate, due to the large genetic redundancy and complexity of the signalling pathways ( Braguy and Zurbriggen, 2016 ).…”

Section: Key Pathways Targeted For Manipulationmentioning

confidence: 99%

Metabolic pathways engineering for drought or/and heat tolerance in cereals

Liu,

Zenda,

Tian

et al. 2023

Front. Plant Sci.

View full text Add to dashboard Cite

Drought (D) and heat (H) are the two major abiotic stresses hindering cereal crop growth and productivity, either singly or in combination (D/+H), by imposing various negative impacts on plant physiological and biochemical processes. Consequently, this decreases overall cereal crop production and impacts global food availability and human nutrition. To achieve global food and nutrition security vis-a-vis global climate change, deployment of new strategies for enhancing crop D/+H stress tolerance and higher nutritive value in cereals is imperative. This depends on first gaining a mechanistic understanding of the mechanisms underlying D/+H stress response. Meanwhile, functional genomics has revealed several stress-related genes that have been successfully used in target-gene approach to generate stress-tolerant cultivars and sustain crop productivity over the past decades. However, the fast-changing climate, coupled with the complexity and multigenic nature of D/+H tolerance suggest that single-gene/trait targeting may not suffice in improving such traits. Hence, in this review-cum-perspective, we advance that targeted multiple-gene or metabolic pathway manipulation could represent the most effective approach for improving D/+H stress tolerance. First, we highlight the impact of D/+H stress on cereal crops, and the elaborate plant physiological and molecular responses. We then discuss how key primary metabolism- and secondary metabolism-related metabolic pathways, including carbon metabolism, starch metabolism, phenylpropanoid biosynthesis, γ-aminobutyric acid (GABA) biosynthesis, and phytohormone biosynthesis and signaling can be modified using modern molecular biotechnology approaches such as CRISPR-Cas9 system and synthetic biology (Synbio) to enhance D/+H tolerance in cereal crops. Understandably, several bottlenecks hinder metabolic pathway modification, including those related to feedback regulation, gene functional annotation, complex crosstalk between pathways, and metabolomics data and spatiotemporal gene expressions analyses. Nonetheless, recent advances in molecular biotechnology, genome-editing, single-cell metabolomics, and data annotation and analysis approaches, when integrated, offer unprecedented opportunities for pathway engineering for enhancing crop D/+H stress tolerance and improved yield. Especially, Synbio-based strategies will accelerate the development of climate resilient and nutrient-dense cereals, critical for achieving global food security and combating malnutrition.

show abstract

Interplay of phytohormones and epigenetic regulation: A recipe for plant development and plasticity

Cited by 10 publications

References 231 publications

Potential Role of DNA Methylation as a Driver of Plastic Responses to the Environment Across Cells, Organisms, and Populations

Potential Role of DNA Methylation as a Driver of Plastic Responses to the Environment Across Cells, Organisms, and Populations

Genome-wide identification and comparative analysis of DNA methyltransferase and demethylase gene families in two ploidy Cyclocarya paliurus and their potential function in heterodichogamy

Metabolic pathways engineering for drought or/and heat tolerance in cereals

Contact Info

Product

Resources

About