Histone H3 lysine4 trimethylation‐regulated <i>GRF11</i> expression is essential for the iron‐deficiency response in <i>Arabidopsis thaliana</i>

Singh, Surjit; Kailasam, Sakthivel; Lo, Jing-Chi; Yeh, Kuo‐Chen

doi:10.1111/nph.17130

Cited by 14 publications

(9 citation statements)

References 77 publications

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“…PRC2-mediated H3K27me3 (histone 3 lysine 27 trimethylation) modulated the expression of FIT-dependent genes under iron deficiency (Park et al, 2019). Recently, NRF2/ELF8 controls the expression of the root-specific gene GRF11 through H3K4me3 and maintains the Fe-uptake machinery (Singh et al, 2021). Taking into account that the Cnr epimutant displayed increased sensitivity to Fe-deficiency response (Figure 1), it is interesting to envision whether epigenetic modifications, especially DNA methylation, play potential roles in Fe-deficiency responses.…”

Section: Discussionmentioning

confidence: 99%

Comparative Physiological and Transcriptomic Analyses Reveal Altered Fe-Deficiency Responses in Tomato Epimutant Colorless Non-ripening

Chen

Zhu²,

Han³

et al. 2022

Front. Plant Sci.

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The mechanisms associated with the regulation of iron (Fe) homeostasis have been extensively examined, however, epigenetic regulation of these processes remains largely unknown. Here, we report that a naturally occurring epigenetic mutant, Colorless non-ripening (Cnr), displayed increased Fe-deficiency responses compared to its wild-type Ailsa Craig (AC). RNA-sequencing revealed that a total of 947 and 1,432 genes were up-regulated by Fe deficiency in AC and Cnr roots, respectively, while 923 and 1,432 genes were, respectively, down-regulated. Gene ontology analysis of differentially expressed genes showed that genes encoding enzymes, transporters, and transcription factors were preferentially affected by Fe deficiency. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis revealed differential metabolic responses to Fe deficiency between AC and Cnr. Based on comparative transcriptomic analyses, 24 genes were identified as potential targets of Cnr epimutation, and many of them were found to be implicated in Fe homeostasis. By developing CRISPR/Cas9 genome editing SlSPL-CNR knockout (KO) lines, we found that some Cnr-mediated Fe-deficiency responsive genes showed similar expression patterns between SlSPL-CNR KO plants and the Cnr epimutant. Moreover, both two KO lines displayed Fe-deficiency-induced chlorosis more severe than AC plants. Additionally, the Cnr mutant displayed hypermethylation in the 286-bp epi-mutated region on the SlSPL-CNR promoter, which contributes to repressed expression of SlSPL-CNR when compared with AC plants. However, Fe-deficiency induced no change in DNA methylation both at the 286-bp epi-allele region and the entire region of SlSPL-CNR gene. Taken together, using RNA-sequencing and genetic approaches, we identified Fe-deficiency responsive genes in tomato roots, and demonstrated that SlSPL-CNR is a novel regulator of Fe-deficiency responses in tomato, thereby, paving the way for further functional characterization and regulatory network dissection.

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Section: Discussionmentioning

confidence: 99%

Comparative Physiological and Transcriptomic Analyses Reveal Altered Fe-Deficiency Responses in Tomato Epimutant Colorless Non-ripening

Chen

Zhu²,

Han³

et al. 2022

Front. Plant Sci.

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“…H3K4me3, the trimethylation of histone 3 lysine 4, generally leads to gene activation (Liu et al, 2010;Xiao et al, 2016). Using a forward genetics screen in Arabidopsis, Singh et al (2021) identified a regulator of iron deficiency response, NON-RESPONSE TO Fe-DEFICIENCY2 (NRF2). In Arabidopsis, NRF2 is known as EARLY FLOWERING8 (ELF8), which regulates FLOWERING LOCUS C (FLC) expression via H3K4me3 (He, 2009).…”

Section: H3k4me3mentioning

confidence: 99%

“…Under iron deficiency, AtNRF2/ELF8 is required for AtGRF11 expression as it modulates H3K4me3 levels at its transcription start site (Singh et al, 2021). While AtGRF11 does not directly interact with AtFIT, it acts downstream of NO to induce AtFIT expression in iron deficient roots (Singh et al, 2021). In the nrf2 mutant, AtGRF11-regulated iron uptake was repressed and iron transport and storage genes were downregulated.…”

Section: H3k4me3mentioning

confidence: 99%

Minireview: Chromatin-based regulation of iron homeostasis in plants

Yao

et al. 2022

Front. Plant Sci.

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Plants utilize delicate mechanisms to effectively respond to changes in the availability of nutrients such as iron. The responses to iron status involve controlling gene expression at multiple levels. The regulation of iron deficiency response by a network of transcriptional regulators has been extensively studied and recent research has shed light on post-translational control of iron homeostasis. Although not as considerably investigated, an increasing number of studies suggest that histone modification and DNA methylation play critical roles during iron deficiency and contribute to fine-tuning iron homeostasis in plants. This review will focus on the current understanding of chromatin-based regulation on iron homeostasis in plants highlighting recent studies in Arabidopsis and rice. Understanding iron homeostasis in plants is vital, as it is not only relevant to fundamental biological questions, but also to agriculture, biofortification, and human health. A comprehensive overview of the effect and mechanism of chromatin-based regulation in response to iron status will ultimately provide critical insights in elucidating the complexities of iron homeostasis and contribute to improving iron nutrition in plants.

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“…Chen et al 2010; Shen et al 2014; J. Li et al 2017; An et al 2020; Gómez-Zambrano et al 2018), and height or size of the plant (CLAVATA, GH9C2, ELF8, NSL1, TUA6) (Glass et al 2015; Markakis et al 2012; Noutoshi et al 2006; Fukunaga et al 2017; Singh et al 2021; Fal et al 2017; He 2004; Hoson et al 2014; Xiong et al 2013; Whitewoods et al 2020).…”

Section: Resultsmentioning

confidence: 99%

The genomic basis of the plant island syndrome in Darwin’s giant daisies

Cerca

Petersen

et al. 2022

Preprint

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Oceanic archipelagos comprise multiple disparate environments over small geographic areas and are isolated from other biotas. These conditions have led to some of the most spectacular adaptive radiations, which have been key to our understanding of evolution, and offer a unique chance to characterise the genomic basis underlying rapid and pronounced phenotypic changes. Repeated patterns of evolutionary change in plants on oceanic archipelagos, i.e. the plant island syndrome, include changes in leaf morphology, acquisition of perennial life-style, and change of ploidy. Here, we describe the genome of the critically endangered and Galapagos endemic Scalesia atractyloides Arnot., obtaining a chromosome-resolved 3.2-Gbp assembly with 43,093 candidate gene models. Using a combination of fossil transposable elements, k-mer spectra analyses and orthologue assignment, we identify the two ancestral subgenomes and date their divergence and the polyploidization event, concluding that the ancestor of all Scalesia species on the Galapagos was an allotetraploid. There are a comparable number of genes and transposable elements across the two subgenomes, and while their synteny has been mostly conserved, we find multiple inversions that may have facilitated adaptation. We identify clear signatures of selection across genes associated with vascular development, life-growth, adaptation to salinity and changes in flowering time, thus finding compelling evidence for a genomic basis of island syndrome in Darwin's giant daisy radiation. This work advances understanding of factors influencing subgenome divergence in polyploid genomes, and characterizes the quick and pronounced genomic changes in a specular and diverse radiation of an iconic island plant radiation.

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Histone H3 lysine4 trimethylation‐regulated GRF11 expression is essential for the iron‐deficiency response in Arabidopsis thaliana

Cited by 14 publications

References 77 publications

Comparative Physiological and Transcriptomic Analyses Reveal Altered Fe-Deficiency Responses in Tomato Epimutant Colorless Non-ripening

Comparative Physiological and Transcriptomic Analyses Reveal Altered Fe-Deficiency Responses in Tomato Epimutant Colorless Non-ripening

Minireview: Chromatin-based regulation of iron homeostasis in plants

The genomic basis of the plant island syndrome in Darwin’s giant daisies

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