Histone modifications and chromatin remodelling in plants in response to salt stress

Yung, Wai‐Shing; Li, Man-Wah; Sze, Ching-Ching; Wang, Qianwen; Lam, Hon‐Ming

doi:10.1111/ppl.13467

Cited by 29 publications

(27 citation statements)

References 129 publications

(240 reference statements)

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“…The modulation of transcriptional responses is important in regulating a broad range of cellular processes underlying salt stress priming. Recent studies have proposed that epigenetic features such as histone marks may be altered as a consequence of priming, which in turn modify the chromatin status and modulate transcriptional responses during subsequent stress exposure (Fu et al., 2021; Sun et al., 2020; Yung et al., 2021; Zheng et al., 2019). In Arabidopsis ( Arabidopsis thaliana ), the increased histone 3 lysine 4 trimethylation (H3K4me3) levels at WRKY6 , WRKY29 , and WRKY53 were followed by higher gene expression levels when the plants were exposed to the wounding stress directly after the priming pre‐treatment (Jaskiewicz et al., 2011).…”

Section: Introductionmentioning

confidence: 99%

Priming‐induced alterations in histone modifications modulate transcriptional responses in soybean under salt stress

et al. 2022

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Plants that have experienced certain abiotic stress may gain tolerance to a similar stress in subsequent exposure. This phenomenon, called priming, was observed here in soybean (Glycine max) seedlings exposed to salt stress. Time-course transcriptomic profiles revealed distinctively different transcriptional responses in the primed seedlings from those in the non-primed seedlings under high salinity stress, indicating a stress response strategy of repressing unhelpful biotic stress responses and focusing on the promotion of those responses important for salt tolerance. To identify histone marks altered by the priming salinity treatment, a genome-wide profiling of histone 3 lysine 4 dimethylation (H3K4me2), H3K4me3, and histone 3 lysine 9 acetylation (H3K9ac) was performed. Our integrative analyses revealed that priming induced drastic alterations in these histone marks, which coordinately modified the stress response, ion homeostasis, and cell wall modification. Furthermore, transcriptional network analyses unveiled epigenetically modified networks which mediate the strategic downregulation of defense responses. Altering the histone acetylation status using a chemical inhibitor could elicit the priming-like transcriptional responses in non-primed seedlings, confirming the importance of histone marks in forming the priming response.

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Section: Introductionmentioning

confidence: 99%

Priming‐induced alterations in histone modifications modulate transcriptional responses in soybean under salt stress

et al. 2022

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“…Long-term adaptation and short-term reaction to environmental factors are underpinned by the changes in gene(s) expression ( Franklin et al, 2014 ). The changes in gene expression and chromatin organization due to histone modifications and nuclear compartmentalization are vital for plant responses to environmental cues ( Sun L. et al, 2020 ; Yung et al, 2021 ). This section focuses on how environmental factors affect histone modifications, chromatin architecture, nuclear localization, and their effects on regulation of gene expression, plant development, and stress tolerance.…”

Section: Modulation In 3d Genome Architecturementioning

confidence: 99%

“…Expressions of some of the chromatin remodeling complexes (e.g., SNF2 and SWR1 factors) have been reported to be responsive to salt stress ( Li et al, 2011 ). Chromatin-remodeling complexes are involved in ATP-dependent repositioning of nucleosomes and changes in the core histone composition of a nucleosome, which regulates chromatin accessibility under stressful conditions ( Clapier et al, 2017 ; Yung et al, 2021 ). Studies also suggest that Topless-like/Topless-like protein (TPL/TPR) interacts with HDAc to regulate stress responses ( Tang et al, 2016 ; Cheng et al, 2018 ) ( Figure 4B ).…”

Section: Modulation In 3d Genome Architecturementioning

confidence: 99%

“…Acetylation of lysine residues in the tails of histone proteins neutralizes the positive charge and reduces electrostatic interaction between histones−DNA, and helps to loosen the DNA packing, allowing the access of transcription machinery to the gene(s) ( Bannister and Kouzarides, 2011 ). In addition, the chromatin-remodeling factor PKL was reported to modulate chromatin accessibility to other transcriptional regulators, leading to altered expression of salt stress-responsive genes ( Yung et al, 2021 ). The accessibility of a gene was reported to be modulated by post-translational modifications of histone proteins as well as the chromatin-remodelling complexes that regulate nucleosome assembly and spacing ( Lusser and Kadonaga, 2003 ; Hargreaves and Crabtree, 2011 ; Clapier et al, 2017 ).…”

Section: Modulation In 3d Genome Architecturementioning

confidence: 99%

“…(Bannister and Kouzarides, 2011). In addition, the chromatinremodeling factor PKL was reported to modulate chromatin accessibility to other transcriptional regulators, leading to altered expression of salt stress-responsive genes (Yung et al, 2021). The accessibility of a gene was reported to be modulated by post-translational modifications of histone proteins as well as the chromatin-remodelling complexes that regulate nucleosome assembly and spacing (Lusser and Kadonaga, 2003;Hargreaves and Crabtree, 2011;Clapier et al, 2017).…”

Section: Salt-induced Chromatin Dynamicsmentioning

confidence: 99%

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Understanding 3D Genome Organization and Its Effect on Transcriptional Gene Regulation Under Environmental Stress in Plant: A Chromatin Perspective

Kumar

Kaur

Seem

et al. 2021

Front. Cell Dev. Biol.

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The genome of a eukaryotic organism is comprised of a supra-molecular complex of chromatin fibers and intricately folded three-dimensional (3D) structures. Chromosomal interactions and topological changes in response to the developmental and/or environmental stimuli affect gene expression. Chromatin architecture plays important roles in DNA replication, gene expression, and genome integrity. Higher-order chromatin organizations like chromosome territories (CTs), A/B compartments, topologically associating domains (TADs), and chromatin loops vary among cells, tissues, and species depending on the developmental stage and/or environmental conditions (4D genomics). Every chromosome occupies a separate territory in the interphase nucleus and forms the top layer of hierarchical structure (CTs) in most of the eukaryotes. While the A and B compartments are associated with active (euchromatic) and inactive (heterochromatic) chromatin, respectively, having well-defined genomic/epigenomic features, TADs are the structural units of chromatin. Chromatin architecture like TADs as well as the local interactions between promoter and regulatory elements correlates with the chromatin activity, which alters during environmental stresses due to relocalization of the architectural proteins. Moreover, chromatin looping brings the gene and regulatory elements in close proximity for interactions. The intricate relationship between nucleotide sequence and chromatin architecture requires a more comprehensive understanding to unravel the genome organization and genetic plasticity. During the last decade, advances in chromatin conformation capture techniques for unravelling 3D genome organizations have improved our understanding of genome biology. However, the recent advances, such as Hi-C and ChIA-PET, have substantially increased the resolution, throughput as well our interest in analysing genome organizations. The present review provides an overview of the historical and contemporary perspectives of chromosome conformation capture technologies, their applications in functional genomics, and the constraints in predicting 3D genome organization. We also discuss the future perspectives of understanding high-order chromatin organizations in deciphering transcriptional regulation of gene expression under environmental stress (4D genomics). These might help design the climate-smart crop to meet the ever-growing demands of food, feed, and fodder.

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Changes in epigenetic features in legumes under abiotic stresses

Yung

Huang

et al. 2022

The Plant Genome

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Legume crops are rich in nutritional value for human and livestock consumption. With global climate change, developing stress‐resilient crops is crucial for ensuring global food security. Because of their nitrogen‐fixing ability, legumes are also important for sustainable agriculture. Various abiotic stresses, such as salt, drought, and elevated temperatures, are known to adversely affect legume production. The responses of plants to abiotic stresses involve complicated cellular processes including stress hormone signaling, metabolic adjustments, and transcriptional regulations. Epigenetic mechanisms play a key role in regulating gene expressions at both transcriptional and posttranscriptional levels. Increasing evidence suggests the importance of epigenetic regulations of abiotic stress responses in legumes, and recent investigations have extended the scope to the epigenomic level using next‐generation sequencing technologies. In this review, the current knowledge on the involvement of epigenetic features, including DNA methylation, histone modification, and noncoding RNAs, in abiotic stress responses in legumes is summarized and discussed. Since most of the available information focuses on a single aspect of these epigenetic features, integrative analyses involving omics data in multiple layers are needed for a better understanding of the dynamic chromatin statuses and their roles in transcriptional regulation. The inheritability of epigenetic modifications should also be assessed in future studies for their applications in improving stress tolerance in legumes through the stable epigenetic optimization of gene expressions.

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Histone modifications and chromatin remodelling in plants in response to salt stress

Cited by 29 publications

References 129 publications

Priming‐induced alterations in histone modifications modulate transcriptional responses in soybean under salt stress

Priming‐induced alterations in histone modifications modulate transcriptional responses in soybean under salt stress

Understanding 3D Genome Organization and Its Effect on Transcriptional Gene Regulation Under Environmental Stress in Plant: A Chromatin Perspective

Changes in epigenetic features in legumes under abiotic stresses

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