Histone Modification and Chromatin Remodeling During the Seed Life Cycle

Ding, Xiali; Jia, Xuhui; Xiang, Yong Bing; Jiang, Wenhui

doi:10.3389/fpls.2022.865361

Cited by 17 publications

(19 citation statements)

References 166 publications

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“…The different seed postgermination stages are not independent of each other; in contrast, they are correlated with each other and are precisely regulated. Specific transcriptional events are closely linked to the chromatin state, which is modulated by epigenetic modifications, including DNA methylation, histone modifications, and chromatin remodeling . The role of histone acetylation and deacetylation in seed behavior has been intensively studied in recent years; however, genome-wide regulation of H3K9ac postgermination has been largely unexplored …”

Section: Discussionmentioning

confidence: 99%

“…Of course, as nutrient-enriched tissue for human consumption, grains of sorghum, particularly seed germination, have been explored as a new strategy to increase nutrient content and reduce antinutrient levels . In this regard, the germination process is intricately regulated to maximize plant survival in response to various environmental stimuli, , In this regard, the germination process is intricately regulated to maximize plant survival in response to various environmental stimuli . Recent studies have revealed the critical role of histone deacetylase in seed germination, implying that dynamic changes in histone acetylation are important to the process .…”

Section: Introductionmentioning

confidence: 99%

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Global Decrease in H3K9 Acetylation in Sorghum Seed Postgermination Stages

Zhou

Zhu

Han

et al. 2023

J. Agric. Food Chem.

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Sorghum seed germination is accompanied by increases in nutrient contents and reduced levels of antinutrients and is therefore being applied to food processing. However, the characterization of acetylated histone H3 at lysine residue 9 (H3K9ac) in sorghum postgermination has lagged. In this study, we performed chromatin immunoprecipitation sequencing (ChIP-seq) to identify H3K9ac enrichment and obtained transcriptome in postgermination stages. More than 10,000 hypoacetylated genes gained H3K9ac marks in the postgermination stages. In addition, we observed that the expression of the main histone deacetylase (HDAC) genes was elevated. The application of the HDAC inhibitor trichostatin A (TSA) resulted in seed growth arrest, suggesting that the repression of the H3K9ac modification is critical for postgermination. Additionally, we obtained a comprehensive view of abundant genomic changes in H3K9ac-marked regions and transcription between the mock and TSA treatment groups, which suggested that H3K9ac was required in the late stage of autotrophic seedling establishment. Metabolic profiling, transcriptome analyses, and ChIPseq revealed that H3K9ac is enriched at genes involved in phenylpropanoid, including lignin and flavonoid, biosynthesis. Our results suggest important roles of H3K9ac in sorghum seed postgermination stages.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Global Decrease in H3K9 Acetylation in Sorghum Seed Postgermination Stages

Zhou

Zhu

Han

et al. 2023

J. Agric. Food Chem.

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“…The repressive mark H3K27me3 is deposited on chromatin, covering thousands of genomic loci, including many developmental and stress-responsive genes in plants ( Shen et al., 2021 ). For seed life cycle, H3K27me3 marks are involved in such as endosperm development, seed size, dormancy and somatic embryogenesis/callus formation after germination by contributing to repression of key regulatory gene expressions for each trait ( Ding et al., 2022 ). As we detected prominent H3K27me3 marks in the DT re-induction related gene in R5, which is after the DT window ( Figures 4B, C ), it is possible that the seed DT switch is also regulated by the expression levels of genes through the H3K27me3 modifications.…”

Section: Discussionmentioning

confidence: 99%

“…Recently, chromatin accessibility profiling in plants using Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq) has been employed in many species and has revealed a wealth of new information regarding the regulatory structure and dynamics of plant genomes ( Bubb and Deal, 2020 ). In the context of epigenetic regulation of seed maturation, dormancy, and germination, different types of histone post-translational modifications have been described to date ( Lepiniec et al., 2018 ; Smolikova et al., 2021 ; Ding et al., 2022 ). It is thus possible that DT window during seed germination is also regulated at the level of histone modifications and chromatin remodeling.…”

Section: Introductionmentioning

confidence: 99%

Chromatin dynamics associated with seed desiccation tolerance/sensitivity at early germination in Medicago truncatula

et al. 2022

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Desiccation tolerance (DT) has contributed greatly to the adaptation of land plants to severe water-deficient conditions. DT is mostly observed in reproductive parts in flowering plants such as seeds. The seed DT is lost at early post germination stage but is temporally re-inducible in 1 mm radicles during the so-called DT window following a PEG treatment before being permanently silenced in 5 mm radicles of germinating seeds. The molecular mechanisms that activate/reactivate/silence DT in developing and germinating seeds have not yet been elucidated. Here, we analyzed chromatin dynamics related to re-inducibility of DT before and after the DT window at early germination in Medicago truncatula radicles to determine if DT-associated genes were transcriptionally regulated at the chromatin levels. Comparative transcriptome analysis of these radicles identified 948 genes as DT re-induction-related genes, positively correlated with DT re-induction. ATAC-Seq analyses revealed that the chromatin state of genomic regions containing these genes was clearly modulated by PEG treatment and affected by growth stages with opened chromatin in 1 mm radicles with PEG (R1P); intermediate openness in 1 mm radicles without PEG (R1); and condensed chromatin in 5 mm radicles without PEG (R5). In contrast, we also showed that the 103 genes negatively correlated with the re-induction of DT did not show any transcriptional regulation at the chromatin level. Additionally, ChIP-Seq analyses for repressive marks H2AK119ub and H3K27me3 detected a prominent signal of H3K27me3 on the DT re-induction-related gene sequences at R5 but not in R1 and R1P. Moreover, no clear H2AK119ub marks was observed on the DT re-induction-related gene sequences at both developmental radicle stages, suggesting that silencing of DT process after germination will be mainly due to H3K27me3 marks by the action of the PRC2 complex, without involvement of PRC1 complex. The dynamic of chromatin changes associated with H3K27me3 were also confirmed on seed-specific genes encoding potential DT-related proteins such as LEAs, oleosins and transcriptional factors. However, several transcriptional factors did not show a clear link between their decrease of chromatin openness and H3K27me3 levels, suggesting that their accessibility may also be regulated by additional factors, such as other histone modifications. Finally, in order to make these comprehensive genome-wide analyses of transcript and chromatin dynamics useful to the scientific community working on early germination and DT, we generated a dedicated genome browser containing all these data and publicly available at https://iris.angers.inrae.fr/mtseedepiatlas/jbrowse/?data=Mtruncatula.

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“…The key factors and molecular mechanisms behind these processes in plants have been widely studied for decades (reviewed in Du et al, 2015; Duan et al, 2018; Zhang et al, 2018b; Song et al, 2019; Chen et al, 2020b; He et al, 2021; Shang and He, 2022). Epigenetic mechanisms are involved in plant phenotypic plasticity during their development and in response to environmental cues, including seed development (Chinnusamy et al, 2008; Markulin et al, 2021; Ding et al, 2022), flowering (He et al, 2020; Luo and He, 2020), fruit development (Tang et al, 2020), and biotic and abiotic stress responses (Zhang et al, 2018b; Alonso et al, 2019; Ashapkin et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

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

Jiang

Guo

Zhai

2022

JIPB

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Both phytohormone signaling and epigenetic mechanisms have long been known to play crucial roles in plant development and plasticity in response to ambient stimuli. Indeed, diverse signaling pathways mediated by phytohormones and epigenetic processes integrate multiple upstream signals to regulate various plant traits. Emerging evidence indicates that phytohormones and epigenetic processes interact at multiple levels. In this review, we summarize the current knowledge of the interplay between phytohormones and epigenetic processes from the perspective of phytohormone biology. We also review chemical regulators used in epigenetic studies and propose strategies for developing novel regulators using multidisciplinary approaches.

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Histone Modification and Chromatin Remodeling During the Seed Life Cycle

Cited by 17 publications

References 166 publications

Global Decrease in H3K9 Acetylation in Sorghum Seed Postgermination Stages

Global Decrease in H3K9 Acetylation in Sorghum Seed Postgermination Stages

Chromatin dynamics associated with seed desiccation tolerance/sensitivity at early germination in Medicago truncatula

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

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