Histone acetylation and deacetylation play essential roles in eukaryotic gene regulation. Reversible modifications of core histones are catalyzed by two intrinsic enzymes, histone acetyltransferase and histone deacetylase (HD). In general, histone deacetylation is related to transcriptional gene silencing, whereas acetylation correlates with gene activation. We produced transgenic plants expressing the antisense Arabidopsis HD (AtHD1) gene. AtHD1 is a homolog of human HD1 and RPD3 global transcriptional regulator in yeast. Expression of the antisense AtHD1 caused dramatic reduction in endogenous AtHD1 transcription, resulting in accumulation of acetylated histones, notably tetraacetylated H4. Reduction in AtHD1 expression and AtHD1 production and changes in acetylation profiles were associated with various developmental abnormalities, including early senescence, ectopic expression of silenced genes, suppression of apical dominance, homeotic changes, heterochronic shift toward juvenility, flower defects, and male and female sterility. Some of the phenotypes could be attributed to ectopic expression of tissue-specific genes (e.g., SUPERMAN) in vegetative tissues. No changes in genomic DNA methylation were detected in the transgenic plants. These results suggest that AtHD1 is a global regulator, which controls gene expression during development through DNA-sequence independent or epigenetic mechanisms in plants. In addition to DNA methylation, histone modifications may be involved in a general regulatory mechanism responsible for plant plasticity and variation in nature.

Blocking histone deacetylation in Arabidopsis induces pleiotropic effects on plant gene regulation and development. [Erratum: June 19, 2001, v. 98 (13), p. 7647.]

Contents Summary 1724 I. Introduction 1725 II. Ripening genes 1725 III. The importance of ethylene in controlling ripening 1727 IV. The importance of MADS-RIN in controlling ripening 1729 V. Interactions between components of the ripening regulatory network 1734 VI. Conclusions 1736 Acknowledgements 1738 Author contributions 1738 References 1738 SUMMARY: Understanding the regulation of fleshy fruit ripening is biologically important and provides insights and opportunities for controlling fruit quality, enhancing nutritional value for animals and humans, and improving storage and waste reduction. The ripening regulatory network involves master and downstream transcription factors (TFs) and hormones. Tomato is a model for ripening regulation, which requires ethylene and master TFs including NAC-NOR and the MADS-box protein MADS-RIN. Recent functional characterization showed that the classical RIN-MC gene fusion, previously believed to be a loss-of-function mutation, is an active TF with repressor activity. This, and other evidence, has highlighted the possibility that MADS-RIN itself is not important for ripening initiation but is required for full ripening. In this review, we discuss the diversity of components in the control network, their targets, and how they interact to control initiation and progression of ripening. Both hormones and individual TFs affect the status and activity of other network participants, which changes overall network signaling and ripening outcomes. MADS-RIN, NAC-NOR and ethylene play critical roles but there are still unanswered questions about these and other TFs. Further attention should be paid to relationships between ethylene, MADS-RIN and NACs in ripening control.

https://nph.onlinelibrary.wiley.com/doi/epdf/10.1111/nph.15545

A critical evaluation of the role of ethylene and MADS transcription factors in the network controlling fleshy fruit ripening

Genetic Control of Glandular Trichome Development.

Fruit ripening is governed by a complex regulatory network. Reversible histone methylation and demethylation regulate chromatin structure and gene expression. However, little is known about the involvement of histone demethylases in regulating fruit ripening. Here, we found that the tomato (Solanum lycopersicum) SlJMJ6 encodes a histone lysine demethylase that specifically demethylates H3K27 methylation. Overexpression of SlJMJ6 accelerates tomato fruit ripening, which is associated with the upregulated expression of a large number of ripening-related genes. Integrated analysis of RNA-seq and chromatin immunoprecipitation followed by sequencing identified 32 genes directly targeted by SlJMJ6 and transcriptionally upregulated with decreased H3K27m3 in SlJMJ6-overexpressed fruit. Numerous SlJMJ6-regulated genes are involved in transcription regulation, ethylene biosynthesis, cell wall degradation and hormone signaling. Eleven ripening-related genes including RIPENING INHIBITOR (RIN), 1-aminocyclopropane 1-carboxylate synthase-4 (ACS4), 1-aminocyclopropane-1-carboxylate oxidase 1 (ACO1), pectate lyase (PL) and beta-galactosidase 4 (TBG4), and a DNA demethylase DML2, were confirmed to be regulated directly by SlJMJ6 through removing H3K27me3. Our results demonstrate that SlJMJ6 is a ripening-prompting H3K27me3 demethylase that activates the expression of the ripening-related genes by modulating H3K27me3, thereby facilitating tomato fruit ripening. Our work also reveals a novel link between histone demethylation and DNA demethylation in regulating fruit ripening. To our knowledge, this is the first report of the involvement of a histone lysine demethylase in the regulation of fruit ripening.

https://nph.onlinelibrary.wiley.com/doi/epdf/10.1111/nph.16590

Histone demethylase SlJMJ6 promotes fruit ripening by removing H3K27 methylation of ripening-related genes in tomato

Fruit development is a complex process that is regulated not only by plant hormones and transcription factors, but also requires epigenetic modifications. Epigenetic modifications include DNA methylation, histone post-translational modifications, chromatin remodeling and noncoding RNAs. Together, these epigenetic modifications, which are controlled during development and in response to the environment, determine the chromatin state of genes and contribute to the transcriptomes of an organism. Recent studies have demonstrated that epigenetic regulation plays an important role in fleshy fruit ripening. Dysfunction of a DNA demethylase delayed ripening in tomato, and the application of a DNA methylation inhibitor altered ripening process in the fruits of several species. These studies indicated that manipulating the epigenome of fruit crops could open new ways for breeding in the future. In this review, we highlight recent progress and address remaining questions and challenges concerning the epigenetic regulation of fruit development and ripening.

https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.16724

Fruit development and epigenetic modifications.

Silencing of histone deacetylase SlHDT3 delays fruit ripening and suppresses carotenoid accumulation in tomato.

The Jasmonate ZIM-domain protein gene SlJAZ2 regulates plant morphology and accelerates flower initiation in Solanum lycopersicum plants.

The MADS-box gene SlMBP11 regulates plant architecture and affects reproductive development in tomato plants.

MADS-box genes have been demonstrated to participate in a number of processes in tomato development, especially fruit ripening. In this study, we reported a novel MADS-box gene, SlMBP15, which is implicated in fruit ripening. Based on statistical analysis, the ripening time of SlMBP15-silenced tomato was delayed by 2-4 days compared with that of the wild-type (WT). The accumulation of carotenoids and biosynthesis of ethylene in fruits were decreased in SlMBP15-silenced tomato. Genes related to carotenoid and ethylene biosynthesis were greatly repressed. SlMBP15 can interact with RIN, a MADS-box regulator affecting the carotenoid accumulation and ethylene biosynthesis in tomato. In addition, SlMBP15-silenced tomato produced dark green leaves, and its plant height was reduced. The gibberellin (GA) content of transgenic plants was lower than that of the WT and GA biosynthesis genes were repressed. These results demonstrated that SlMBP15 not only positively regulated tomato fruit ripening but also affected the morphogenesis of the vegetative organs.

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Suppression of SlMBP15 Inhibits Plant Vegetative Growth and Delays Fruit Ripening in Tomato

Histone deacetylation catalyzed by histone deacetylases is an important type of histone modification. Histone deacetylases affect various processes of plant development and involve in responding to hormones and biotic and abiotic stresses. Here, we report a tomato PRD3/HDA1 histone deacetylase gene, SlHDA5, which is expressed ubiquitously in different tissues and development stages. Expression profiles in hormone treatments showed that SlHDA5 was induced by abscisic acid (ABA) and methyl jasmonate (MeJA). Seedlings growth of SlHDA5-RNAi lines were more inhibited on the medium containing salt compared with wild type (WT). Under salt stress, chlorophyll in mature leaves degraded earlier in transgenic leaves than that in WT, and transgenic plants displayed wilting earlier and more severe than WT. After drought treatment, transgenic plants wilted and dehydrated earlier than WT, which was confirmed by lower water and chlorophyll content, and higher malondialdehyde (MDA) content in transgenic plants manifesting that the tolerance of transgenic plants to drought receded. Under the treatment of ABA, root length of transgenic seedlings was more strongly repressed by contrast with WT, suggesting repression of SlHDA5 increased seedling sensibility to ABA. Our study indicated that silencing of SlHDA5 resulted in decreasing tolerance to salt, drought, and ABA.

Boyan Tang

Papers

Silencing of histone deacetylase SlHDT3 delays fruit ripening and suppresses carotenoid accumulation in tomato.

The Jasmonate ZIM-domain protein gene SlJAZ2 regulates plant morphology and accelerates flower initiation in Solanum lycopersicum plants.

The MADS-box gene SlMBP11 regulates plant architecture and affects reproductive development in tomato plants.

Suppression of SlMBP15 Inhibits Plant Vegetative Growth and Delays Fruit Ripening in Tomato

SlHDA5 , a Tomato Histone Deacetylase Gene, Is Involved in Responding to Salt, Drought, and ABA