Differential expression of histone deacetylases during banana ripening and identification of MaHDA6 in regulating ripening-associated genes

Fu, Changchun; Han, Yanchao; Guo, Yufan; Kuang, Jian-fei; Chen, Jian-Ye; Shan, Wei; Lu, Wang-jin

doi:10.1016/j.postharvbio.2018.03.010

Cited by 26 publications

(26 citation statements)

References 60 publications

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“…In tomato, 32 HAT family members and 15 HDAC family members were identified based on whole genome sequencing ( Cigliano et al, 2013 ). For example, tomato HDAC proteins have been shown to accumulate during fruit development ( Cigliano et al, 2013 ), and MaHDA6 may be involved in banana ripening through binding to the MaERF11/15 promoters ( Fu et al, 2018 ). Moreover, EAR motif-containing proteins have been proposed to form transcriptional repression complexes by recruiting other co-repressors, such as HDAC proteins ( Kagale and Rozwadowski, 2011 ), and it has been suggested that MaERF11 may recruit MaHDA1 to transcriptionally repress its MaACO1 target ( Han et al, 2016 ).…”

Section: Discussionmentioning

confidence: 99%

“…HDACs have been reported to play important roles in plant growth and development, including seed ( Chhun et al, 2016 ) and flower development ( Kang et al, 2015 ; Bollier et al, 2018 ), as well as stress responses ( Luo et al, 2012 ) in Arabidopsis thaliana . In recent years, the involvement of HDACs in the regulation of fruit development has been studied in tomato (Guo et al, 2017 , 2018 ), cucumber ( Cucumis sativus ; Zhang et al, 2020 ), pear ( Pyrus communis L.; Li et al, 2020 ), and banana ( Xiao et al, 2013 ; Han et al, 2016 ; Fu et al, 2018 ). However, much remains to be learnt about the scale and direct targets of HDAC-mediated gene repression in fruit development.…”

Section: Introductionmentioning

confidence: 99%

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Ethylene response factor MdERF4 and histone deacetylase MdHDA19 suppress apple fruit ripening through histone deacetylation of ripening-related genes

Han

Wang

et al. 2022

Plant Physiology

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Histone deacetylase enzymes participate in the regulation of many aspects of plant development. However, the genome-level targets of histone deacetylation during apple (Malus domestica) fruit development have not been resolved in detail, and the mechanisms of regulation of such a process are unknown. We previously showed that the complex of ethylene response factor 4 (MdERF4) and the TOPLESS co-repressor (MdTPL4) (MdERF4-MdTPL4) is constitutively active during apple fruit development, but whether this transcriptional repression complex is coupled to chromatin modification is unknown. Here, we show that a histone deacetylase (MdHDA19) is recruited to the MdERF4-MdTPL4 complex, thereby impacting fruit ethylene biosynthesis. Transient suppression of MdHDA19 expression promoted fruit ripening and ethylene production. To identify potential downstream target genes regulated by MdHDA19, we conducted chromatin immunoprecipitation (ChIP) sequencing of H3K9 and ChIP-quantitative PCR assays. We found that MdHDA19 affects ethylene production by facilitating H3K9 deacetylation and forms a complex with MdERF4-MdTPL4 to directly repress MdACS3a expression by decreasing the degree of acetylation. We demonstrate that an early-maturing-specific acetylation H3K9ac peak in MdACS3a and expression of MdACS3a were specifically up-regulated in fruit of an early-maturing, but not a late-maturing, cultivar. We provide evidence that a C-to-G mutation in the EAR motif of MdERF4 reduces the repression of MdACS3a by the MdERF4-MdTPL4-MdHDA19 complex. Taken together, our results reveal that the MdERF4-MdTPL-MdHDA19 repressor complex participates in the epigenetic regulation of apple fruit ripening.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Ethylene response factor MdERF4 and histone deacetylase MdHDA19 suppress apple fruit ripening through histone deacetylation of ripening-related genes

Han

Wang

et al. 2022

Plant Physiology

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“…Based on sequence homology with yeast HDACs, plant HDACs are classified into three different groups, including Reduced Potassium Dependency-3/Histone Deacetylase 1 (RPD3/HDA1), which requires a zinc ion cofactor for deacetylase activity ( Yang & Seto, 2007 ), Silent Information Regulator 2 (SIR2), which depends on nicotinamide adenine dinucleotide (NAD + ), and Histone Deacetylase 2 (HD2), which is unique in plants ( Hirschey, 2011 ; Pandey et al., 2002 ). Researchers have identified and characterized some HDAC genes in a wide range of plant species, such as maize ( Zea mays ) ( Forestan et al, 2018 ), A. thaliana ( Hollender & Liu, 2008 ), rice ( Oryza sativa ) ( Fu, Wu & Duan, 2007 ), barley ( Hordeum vulgare ) ( Demetriou et al, 2009 ), potato ( Solanum chacoense ) ( Lagacé et al, 2003 ), grape ( Vitis vinifera ) ( Busconi et al, 2009 ), tobacco ( Nicotiana tabacum ) ( Bourque et al, 2011 ), black cottonwood ( Populus trichocarpa ) ( Alinsug, Yu & Wu, 2009 ), banana ( Musa acuminata ) ( Fu et al, 2018 ), soybean ( Glycine max ) ( Yang et al, 2018 ), litchi ( Litchi chinensis ) ( Peng et al, 2017 ), common bean ( Phaseolus vulgaris ) ( Hayford et al, 2017 ), common liverwort ( Marchantia polymorpha ) ( Chu & Chen, 2018 ) and tomato ( Solanum lycopersicum ) ( Zhao et al, 2015 ), and have studied the functions of certain HDAC genes. For example, HDAC genes are involved in plant responses to stress-related hormones such as salicylic acid (SA), abscisic acid (ABA) or jasmonic acid (JA) and stress stimuli such as drought, cold, salt, and pathogens ( Ma et al, 2013 ).…”

Section: Introductionmentioning

confidence: 99%

Identification of histone deacetylase genes in Dendrobium officinale and their expression profiles under phytohormone and abiotic stress treatments

Zhang

Silva²,

et al. 2020

PeerJ

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The deacetylation of core histones controlled by the action of histone deacetylases (HDACs) plays an important role in the epigenetic regulation of plant gene transcription. However, no systematic analysis of HDAC genes in Dendrobium officinale, a medicinal orchid, has been performed. In the current study, a total of 14 histone deacetylases in D. officinale were identified and characterized using bioinformatics-based methods. These genes were classified into RPD3/HDA1, SIR2, and HD2 subfamilies. Most DoHDAC genes in the same subfamily shared similar structures, and their encoded proteins contained similar motifs, suggesting that the HDAC family members are highly conserved and might have similar functions. Different cis-acting elements in promoters were related to abiotic stresses and exogenous plant hormones. A transient expression assay in onion epidermal cells by Agrobacterium-mediated transformation indicated that all of the detected histone deacetylases such as DoHDA7, DoHDA9, DoHDA10, DoHDT3, DoHDT4, DoSRT1 and DoSRT2, were localized in the nucleus. A tissue-specific analysis based on RNA-seq suggested that DoHDAC genes play a role in growth and development in D. officinale. The expression profiles of selected DoHDAC genes under abiotic stresses and plant hormone treatments were analyzed by qRT-PCR. DoHDA3, DoHDA8, DoHDA10 and DoHDT4 were modulated by multiple abiotic stresses and phytohormones, indicating that these genes were involved in abiotic stress response and phytohormone signaling pathways. These results provide valuable information for molecular studies to further elucidate the function of DoHDAC genes.

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“…Histone deacetylases (HDACs) are involved in deacetylation of major histone proteins. Seventeen MaHDACs were identified, among which MaHDA6 was found to control fruit ripening by histone deacetylation of the transcription factor genes, MaERF11/15 [ 85 ]. Similarly, CpHDA3 mediated the expression of pectin methylesterase and polygalacturonase genes during papaya fruit ripening and softening by forming a histone deacetylase repressor complex with CpERF9 transcription factor [ 86 ].…”

Section: Fruit Ripeningmentioning

confidence: 99%

Genomic Approaches for Improvement of Tropical Fruits: Fruit Quality, Shelf Life and Nutrient Content

Mathiazhagan

Chidambara

Laxman

et al. 2021

Genes

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The breeding of tropical fruit trees for improving fruit traits is complicated, due to the long juvenile phase, generation cycle, parthenocarpy, polyploidy, polyembryony, heterozygosity and biotic and abiotic factors, as well as a lack of good genomic resources. Many molecular techniques have recently evolved to assist and hasten conventional breeding efforts. Molecular markers linked to fruit development and fruit quality traits such as fruit shape, size, texture, aroma, peel and pulp colour were identified in tropical fruit crops, facilitating Marker-assisted breeding (MAB). An increase in the availability of genome sequences of tropical fruits further aided in the discovery of SNP variants/Indels, QTLs and genes that can ascertain the genetic determinants of fruit characters. Through multi-omics approaches such as genomics, transcriptomics, metabolomics and proteomics, the identification and quantification of transcripts, including non-coding RNAs, involved in sugar metabolism, fruit development and ripening, shelf life, and the biotic and abiotic stress that impacts fruit quality were made possible. Utilizing genomic assisted breeding methods such as genome wide association (GWAS), genomic selection (GS) and genetic modifications using CRISPR/Cas9 and transgenics has paved the way to studying gene function and developing cultivars with desirable fruit traits by overcoming long breeding cycles. Such comprehensive multi-omics approaches related to fruit characters in tropical fruits and their applications in breeding strategies and crop improvement are reviewed, discussed and presented here.

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Differential expression of histone deacetylases during banana ripening and identification of MaHDA6 in regulating ripening-associated genes

Cited by 26 publications

References 60 publications

Ethylene response factor MdERF4 and histone deacetylase MdHDA19 suppress apple fruit ripening through histone deacetylation of ripening-related genes

Ethylene response factor MdERF4 and histone deacetylase MdHDA19 suppress apple fruit ripening through histone deacetylation of ripening-related genes

Identification of histone deacetylase genes in Dendrobium officinale and their expression profiles under phytohormone and abiotic stress treatments

Genomic Approaches for Improvement of Tropical Fruits: Fruit Quality, Shelf Life and Nutrient Content

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