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Li J, Zhang Q, Wang Z, Liu Q. The roles of epigenetic regulators in plant regeneration: Exploring patterns amidst complex conditions. PLANT PHYSIOLOGY 2024; 194:2022-2038. [PMID: 38290051 PMCID: PMC10980418 DOI: 10.1093/plphys/kiae042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/06/2023] [Accepted: 12/17/2023] [Indexed: 02/01/2024]
Abstract
Plants possess remarkable capability to regenerate upon tissue damage or optimal environmental stimuli. This ability not only serves as a crucial strategy for immobile plants to survive through harsh environments, but also made numerous modern plant improvements techniques possible. At the cellular level, this biological process involves dynamic changes in gene expression that redirect cell fate transitions. It is increasingly recognized that chromatin epigenetic modifications, both activating and repressive, intricately interact to regulate this process. Moreover, the outcomes of epigenetic regulation on regeneration are influenced by factors such as the differences in regenerative plant species and donor tissue types, as well as the concentration and timing of hormone treatments. In this review, we focus on several well-characterized epigenetic modifications and their regulatory roles in the expression of widely studied morphogenic regulators, aiming to enhance our understanding of the mechanisms by which epigenetic modifications govern plant regeneration.
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Affiliation(s)
- Jiawen Li
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Qiyan Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Zejia Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Qikun Liu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
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2
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Liu X, Bie XM, Lin X, Li M, Wang H, Zhang X, Yang Y, Zhang C, Zhang XS, Xiao J. Uncovering the transcriptional regulatory network involved in boosting wheat regeneration and transformation. NATURE PLANTS 2023; 9:908-925. [PMID: 37142750 DOI: 10.1038/s41477-023-01406-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 03/29/2023] [Indexed: 05/06/2023]
Abstract
Genetic transformation is important for gene functional study and crop improvement. However, it is less effective in wheat. Here we employed a multi-omic analysis strategy to uncover the transcriptional regulatory network (TRN) responsible for wheat regeneration. RNA-seq, ATAC-seq and CUT&Tag techniques were utilized to profile the transcriptional and chromatin dynamics during early regeneration from the scutellum of immature embryos in the wheat variety Fielder. Our results demonstrate that the sequential expression of genes mediating cell fate transition during regeneration is induced by auxin, in coordination with changes in chromatin accessibility, H3K27me3 and H3K4me3 status. The built-up TRN driving wheat regeneration was found to be dominated by 446 key transcription factors (TFs). Further comparisons between wheat and Arabidopsis revealed distinct patterns of DNA binding with one finger (DOF) TFs in the two species. Experimental validations highlighted TaDOF5.6 (TraesCS6A02G274000) and TaDOF3.4 (TraesCS2B02G592600) as potential enhancers of transformation efficiency in different wheat varieties.
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Affiliation(s)
- Xuemei Liu
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xiao Min Bie
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Xuelei Lin
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Menglu Li
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Hongzhe Wang
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xiaoyu Zhang
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yiman Yang
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- Nanjing Agricultural University, Nanjing, China
| | - Chunyan Zhang
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Xian Sheng Zhang
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, China.
| | - Jun Xiao
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, CAS, Beijing, China.
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3
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Guo F, Wang H, Lian G, Cai G, Liu W, Zhang H, Li D, Zhou C, Han N, Zhu M, Su Y, Seo PJ, Xu L, Bian H. Initiation of scutellum-derived callus is regulated by an embryo-like developmental pathway in rice. Commun Biol 2023; 6:457. [PMID: 37100819 PMCID: PMC10130139 DOI: 10.1038/s42003-023-04835-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 04/12/2023] [Indexed: 04/28/2023] Open
Abstract
In rice (Oryza sativa) tissue culture, callus can be induced from the scutellum in embryo or from the vasculature of non-embryonic organs such as leaves, nodes, or roots. Here we show that the auxin signaling pathway triggers cell division in the epidermis of the scutellum to form an embryo-like structure, which leads to callus formation. Our transcriptome data show that embryo-, stem cell-, and auxin-related genes are upregulated during scutellum-derived callus initiation. Among those genes, the embryo-specific gene OsLEC1 is activated by auxin and involved in scutellum-derived callus initiation. However, OsLEC1 is not required for vasculature-derived callus initiation from roots. In addition, OsIAA11 and OsCRL1, which are involved in root development, are required for vasculature-derived callus formation but not for scutellum-derived callus formation. Overall, our data indicate that scutellum-derived callus initiation is regulated by an embryo-like development program, and this is different from vasculature-derived callus initiation which borrows a root development program.
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Affiliation(s)
- Fu Guo
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, 572025, China
- Yazhou Bay Seed Laboratory, Yazhou Bay Science and Technology City, Yazhou District, Sanya, 572025, China
| | - Hua Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
| | - Guiwei Lian
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Gui Cai
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
| | - Wu Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
| | - Haidao Zhang
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Dandan Li
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, 572025, China
| | - Chun Zhou
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ning Han
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Muyuan Zhu
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yinghua Su
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Korea
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China.
| | - Hongwu Bian
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
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Liu X, Zhu K, Xiao J. Recent advances in understanding of the epigenetic regulation of plant regeneration. ABIOTECH 2023; 4:31-46. [PMID: 37220541 PMCID: PMC10199984 DOI: 10.1007/s42994-022-00093-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/27/2022] [Indexed: 05/22/2023]
Abstract
Ever since the concept of "plant cell totipotency" was first proposed in the early twentieth century, plant regeneration has been a major focus of study. Regeneration-mediated organogenesis and genetic transformation are important topics in both basic research and modern agriculture. Recent studies in the model plant Arabidopsis thaliana and other species have expanded our understanding of the molecular regulation of plant regeneration. The hierarchy of transcriptional regulation driven by phytohormone signaling during regeneration is associated with changes in chromatin dynamics and DNA methylation. Here, we summarize how various aspects of epigenetic regulation, including histone modifications and variants, chromatin accessibility dynamics, DNA methylation, and microRNAs, modulate plant regeneration. As the mechanisms of epigenetic regulation are conserved in many plants, research in this field has potential applications in boosting crop breeding, especially if coupled with emerging single-cell omics technologies.
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Affiliation(s)
- Xuemei Liu
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Kehui Zhu
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Jun Xiao
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
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Wan Q, Zhai N, Xie D, Liu W, Xu L. WOX11: the founder of plant organ regeneration. CELL REGENERATION (LONDON, ENGLAND) 2023; 12:1. [PMID: 36596978 PMCID: PMC9810776 DOI: 10.1186/s13619-022-00140-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/29/2022] [Indexed: 01/05/2023]
Abstract
De novo organ regeneration is the process in which adventitious roots or shoots regenerate from detached or wounded organs. De novo organ regeneration can occur either in natural conditions, e.g. adventitious root regeneration from the wounded sites of detached leaves or stems, or in in-vitro tissue culture, e.g. organ regeneration from callus. In this review, we summarize recent advances in research on the molecular mechanism of de novo organ regeneration, focusing on the role of the WUSCHEL-RELATED HOMEOBOX11 (WOX11) gene in the model plant Arabidopsis thaliana. WOX11 is a direct target of the auxin signaling pathway, and it is expressed in, and regulates the establishment of, the founder cell during de novo root regeneration and callus formation. WOX11 activates the expression of its target genes to initiate root and callus primordia. Therefore, WOX11 links upstream auxin signaling to downstream cell fate transition during regeneration. We also discuss the role of WOX11 in diverse species and its evolution in plants.
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Affiliation(s)
- Qihui Wan
- grid.9227.e0000000119573309National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049 China
| | - Ning Zhai
- grid.9227.e0000000119573309National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032 China
| | - Dixiang Xie
- grid.9227.e0000000119573309National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049 China
| | - Wu Liu
- grid.9227.e0000000119573309National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032 China
| | - Lin Xu
- grid.9227.e0000000119573309National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032 China
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Dasgupta P, Prasad P, Bag SK, Chaudhuri S. Dynamicity of histone H3K27ac and H3K27me3 modifications regulate the cold-responsive gene expression in Oryza sativa L. ssp. indica. Genomics 2022; 114:110433. [PMID: 35863676 DOI: 10.1016/j.ygeno.2022.110433] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 06/15/2022] [Accepted: 07/10/2022] [Indexed: 11/29/2022]
Abstract
Cultivated in tropical and subtropical regions, Oryza sativa L. ssp. indica is largely affected by cold-stress, especially at the seedling stage. The present model of the stress-responsive regulatory network in plants entails the role of genetic and epigenetic factors in stress-responsive gene expression. Despite extensive transcriptomic studies, the regulation of various epigenetic factors in plants cold-stress response is less explored. The present study addresses the effect of genome-wide changes of H3K27 modifications on gene expression in IR64 rice, during cold-stress. Our results suggest a positive correlation between the changes in H3K27 modifications and stress-responsive gene activation in indica rice. Cold-induced enrichment of H3K27 acetylation promotes nucleosomal rearrangement, thereby facilitating the accessibility of the transcriptional machinery at the stress-responsive loci for transcription activation. Although H3K27ac exhibits uniform distribution throughout the loci of enriched genes; occupancy of H3K27me3 is biased to intergenic regions. Integration of the ChIP-seq data with transcriptome indicated that upregulation of stress-responsive TFs, photosynthesis-TCA-related, water-deficit genes, redox and JA signalling components, was associated with differential changes of H3K27ac and H3K27me3 levels. Furthermore, cold-induced upregulation of histone acetyltransferases and downregulation of DNA methyltransferases was noted through the antagonistic switch of H3K27ac and H3K27me3. Moreover, motif analysis of H3K27ac and H3K27me3 enriched regions are associated with putative stress responsive transcription factors binding sites, GAGA element and histone H3K27demethylase. Collectively our analysis suggests that differential expression of various chromatin and DNA modifiers coupled with increased H3K27ac and depleted H3K27me3 increases DNA accessibility, thereby promoting transcription of the cold-responsive genes in indica rice.
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Affiliation(s)
- Pratiti Dasgupta
- Division of Plant Biology, Bose Institute, Unified Academic Campus, EN 80, Sector V, Bidhan Nagar, Kolkata 700091, WB, India
| | - Priti Prasad
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, Uttar Pradesh 226001, India
| | - Sumit K Bag
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, Uttar Pradesh 226001, India
| | - Shubho Chaudhuri
- Division of Plant Biology, Bose Institute, Unified Academic Campus, EN 80, Sector V, Bidhan Nagar, Kolkata 700091, WB, India.
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Zheng B, Liu J, Gao A, Chen X, Gao L, Liao L, Luo B, Ogutu CO, Han Y. Epigenetic reprogramming of H3K27me3 and DNA methylation during leaf-to-callus transition in peach. HORTICULTURE RESEARCH 2022; 9:uhac132. [PMID: 35937864 PMCID: PMC9350832 DOI: 10.1093/hr/uhac132] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 05/29/2022] [Indexed: 05/30/2023]
Abstract
Plant tissues are capable of developing unorganized cell masses termed calluses in response to the appropriate combination of auxin and cytokinin. Revealing the potential epigenetic mechanisms involved in callus development can improve our understanding of the regeneration process of plant cells, which will be beneficial for overcoming regeneration recalcitrance in peach. In this study, we report on single-base resolution mapping of DNA methylation and reprogramming of the pattern of trimethylation of histone H3 at lysine 27 (H3K27me3) at the genome-wide level during the leaf-to-callus transition in peach. Overall, mCG and mCHH were predominant at the genome-wide level and mCG was predominant in genic regions. H3K27me3 deposition was mainly detected in the gene body and at the TSS site, and GAGA repetitive sequences were prone to recruit H3K27me3 modification. H3K27me3 methylation was negatively correlated with gene expression. In vitro culture of leaf explants was accompanied by DNA hypomethylation and H3K27me3 demethylation, which could activate auxin- and cytokinin-related regulators to induce callus development. The DNA methylation inhibitor 5-azacytidine could significantly increase callus development, while the H3K27me3 demethylase inhibitor GSK-J4 dramatically reduced callus development. These results demonstrate the roles of DNA methylation and H3K27me3 modification in mediating chromatin status during callus development. Our study provides new insights into the epigenetic mechanisms through which differentiated cells acquire proliferative competence to induce callus development in plants.
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Affiliation(s)
- Beibei Zheng
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jingjing Liu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Anqi Gao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Xiaomei Chen
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Lingling Gao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Liao Liao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Binwen Luo
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Collins Otieno Ogutu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Yuepeng Han
- Corresponding author. E-mail:
Equal contribution
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Canton M, Farinati S, Forestan C, Joseph J, Bonghi C, Varotto S. An efficient chromatin immunoprecipitation (ChIP) protocol for studying histone modifications in peach reproductive tissues. PLANT METHODS 2022; 18:43. [PMID: 35361223 PMCID: PMC8973749 DOI: 10.1186/s13007-022-00876-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/15/2022] [Indexed: 05/12/2023]
Abstract
BACKGROUND Perennial fruit trees display a growth behaviour characterized by annual cycling between growth and dormancy, with complex physiological features. Rosaceae fruit trees represent excellent models for studying not only the fruit growth/patterning but also the progression of the reproductive cycle depending upon the impact of climate conditions. Additionally, current developments in high-throughput technologies have impacted Rosaceae tree research while investigating genome structure and function as well as (epi)genetic mechanisms involved in important developmental and environmental response processes during fruit tree growth. Among epigenetic mechanisms, chromatin remodelling mediated by histone modifications and other chromatin-related processes play a crucial role in gene modulation, controlling gene expression. Chromatin immunoprecipitation is an effective technique to investigate chromatin dynamics in plants. This technique is generally applied for studies on chromatin states and enrichment of post-transcriptional modifications (PTMs) in histone proteins. RESULTS Peach is considered a model organism among climacteric fruits in the Rosaceae family for studies on bud formation, dormancy, and organ differentiation. In our work, we have primarily established specific protocols for chromatin extraction and immunoprecipitation in reproductive tissues of peach (Prunus persica). Subsequently, we focused our investigations on the role of two chromatin marks, namely the trimethylation of histone H3 at lysine in position 4 (H3K4me3) and trimethylation of histone H3 at lysine 27 (H3K27me3) in modulating specific gene expression. Bud dormancy and fruit growth were investigated in a nectarine genotype called Fantasia as our model system. CONCLUSIONS We present general strategies to optimize ChIP protocols for buds and mesocarp tissues of peach and analyze the correlation between gene expression and chromatin mark enrichment/depletion. The procedures proposed may be useful to evaluate any involvement of histone modifications in the regulation of gene expression during bud dormancy progression and core ripening in fruits.
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Affiliation(s)
- Monica Canton
- Department of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE), University of Padova, Legnaro, PD Italy
| | - Silvia Farinati
- Department of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE), University of Padova, Legnaro, PD Italy
| | - Cristian Forestan
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
| | - Justin Joseph
- Department of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE), University of Padova, Legnaro, PD Italy
| | - Claudio Bonghi
- Department of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE), University of Padova, Legnaro, PD Italy
| | - Serena Varotto
- Department of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE), University of Padova, Legnaro, PD Italy
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Zhang Y, Yang X, Nvsvrot T, Huang L, Cai G, Ding Y, Ren W, Wang N. The transcription factor WRKY75 regulates the development of adventitious roots, lateral buds and callus by modulating hydrogen peroxide content in poplar. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:1483-1498. [PMID: 34791155 DOI: 10.1093/jxb/erab501] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 11/12/2021] [Indexed: 06/13/2023]
Abstract
Hydrogen peroxide (H2O2) plays important roles in plant development. Adventitious roots (AR), lateral buds (LB) and callus formation are important traits for plants. Here, a gene encoding RESPIRATORY BURST OXIDASE HOMOLOG B (PdeRBOHB) from poplar line 'NL895' (Populus. deltoides × P. euramericana) was predicted to be involved in H2O2 accumulation, and lines with reduced expression were generated. H2O2 content was decreased, and the development of adventitious roots, lateral buds, and callus was inhibited in reduced expression PdeRBOHB lines. A gene encoding PdeWRKY75 was identified as the upstream transcription factor positively regulating PdeRBOHB. This regulation was confirmed by dual luciferase reporter assay, GUS transient expression analysis and electrophoretic mobility shift assay. In the reduced expression PdeWRKY75 lines, H2O2 content was decreased and the development of adventitious roots, lateral buds, and callus development was inhibited, while in the overexpression lines, H2O2 content was increased and the development of adventitious roots and lateral buds was inhibited, but callus formation was enhanced. Additionally, reduced expression PdeRBOHB lines showed lowered expression of PdeWRKY75, while exogenous application of H2O2 showed the opposite effect. Together, these results suggest that PdeWRKY75 and PdeRBOHB are part of a regulatory module in H2O2 accumulation, which is involved in the regulation of multiple biological processes.
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Affiliation(s)
- Yan Zhang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaoqing Yang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tashbek Nvsvrot
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Liyu Huang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guanghua Cai
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yiwei Ding
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenyu Ren
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Nian Wang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan, 430070, China
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