1
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Xue Y, Cao X, Chen X, Deng X, Deng XW, Ding Y, Dong A, Duan CG, Fang X, Gong L, Gong Z, Gu X, He C, He H, He S, He XJ, He Y, He Y, Jia G, Jiang D, Jiang J, Lai J, Lang Z, Li C, Li Q, Li X, Liu B, Liu B, Luo X, Qi Y, Qian W, Ren G, Song Q, Song X, Tian Z, Wang JW, Wang Y, Wu L, Wu Z, Xia R, Xiao J, Xu L, Xu ZY, Yan W, Yang H, Zhai J, Zhang Y, Zhao Y, Zhong X, Zhou DX, Zhou M, Zhou Y, Zhu B, Zhu JK, Liu Q. Epigenetics in the modern era of crop improvements. SCIENCE CHINA. LIFE SCIENCES 2025; 68:1570-1609. [PMID: 39808224 DOI: 10.1007/s11427-024-2784-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2024] [Accepted: 11/15/2024] [Indexed: 01/16/2025]
Abstract
Epigenetic mechanisms are integral to plant growth, development, and adaptation to environmental stimuli. Over the past two decades, our comprehension of these complex regulatory processes has expanded remarkably, producing a substantial body of knowledge on both locus-specific mechanisms and genome-wide regulatory patterns. Studies initially grounded in the model plant Arabidopsis have been broadened to encompass a diverse array of crop species, revealing the multifaceted roles of epigenetics in physiological and agronomic traits. With recent technological advancements, epigenetic regulations at the single-cell level and at the large-scale population level are emerging as new focuses. This review offers an in-depth synthesis of the diverse epigenetic regulations, detailing the catalytic machinery and regulatory functions. It delves into the intricate interplay among various epigenetic elements and their collective influence on the modulation of crop traits. Furthermore, it examines recent breakthroughs in technologies for epigenetic modifications and their integration into strategies for crop improvement. The review underscores the transformative potential of epigenetic strategies in bolstering crop performance, advocating for the development of efficient tools to fully exploit the agricultural benefits of epigenetic insights.
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Affiliation(s)
- Yan Xue
- State Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China.
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Xiangsong Chen
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
| | - Xian Deng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Xing Wang Deng
- State Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China.
| | - Yong Ding
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China.
| | - Aiwu Dong
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China.
| | - Cheng-Guo Duan
- Key Laboratory of Plant Design, National Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Xiaofeng Fang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.
| | - Zhizhong Gong
- State Key Laboratory of Plant Environmental Resilience, Frontiers Science Center for Molecular Design Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
- College of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China.
| | - Xiaofeng Gu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Chongsheng He
- College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan Engineering and Technology Research Center of Hybrid Rapeseed, Hunan University, Changsha, 410082, China.
| | - Hang He
- Institute of Advanced Agricultural Sciences, School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China.
| | - Shengbo He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China.
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing, 102206, China.
| | - Yan He
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Yuehui He
- School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
| | - Guifang Jia
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
| | - Danhua Jiang
- Key Laboratory of Seed Innovation, State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jianjun Jiang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Zhengzhou, 450046, China.
| | - Jinsheng Lai
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China.
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China.
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China.
- Sanya Institute of China Agricultural University, Sanya, 572025, China.
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China.
| | - Zhaobo Lang
- Institute of Advanced Biotechnology and School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Chenlong Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.
| | - Qing Li
- National Key Laboratory of Crop Genetic Improvement, Huebei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Xingwang Li
- National Key Laboratory of Crop Genetic Improvement, Huebei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.
| | - Bing Liu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China.
| | - Xiao Luo
- Shandong Provincial Key Laboratory of Precision Molecular Crop Design and Breeding, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China.
| | - Yijun Qi
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Weiqiang Qian
- School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China.
| | - Guodong Ren
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China.
| | - Qingxin Song
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Xianwei Song
- Key Laboratory of Seed Innovation, State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Zhixi Tian
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jia-Wei 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, Shanghai, 200032, China.
| | - Yuan Wang
- Key Laboratory of Seed Innovation, State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Liang Wu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
| | - Zhe Wu
- Shenzhen Key Laboratory of Plant Genetic Engineering and Molecular Design, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Rui Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, 510640, China.
| | - Jun Xiao
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - 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, Shanghai, 200032, China.
| | - Zheng-Yi Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.
| | - Wenhao Yan
- National Key Laboratory of Crop Genetic Improvement, Huebei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Hongchun Yang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
| | - Jixian Zhai
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Yijing Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China.
| | - Yusheng Zhao
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Xuehua Zhong
- Department of Biology, Washington University in St. Louis, St. Louis, 63130, USA.
| | - Dao-Xiu Zhou
- National Key Laboratory of Crop Genetic Improvement, Huebei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, University Paris-Saclay, Orsay, 91405, France.
| | - Ming Zhou
- State Key Laboratory of Plant Environmental Resilience, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Yue Zhou
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
| | - Bo Zhu
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, 610101, China.
| | - Jian-Kang Zhu
- Institute of Advanced Biotechnology and School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, 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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Parker MT, Amar S, Campoy JA, Krause K, Tusso S, Marek M, Huettel B, Schneeberger K. Scalable eQTL mapping using single-nucleus RNA-sequencing of recombined gametes from a small number of individuals. PLoS Biol 2025; 23:e3003085. [PMID: 40279341 PMCID: PMC12119024 DOI: 10.1371/journal.pbio.3003085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2025] [Revised: 05/28/2025] [Accepted: 02/25/2025] [Indexed: 04/27/2025] Open
Abstract
Phenotypic differences between individuals of a species are often caused by differences in gene expression, which are in turn caused by genetic variation. Expression quantitative trait locus (eQTL) analysis is a methodology by which we can identify such causal variants. Scaling eQTL analysis is costly due to the expense of generating mapping populations, and the collection of matched transcriptomic and genomic information. We developed a rapid eQTL analysis approach using single-cell/nucleus RNA sequencing of gametes from a small number of heterozygous individuals. Patterns of inherited polymorphisms are used to infer the recombinant genomes of thousands of individual gametes and identify how different haplotypes correlate with variation in gene expression. Applied to Arabidopsis pollen nuclei, our approach uncovers both cis- and trans-eQTLs, ultimately mapping variation in a master regulator of sperm cell development that affects the expression of hundreds of genes. This establishes snRNA-sequencing as a powerful, cost-effective method for the mapping of meiotic recombination, addressing the scalability challenges of eQTL analysis and enabling eQTL mapping in specific cell-types.
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Affiliation(s)
- Matthew T. Parker
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Samija Amar
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - José A. Campoy
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Kristin Krause
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Sergio Tusso
- Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | | | | | - Korbinian Schneeberger
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine University, Düsseldorf, Germany
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3
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Sivakumar P, Pandey S, Ramesha A, Davda JN, Singh A, Kumar C, Gala H, Subbiah V, Adicherla H, Dhawan J, Aravind L, Siddiqi I. Sporophyte-directed gametogenesis in Arabidopsis. NATURE PLANTS 2025; 11:398-409. [PMID: 40087543 DOI: 10.1038/s41477-025-01932-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 01/30/2025] [Indexed: 03/17/2025]
Abstract
Plants alternate between diploid sporophyte and haploid gametophyte generations1. In mosses, which retain features of ancestral land plants, the gametophyte is dominant and has an independent existence. However, in flowering plants the gametophyte has undergone evolutionary reduction to just a few cells enclosed within the sporophyte. The gametophyte is thought to retain genetic control of its development even after reduction2. Here we show that male gametophyte development in Arabidopsis, long considered to be autonomous, is also under genetic control of the sporophyte via a repressive mechanism that includes large-scale regulation of protein turnover. We identify an Arabidopsis gene SHUKR as an inhibitor of male gametic gene expression. SHUKR is unrelated to proteins of known function and acts sporophytically in meiosis to control gametophyte development by negatively regulating expression of a large set of genes specific to postmeiotic gametogenesis. This control emerged late in evolution as SHUKR homologues are found only in eudicots. We show that SHUKR is rapidly evolving under positive selection, suggesting that variation in control of protein turnover during male gametogenesis has played an important role in evolution within eudicots.
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Affiliation(s)
- Prakash Sivakumar
- Centre for Cellular and Molecular Biology, CSIR, Hyderabad, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Saurabh Pandey
- Centre for Cellular and Molecular Biology, CSIR, Hyderabad, India
- databaum GmbH, Hamburg, Germany
| | - A Ramesha
- Centre for Cellular and Molecular Biology, CSIR, Hyderabad, India
- Seri-Biotech Research Laboratory, Central Silk Board, Bangalore, India
| | | | - Aparna Singh
- Centre for Cellular and Molecular Biology, CSIR, Hyderabad, India
- Department of Botany, MMV, Banaras Hindu University, Varanasi, India
| | - Chandan Kumar
- Centre for Cellular and Molecular Biology, CSIR, Hyderabad, India
- University of Texas at Austin, Austin, TX, USA
| | - Hardik Gala
- Centre for Cellular and Molecular Biology, CSIR, Hyderabad, India
| | | | | | - Jyotsna Dhawan
- Centre for Cellular and Molecular Biology, CSIR, Hyderabad, India
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Imran Siddiqi
- Centre for Cellular and Molecular Biology, CSIR, Hyderabad, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
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4
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Schenk ST, Brehaut V, Chardin C, Boudsocq M, Marmagne A, Colcombet J, Krapp A. Nitrate activates an MKK3-dependent MAPK module via NLP transcription factors in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2025; 121:e70010. [PMID: 39962336 PMCID: PMC11832804 DOI: 10.1111/tpj.70010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2024] [Revised: 12/06/2024] [Accepted: 01/11/2025] [Indexed: 02/20/2025]
Abstract
Plant responses to nutrient availability are critical for plant development and yield. Nitrate, the major form of nitrogen in most soils, serves as both a nutrient and signaling molecule. Nitrate itself triggers rapid, major changes in gene expression, especially via nodule inception (NIN)-like protein (NLP) transcription factors, and stimulates protein phosphorylation. Mitogen-activated protein kinase (MAPK)-related genes are among the early nitrate-responsive genes; however, little is known about their roles in nitrate signaling pathways. Here, we show that nitrate resupply to nitrogen-depleted Arabidopsis (Arabidopsis thaliana) plants triggers, within minutes, an MAPK cascade that requires NLP-dependent transcriptional induction of mitogen-activated protein kinase kinase kinase 13 (MAP3K13) and MAP3K14 and that the MAPK cascade is composed of MKK3 and likely C-clade MAPKs (MPK1/2/7/14). Importantly, nitrate reductase-deficient mutants exhibited nitrate-induced MPK7 activities comparable to those observed in wild-type plants, indicating that nitrate itself is the signal that stimulates the cascade. We show that the modified expression of MAP3K13 and MAP3K14 affects nitrate-stimulated BT2 expression and modulates plant responses to nitrogen availability, such as nitrate uptake and senescence. Our finding that an MAPK cascade involving MAP3K13 and MAP3K14 functions in the complex regulatory network governing responses to nitrate availability will guide future strategies to optimize plant responses to nitrogen fertilization and nitrogen use efficiency.
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Affiliation(s)
- Sebastian T. Schenk
- Université Paris‐Saclay, CNRS, INRAE, Institute of Plant Sciences Paris‐Saclay (IPS2)91190Gif sur YvetteFrance
- Present address:
Rubin Mühle GmbH, Unit for Research and Development, Quality AssuranceHugsweierer Hauptstr. 32D‐77933Lahr‐HugsweierGermany
| | - Virginie Brehaut
- Université Paris‐Saclay, INRAE, AgroParisTech, Institut Jean‐Pierre Bourgin for Plant Sciences (IJPB)78000VersaillesFrance
| | - Camille Chardin
- Université Paris‐Saclay, INRAE, AgroParisTech, Institut Jean‐Pierre Bourgin for Plant Sciences (IJPB)78000VersaillesFrance
- Present address:
Labcorp B.V, 2800MechelenBelgium
| | - Marie Boudsocq
- Université Paris‐Saclay, CNRS, INRAE, Institute of Plant Sciences Paris‐Saclay (IPS2)91190Gif sur YvetteFrance
| | - Anne Marmagne
- Université Paris‐Saclay, INRAE, AgroParisTech, Institut Jean‐Pierre Bourgin for Plant Sciences (IJPB)78000VersaillesFrance
| | - Jean Colcombet
- Université Paris‐Saclay, CNRS, INRAE, Institute of Plant Sciences Paris‐Saclay (IPS2)91190Gif sur YvetteFrance
| | - Anne Krapp
- Université Paris‐Saclay, INRAE, AgroParisTech, Institut Jean‐Pierre Bourgin for Plant Sciences (IJPB)78000VersaillesFrance
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5
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Cahn J, Lloyd JPB, Karemaker ID, Jansen PWTC, Pflueger J, Duncan O, Petereit J, Bogdanovic O, Millar AH, Vermeulen M, Lister R. Characterization of DNA methylation reader proteins in Arabidopsis thaliana. Genome Res 2024; 34:2229-2243. [PMID: 39632087 PMCID: PMC11694752 DOI: 10.1101/gr.279379.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 10/17/2024] [Indexed: 12/07/2024]
Abstract
In plants, cytosine DNA methylation (mC) is largely associated with transcriptional repression of transposable elements, but it can also be found in the body of expressed genes, referred to as gene body methylation (gbM). gbM is correlated with ubiquitously expressed genes; however, its function, or absence thereof, is highly debated. The different outputs that mC can have raise questions as to how it is interpreted-or read-differently in these sequence and genomic contexts. To screen for potential mC-binding proteins, we performed an unbiased DNA affinity pull-down assay combined with quantitative mass spectrometry using methylated DNA probes for each DNA sequence context. All mC readers known to date preferentially bind to the methylated probes, along with a range of new mC-binding protein candidates. Functional characterization of these mC readers, focused on the MBD and SUVH families, was undertaken by ChIP-seq mapping of genome-wide binding sites, their protein interactors, and the impact of high-order mutations on transcriptomic and epigenomic profiles. Together, these results highlight specific context preferences for these proteins, and in particular the ability of MBD2 to bind predominantly to gbM. This comprehensive analysis of Arabidopsis mC readers emphasizes the complexity and interconnectivity between DNA methylation and chromatin remodeling processes in plants.
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Affiliation(s)
- Jonathan Cahn
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - James P B Lloyd
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
- ARC Centre of Excellence in Plants for Space, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Ino D Karemaker
- Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen 6525 GA, The Netherlands
| | - Pascal W T C Jansen
- Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen 6525 GA, The Netherlands
| | - Jahnvi Pflueger
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia
| | - Owen Duncan
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Jakob Petereit
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Ozren Bogdanovic
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
- ARC Centre of Excellence in Plants for Space, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Michiel Vermeulen
- Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen 6525 GA, The Netherlands
- Division of Molecular Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Ryan Lister
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia;
- ARC Centre of Excellence in Plants for Space, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia
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6
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Zeng Y, Somers J, Bell HS, Vejlupkova Z, Kelly Dawe R, Fowler JE, Nelms B, Gent JI. Potent pollen gene regulation by DNA glycosylases in maize. Nat Commun 2024; 15:8352. [PMID: 39333110 PMCID: PMC11436724 DOI: 10.1038/s41467-024-52620-y] [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: 02/24/2024] [Accepted: 09/13/2024] [Indexed: 09/29/2024] Open
Abstract
Although DNA methylation primarily represses TEs, it also represses select genes that are methylated in plant body tissues but demethylated by DNA glycosylases (DNGs) in endosperm or pollen. Either one of two DNGs, MATERNAL DEREPRESSION OF R1 (MDR1) or DNG102, is essential for pollen viability in maize. Using single-pollen mRNA sequencing on pollen-segregating mutations in both genes, we identify 58 candidate DNG target genes that account for 11.1% of the wild-type transcriptome but are silent or barely detectable in other tissues. They are unusual in their tendency to lack introns but even more so in their TE-like methylation (teM) in coding DNA. The majority have predicted functions in cell wall modification, and they likely support the rapid tip growth characteristic of pollen tubes. These results suggest a critical role for DNA methylation and demethylation in regulating maize genes with the potential for extremely high expression in pollen but constitutive silencing elsewhere.
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Affiliation(s)
- Yibing Zeng
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Julian Somers
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Harrison S Bell
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Zuzana Vejlupkova
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - R Kelly Dawe
- Department of Genetics, University of Georgia, Athens, GA, USA
- Department of Plant Biology, University of Georgia, Athens, GA, USA
| | - John E Fowler
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Brad Nelms
- Department of Plant Biology, University of Georgia, Athens, GA, USA.
| | - Jonathan I Gent
- Department of Plant Biology, University of Georgia, Athens, GA, USA.
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7
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Zeng Y, Somers J, Bell HS, Vejlupkova Z, Dawe RK, Fowler JE, Nelms B, Gent JI. Potent pollen gene regulation by DNA glycosylases in maize. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.13.580204. [PMID: 38405940 PMCID: PMC10888782 DOI: 10.1101/2024.02.13.580204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Although DNA methylation primarily represses TEs, it also represses select genes that are methylated in plant body tissues but demethylated by DNA glycosylases (DNGs) in endosperm or pollen. Activity of either one of two DNGs, MDR1 or DNG102, is essential for pollen viability in maize. Using single-pollen mRNA sequencing on pollen segregating mutations in both genes, we identified 58 candidate DNG target genes that account for 11.1% of the wild-type transcriptome but are silent or barely detectable in the plant body (sporophyte). They are unusual in their tendency to lack introns but even more so in their having TE-like methylation in their CDS. The majority have predicted functions in cell wall modification, and they likely support the rapid tip growth characteristic of pollen tubes. These results suggest a critical role for DNA methylation and demethylation in regulating maize genes with potential for extremely high expression in pollen but constitutive silencing elsewhere.
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8
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Li Y, Kamiyama Y, Minegishi F, Tamura Y, Yamashita K, Katagiri S, Takase H, Otani M, Tojo R, Rupp GE, Suzuki T, Kawakami N, Peck SC, Umezawa T. Group C MAP kinases phosphorylate MBD10 to regulate ABA-induced leaf senescence in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1747-1759. [PMID: 38477703 DOI: 10.1111/tpj.16706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 02/15/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024]
Abstract
Abscisic acid (ABA) is a phytohormone that promotes leaf senescence in response to environmental stress. We previously identified methyl CpG-binding domain 10 (MBD10) as a phosphoprotein that becomes differentially phosphorylated after ABA treatment in Arabidopsis. ABA-induced leaf senescence was delayed in mbd10 knockout plants but accelerated in MBD10-overexpressing plants, suggesting that MBD10 positively regulates ABA-induced leaf senescence. ABA-induced phosphorylation of MBD10 occurs in planta on Thr-89, and our results demonstrated that Thr-89 phosphorylation is essential for MBD10's function in leaf senescence. The in vivo phosphorylation of Thr-89 in MBD10 was significantly downregulated in a quadruple mutant of group C MAPKs (mpk1/2/7/14), and group C MAPKs directly phosphorylated MBD10 in vitro. Furthermore, mpk1/2/7/14 showed a similar phenotype as seen in mbd10 for ABA-induced leaf senescence, suggesting that group C MAPKs are the cognate kinases of MBD10 for Thr-89. Because group C MAPKs have been reported to function downstream of SnRK2s, our results indicate that group C MAPKs and MBD10 constitute a regulatory pathway for ABA-induced leaf senescence.
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Grants
- KAKENHI JP21H05654 Ministry of Education, Culture, Sports, Science and Technology
- KAKENHI JP22K19170 Ministry of Education, Culture, Sports, Science and Technology
- KAKENHI JP23H02497 Ministry of Education, Culture, Sports, Science and Technology
- KAKENHI JP23H04192 Ministry of Education, Culture, Sports, Science and Technology
- 20350427 Moonshot Research and Development Program
- JP21J10962 Japan Society for the Promotion of Science
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Affiliation(s)
- Yangdan Li
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei, 184-8588, Tokyo, Japan
| | - Yoshiaki Kamiyama
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei, 184-8588, Tokyo, Japan
| | - Fuko Minegishi
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei, 184-8588, Tokyo, Japan
| | - Yuki Tamura
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei, 184-8588, Tokyo, Japan
| | - Kota Yamashita
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei, 184-8588, Tokyo, Japan
| | - Sotaro Katagiri
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei, 184-8588, Tokyo, Japan
| | - Hinano Takase
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei, 184-8588, Tokyo, Japan
| | - Masahiko Otani
- School of Agriculture, Meiji University, Kawasaki, 214-8571, Kanagawa, Japan
| | - Ryo Tojo
- School of Agriculture, Meiji University, Kawasaki, 214-8571, Kanagawa, Japan
| | - Gabrielle E Rupp
- Department of Biochemistry, University of Missouri, Columbia, 65211, Missouri, USA
| | - Takamasa Suzuki
- College of Bioscience and Biotechnology, Chubu University, Kasugai, 487-8501, Aichi, Japan
| | - Naoto Kawakami
- School of Agriculture, Meiji University, Kawasaki, 214-8571, Kanagawa, Japan
| | - Scott C Peck
- Department of Biochemistry, University of Missouri, Columbia, 65211, Missouri, USA
| | - Taishi Umezawa
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei, 184-8588, Tokyo, Japan
- Faculty of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, 183-8538, Tokyo, Japan
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9
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Ren Z, Gou R, Zhuo W, Chen Z, Yin X, Cao Y, Wang Y, Mi Y, Liu Y, Wang Y, Fan LM, Deng XW, Qian W. The MBD-ACD DNA methylation reader complex recruits MICRORCHIDIA6 to regulate ribosomal RNA gene expression in Arabidopsis. THE PLANT CELL 2024; 36:1098-1118. [PMID: 38092516 PMCID: PMC10980342 DOI: 10.1093/plcell/koad313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 12/11/2023] [Indexed: 04/01/2024]
Abstract
DNA methylation is an important epigenetic mark implicated in selective rRNA gene expression, but the DNA methylation readers and effectors remain largely unknown. Here, we report a protein complex that reads DNA methylation to regulate variant-specific 45S ribosomal RNA (rRNA) gene expression in Arabidopsis (Arabidopsis thaliana). The complex, consisting of METHYL-CpG-BINDING DOMAIN PROTEIN5 (MBD5), MBD6, ALPHA-CRYSTALLIN DOMAIN PROTEIN15.5 (ACD15.5), and ACD21.4, directly binds to 45S rDNA. While MBD5 and MBD6 function redundantly, ACD15.5 and ACD21.4 are indispensable for variant-specific rRNA gene expression. These 4 proteins undergo phase separation in vitro and in vivo and are interdependent for their phase separation. The α-crystallin domain of ACD15.5 and ACD21.4, which is essential for their function, enables phase separation of the complex, likely by mediating multivalent protein interactions. The effector MICRORCHIDIA6 directly interacts with ACD15.5 and ACD21.4, but not with MBD5 and MBD6, and is recruited to 45S rDNA by the MBD-ACD complex to regulate variant-specific 45S rRNA expression. Our study reveals a pathway in Arabidopsis through which certain 45S rRNA gene variants are silenced, while others are activated.
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Affiliation(s)
- Zhitong Ren
- National Key Laboratory of Wheat Improvement, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Peking University Institute of advanced Agricultural Sciences, Weifang, Shandong 261325, China
- College of Agronomy, Sichuan Agriculture University, Chengdu 611130, China
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Runyu Gou
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Wanqing Zhuo
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Zhiyu Chen
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xiaochang Yin
- National Key Laboratory of Wheat Improvement, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Peking University Institute of advanced Agricultural Sciences, Weifang, Shandong 261325, China
| | - Yuxin Cao
- National Key Laboratory of Wheat Improvement, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Peking University Institute of advanced Agricultural Sciences, Weifang, Shandong 261325, China
| | - Yue Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yingjie Mi
- National Key Laboratory of Wheat Improvement, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Peking University Institute of advanced Agricultural Sciences, Weifang, Shandong 261325, China
| | - Yannan Liu
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Yingxiang Wang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
- College of Life Sciences, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Liu-Min Fan
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xing Wang Deng
- National Key Laboratory of Wheat Improvement, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Peking University Institute of advanced Agricultural Sciences, Weifang, Shandong 261325, China
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Weiqiang Qian
- National Key Laboratory of Wheat Improvement, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Peking University Institute of advanced Agricultural Sciences, Weifang, Shandong 261325, China
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
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10
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Candela-Ferre J, Diego-Martin B, Pérez-Alemany J, Gallego-Bartolomé J. Mind the gap: Epigenetic regulation of chromatin accessibility in plants. PLANT PHYSIOLOGY 2024; 194:1998-2016. [PMID: 38236303 PMCID: PMC10980423 DOI: 10.1093/plphys/kiae024] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/07/2023] [Accepted: 11/23/2023] [Indexed: 01/19/2024]
Abstract
Chromatin plays a crucial role in genome compaction and is fundamental for regulating multiple nuclear processes. Nucleosomes, the basic building blocks of chromatin, are central in regulating these processes, determining chromatin accessibility by limiting access to DNA for various proteins and acting as important signaling hubs. The association of histones with DNA in nucleosomes and the folding of chromatin into higher-order structures are strongly influenced by a variety of epigenetic marks, including DNA methylation, histone variants, and histone post-translational modifications. Additionally, a wide array of chaperones and ATP-dependent remodelers regulate various aspects of nucleosome biology, including assembly, deposition, and positioning. This review provides an overview of recent advances in our mechanistic understanding of how nucleosomes and chromatin organization are regulated by epigenetic marks and remodelers in plants. Furthermore, we present current technologies for profiling chromatin accessibility and organization.
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Affiliation(s)
- Joan Candela-Ferre
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, 46022Spain
| | - Borja Diego-Martin
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, 46022Spain
| | - Jaime Pérez-Alemany
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, 46022Spain
| | - Javier Gallego-Bartolomé
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, 46022Spain
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11
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Wang S, Wang M, Ichino L, Boone BA, Zhong Z, Papareddy RK, Lin EK, Yun J, Feng S, Jacobsen SE. MBD2 couples DNA methylation to transposable element silencing during male gametogenesis. NATURE PLANTS 2024; 10:13-24. [PMID: 38225352 PMCID: PMC10808059 DOI: 10.1038/s41477-023-01599-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 11/27/2023] [Indexed: 01/17/2024]
Abstract
DNA methylation is an essential component of transposable element (TE) silencing, yet the mechanism by which methylation causes transcriptional repression remains poorly understood1-5. Here we study the Arabidopsis thaliana Methyl-CpG Binding Domain (MBD) proteins MBD1, MBD2 and MBD4 and show that MBD2 acts as a TE repressor during male gametogenesis. MBD2 bound chromatin regions containing high levels of CG methylation, and MBD2 was capable of silencing the FWA gene when tethered to its promoter. MBD2 loss caused activation at a small subset of TEs in the vegetative cell of mature pollen without affecting DNA methylation levels, demonstrating that MBD2-mediated silencing acts strictly downstream of DNA methylation. TE activation in mbd2 became more significant in the mbd5 mbd6 and adcp1 mutant backgrounds, suggesting that MBD2 acts redundantly with other silencing pathways to repress TEs. Overall, our study identifies MBD2 as a methyl reader that acts downstream of DNA methylation to silence TEs during male gametogenesis.
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Affiliation(s)
- Shuya Wang
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ming Wang
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Lucia Ichino
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Brandon A Boone
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Zhenhui Zhong
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ranjith K Papareddy
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Evan K Lin
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jaewon Yun
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Suhua Feng
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
- Eli & Edythe Broad Center of Regenerative Medicine & Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA
| | - Steven E Jacobsen
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA.
- Eli & Edythe Broad Center of Regenerative Medicine & Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA.
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, USA.
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12
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Kramer MC, Swanson R, Slotkin RK. Reading banned regions of genomes. NATURE PLANTS 2024; 10:7-8. [PMID: 38225351 DOI: 10.1038/s41477-023-01600-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Affiliation(s)
| | - Ryan Swanson
- Donald Danforth Plant Science Center, St Louis, MO, USA
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | - R Keith Slotkin
- Donald Danforth Plant Science Center, St Louis, MO, USA.
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA.
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13
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Boone BA, Ichino L, Wang S, Gardiner J, Yun J, Jami-Alahmadi Y, Sha J, Mendoza CP, Steelman BJ, van Aardenne A, Kira-Lucas S, Trentchev I, Wohlschlegel JA, Jacobsen SE. ACD15, ACD21, and SLN regulate the accumulation and mobility of MBD6 to silence genes and transposable elements. SCIENCE ADVANCES 2023; 9:eadi9036. [PMID: 37967186 PMCID: PMC10651127 DOI: 10.1126/sciadv.adi9036] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 10/13/2023] [Indexed: 11/17/2023]
Abstract
DNA methylation mediates silencing of transposable elements and genes in part via recruitment of the Arabidopsis MBD5/6 complex, which contains the methyl-CpG binding domain (MBD) proteins MBD5 and MBD6, and the J-domain containing protein SILENZIO (SLN). Here, we characterize two additional complex members: α-crystalline domain (ACD) containing proteins ACD15 and ACD21. We show that they are necessary for gene silencing, bridge SLN to the complex, and promote higher-order multimerization of MBD5/6 complexes within heterochromatin. These complexes are also highly dynamic, with the mobility of MBD5/6 complexes regulated by the activity of SLN. Using a dCas9 system, we demonstrate that tethering the ACDs to an ectopic site outside of heterochromatin can drive a massive accumulation of MBD5/6 complexes into large nuclear bodies. These results demonstrate that ACD15 and ACD21 are critical components of the gene-silencing MBD5/6 complex and act to drive the formation of higher-order, dynamic assemblies at CG methylation (meCG) sites.
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Affiliation(s)
- Brandon A. Boone
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Lucia Ichino
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Shuya Wang
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Jason Gardiner
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Jaewon Yun
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Yasaman Jami-Alahmadi
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Jihui Sha
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Cristy P. Mendoza
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Bailey J. Steelman
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Aliya van Aardenne
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Sophia Kira-Lucas
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Isabelle Trentchev
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - James A. Wohlschlegel
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Steven E. Jacobsen
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edyth Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA 90095, USA
- Howard Hughes Medical Institute (HHMI), University of California Los Angeles, Los Angeles, CA 90095, USA
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14
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Boone BA, Ichino L, Wang S, Gardiner J, Yun J, Jami-Alahmadi Y, Sha J, Mendoza CP, Steelman BJ, van Aardenne A, Kira-Lucas S, Trentchev I, Wohlschlegel JA, Jacobsen SE. ACD15, ACD21 and SLN regulate accumulation and mobility of MBD6 to silence genes and transposable elements. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.23.554494. [PMID: 37662299 PMCID: PMC10473691 DOI: 10.1101/2023.08.23.554494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
DNA methylation mediates silencing of transposable elements and genes in part via recruitment of the Arabidopsis MBD5/6 complex, which contains the methyl-CpG-binding domain (MBD) proteins MBD5 and MBD6, and the J-domain containing protein SILENZIO (SLN). Here we characterize two additional complex members: α-crystalline domain containing proteins ACD15 and ACD21. We show that they are necessary for gene silencing, bridge SLN to the complex, and promote higher order multimerization of MBD5/6 complexes within heterochromatin. These complexes are also highly dynamic, with the mobility of complex components regulated by the activity of SLN. Using a dCas9 system, we demonstrate that tethering the ACDs to an ectopic site outside of heterochromatin can drive massive accumulation of MBD5/6 complexes into large nuclear bodies. These results demonstrate that ACD15 and ACD21 are critical components of gene silencing complexes that act to drive the formation of higher order, dynamic assemblies.
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Affiliation(s)
- Brandon A. Boone
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
- These authors contributed equally
| | - Lucia Ichino
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
- These authors contributed equally
| | - Shuya Wang
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Jason Gardiner
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
- Translational Plant Biology, Department of Biology, Utrecht University, 3584CH, Utrecht, The Netherlands
| | - Jaewon Yun
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Yasaman Jami-Alahmadi
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Jihui Sha
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Cristy P. Mendoza
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Bailey J. Steelman
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Aliya van Aardenne
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Sophia Kira-Lucas
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Isabelle Trentchev
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - James A. Wohlschlegel
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Steven E. Jacobsen
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edyth Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA 90095, USA
- Howard Hughes Medical Institute (HHMI), UCLA; Los Angeles, CA 90095, USA
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15
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Shu J, Yin X, Liu Y, Mi Y, Zhang B, Zhang A, Guo H, Dong J. MBD3 Regulates Male Germ Cell Division and Sperm Fertility in Arabidopsis thaliana. PLANTS (BASEL, SWITZERLAND) 2023; 12:2654. [PMID: 37514268 PMCID: PMC10384339 DOI: 10.3390/plants12142654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/03/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023]
Abstract
DNA methylation plays important roles through the methyl-CpG-binding domain (MBD) to realize epigenetic modifications. Thirteen AtMBD proteins have been identified from the Arabidopsis thaliana genome, but the functions of some members are unclear. AtMBD3 was found to be highly expressed in pollen and seeds and it preferably binds methylated CG, CHG, and unmethylated DNA sequences. Then, two mutant alleles at the AtMBD3 locus were obtained in order to further explore its function using CRISPR/Cas9. When compared with 92.17% mature pollen production in the wild type, significantly lower percentages of 84.31% and 78.91% were observed in the mbd3-1 and mbd3-2 mutants, respectively. About 16-21% of pollen from the mbd3 mutants suffered a collapse in reproductive transmission, whereas the other pollen was found to be normal. After pollination, about 16% and 24% of mbd3-1 and mbd3-2 mutant seeds underwent early or late abortion, respectively. Among all the late abortion seeds in mbd3-2 plants, 25% of the abnormal seeds were at the globular stage, 31.25% were at the transition stage, and 43.75% were at the heart stage. A transcriptome analysis of the seeds found 950 upregulated genes and 1128 downregulated genes between wild type and mbd3-2 mutants. Some transcriptional factors involved in embryo development were selected to be expressed, and we found significant differences between wild type and mbd3 mutants, such as WOXs, CUC1, AIB4, and RGL3. Furthermore, we found a gene that is specifically expressed in pollen, named PBL6. PBL6 was found to directly interact with AtMBD3. Our results provide insights into the function of AtMBD3 in plants, especially in sperm fertility.
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Affiliation(s)
- Jia Shu
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Xiaochang Yin
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Yannan Liu
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Yingjie Mi
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Bin Zhang
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Aoyuan Zhang
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Hongbo Guo
- College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China
| | - Juane Dong
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
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16
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Flores-Tornero M, Becker JD. 50 years of sperm cell isolations: from structural to omic studies. JOURNAL OF EXPERIMENTAL BOTANY 2023:erad117. [PMID: 37025026 DOI: 10.1093/jxb/erad117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Indexed: 06/19/2023]
Abstract
The fusion of male and female gametes is a fundamental process in the perpetuation and diversification of species. During the last 50 years, significant efforts have been made to isolate and characterize sperm cells from flowering plants, and to identify how these cells interact with female gametes to achieve double fertilization. The first techniques and analytical approaches not only provided structural and biochemical characterizations of plant sperm cells but also paved the way for in vitro fertilization studies. Further technological advances then led to unique insights into sperm biology at transcriptomic, proteomic and epigenetic level. Starting with a historical overview of sperm cell isolation techniques, we provide examples of how these contributed to create our current knowledge of sperm cell biology, and point out remaining challenges.
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Affiliation(s)
- María Flores-Tornero
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, Oeiras, 2780-157 Portugal
| | - Jörg D Becker
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, Oeiras, 2780-157 Portugal
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