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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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Kurbidaeva A, Gupta S, Zaidem M, Castanera R, Sato Y, Joly‐Lopez Z, Casacuberta JM, Purugganan MD. Topologically associating domains and the evolution of three-dimensional genome architecture in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2025; 122:e70139. [PMID: 40384625 PMCID: PMC12086760 DOI: 10.1111/tpj.70139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2024] [Revised: 02/17/2025] [Accepted: 03/25/2025] [Indexed: 05/20/2025]
Abstract
We examined the nature and evolution of three-dimensional (3D) genome conformation, including topologically associating domains (TADs), in five genomes within the genus Oryza. These included three varieties from subspecies within domesticated Asian rice O. sativa as well as their closely related wild relatives O. rufipogon and O. meridionalis. We used the high-resolution chromosome conformation capture technique Micro-C, which we modified for use in rice. Our analysis of rice TADs shows that TAD boundaries have high transcriptional activity, low methylation levels, low transposable element (TE) content, and increased gene density. We also find a significant correlation of expression levels for genes within TADs, suggesting that they do function as genomic domains with shared regulatory features. Our findings indicate that animal and plant TADs may share more commonalities than were initially thought, as evidenced by similar genetic and epigenetic signatures associated with TADs and boundaries. To examine 3D genome divergence, we employed a computer vision-based algorithm for the comparison of chromatin contact maps and complemented this analysis by assessing the evolutionary conservation of individual TADs and their boundaries. We conclude that overall chromatin organization is conserved in rice, and 3D structural divergence correlates with evolutionary distance between genomes. We also note that individual TADs are not well conserved, even at short evolutionary timescales.
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Affiliation(s)
- Amina Kurbidaeva
- Center for Genomics and Systems BiologyNew York UniversityNew YorkNew York10003USA
| | - Sonal Gupta
- Center for Genomics and Systems BiologyNew York UniversityNew YorkNew York10003USA
- Trivedi School of BioscienceAshoka UniversitySonipatIndia
| | - Maricris Zaidem
- Center for Genomics and Systems BiologyNew York UniversityNew YorkNew York10003USA
- Department of BiologyUniversity of OxfordOxfordUK
| | - Raúl Castanera
- Centre for Research in Agricultural GenomicsCerdanyola del VallèsBarcelonaSpain
- IRTA, Genomics and BiotechnologyEdifici CRAG, Campus UABBellaterraCatalonia08193Spain
| | | | - Zoé Joly‐Lopez
- Center for Genomics and Systems BiologyNew York UniversityNew YorkNew York10003USA
- Département de ChimieUniversité du Quebéc à MontréalMontrealQuebecCanada
| | | | - Michael D. Purugganan
- Center for Genomics and Systems BiologyNew York UniversityNew YorkNew York10003USA
- Center for Genomics and Systems BiologyNew York University Abu DhabiAbu DhabiUnited Arab Emirates
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3
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Liu Y, Xiao S, Yang M, Guo G, Zhou Y. The Impact of Polycomb Group Proteins on 3D Chromatin Structure and Environmental Stresses in Plants. PLANTS (BASEL, SWITZERLAND) 2025; 14:1038. [PMID: 40219106 PMCID: PMC11990978 DOI: 10.3390/plants14071038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2025] [Revised: 03/19/2025] [Accepted: 03/25/2025] [Indexed: 04/14/2025]
Abstract
The two multi-subunit complexes, Polycomb Repressive Complex 1 and 2 (PRC1/2), act synergistically during development to maintain the gene silencing state among different species. In contrast with mammals and Drosophila melanogaster, the enzyme activities and components of the PRC1 complex in plants are not fully conserved. In addition, the mutual recruitment of PRC1 and PRC2 in plants differs from that observed in mammals and Drosophila. Polycomb Group (PcG) proteins and their catalytic activity play an indispensable role in transcriptional regulation, developmental processes, and the maintenance of cellular identity. In plants, PRC1 and PRC2 deposit H2Aub and H3K27me3, respectively, and also play an important role in influencing three-dimensional (3D) chromatin structure. With the development of high-throughput sequencing techniques and computational biology, remarkable progress has been made in the field of plant 3D chromatin structure, and PcG has been found to be involved in the epigenetic regulation of gene expression by mediating the formation of 3D chromatin structures. At the same time, some genetic evidence indicates that PcG enables plants to better adapt to and resist a wide range of stresses by dynamically regulating gene expression. In the following review, we focus on the recruitment relationship between PRC1 and PRC2, the crucial role of PcG enzyme activity, the effect of PcG on 3D chromatin structure, and the vital role of PcG in environmental stress in plants.
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Affiliation(s)
- Yali Liu
- Institute of Cell Biology and MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China;
| | - Suxin Xiao
- State Key Laboratory of Gene Function and Modulation Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; (S.X.); (M.Y.)
| | - Minqi Yang
- State Key Laboratory of Gene Function and Modulation Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; (S.X.); (M.Y.)
| | - Guangqin Guo
- Institute of Cell Biology and MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China;
| | - Yue Zhou
- State Key Laboratory of Gene Function and Modulation Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; (S.X.); (M.Y.)
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4
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Shu J, Xiao S, Wang D, Yang M, Zhou Y. Protocol for capturing genome-wide chromatin interactions in Arabidopsis. STAR Protoc 2025; 6:103702. [PMID: 40096089 PMCID: PMC11957576 DOI: 10.1016/j.xpro.2025.103702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2024] [Revised: 02/18/2025] [Accepted: 02/25/2025] [Indexed: 03/19/2025] Open
Abstract
High-order chromatin structure is essential for the regulation of plant growth and development. Here, we present a protocol for capturing genome-wide chromatin interactions in Arabidopsis. We describe steps for tissue fixation, nuclei isolation, chromatin digestion, ligation, sonication, and library preparation. This protocol has potential application in 3D chromatin analysis in many species of plants. For complete details on the use and execution of this protocol, please refer to Shu et al.,1 Yin et al.,2 and Yang et al.3,4.
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Affiliation(s)
- Jiayue Shu
- State Key Laboratory of Gene Function and Modulation Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Suxin Xiao
- State Key Laboratory of Gene Function and Modulation Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Dingyue Wang
- State Key Laboratory of Gene Function and Modulation Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Minqi Yang
- State Key Laboratory of Gene Function and Modulation Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yue Zhou
- State Key Laboratory of Gene Function and Modulation Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
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Song Z, Xia Q, Yang M, Yang T, Liu Y, Wang D, Shu J, Liu Z, Chi Y, Xu H, Xing D, Zhou Y. Dynamic changes in 3D chromatin structure during male gametogenesis in Arabidopsis thaliana. Genome Biol 2025; 26:27. [PMID: 39930459 PMCID: PMC11808980 DOI: 10.1186/s13059-025-03496-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 02/05/2025] [Indexed: 02/14/2025] Open
Abstract
BACKGROUND Chromatin higher-order structure plays an important role in genome stability maintenance and gene transcriptional regulation; however, the dynamics of the three-dimensional (3D) chromatin in male gametophytes during the two rounds of mitosis remains elusive. RESULTS Here, we use the optimized single-nucleus and low-input Hi-C methods to investigate changes in 3D chromatin structure in four types of male gametophyte nucleus at different stages. The reconstructed genome structures show that microspore nuclei develop towards two different directions. Although the 3D chromatin organization in generative nuclei is similar to that in microspore nuclei, vegetative nuclei lose chromosome territories, display dispersed centromeres, and switched A/B compartments, which are associated with vegetative specific gene expression. Additionally, we find that there is an active transcriptional center in sperm nuclei, emphasizing the transcription in Arabidopsis sperm is not completely inhibited despite the chromosomes being condensed. CONCLUSIONS Our data suggest that the special 3D structures of vegetative and sperm nuclei contribute to cell type-specific expression patterns.
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Affiliation(s)
- Zhihan Song
- State Key Laboratory of Gene Function and Modulation Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Qimin Xia
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Minqi Yang
- State Key Laboratory of Gene Function and Modulation Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Tingting Yang
- State Key Laboratory of Gene Function and Modulation Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Yali Liu
- Institute of Cell Biologyand, MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences , Lanzhou University, Lanzhou, 730000, China
| | - Dingyue Wang
- State Key Laboratory of Gene Function and Modulation Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Jiayue Shu
- State Key Laboratory of Gene Function and Modulation Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Zhiyuan Liu
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
- Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, 100871, China
| | - Yi Chi
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Heming Xu
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Dong Xing
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China.
- Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, 100871, China.
| | - Yue Zhou
- State Key Laboratory of Gene Function and Modulation Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
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Lee H, Seo PJ. Hi-GDT: A Hi-C-based 3D gene domain analysis tool for analyzing local chromatin contacts in plants. Gigascience 2025; 14:giaf020. [PMID: 40117178 PMCID: PMC11927400 DOI: 10.1093/gigascience/giaf020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2024] [Revised: 01/06/2025] [Accepted: 02/12/2025] [Indexed: 03/23/2025] Open
Abstract
BACKGROUND Three-dimensional (3D) chromatin organization is emerging as a key factor in gene regulation in eukaryotes. Recent studies using high-resolution Hi-C analysis have explored fine-scale local chromatin contact domains in plants, as exemplified by the basic contact domains established at accessible gene border regions in Arabidopsis (Arabidopsis thaliana). However, we lack effective tools to identify these contact domains and examine their structural dynamics. RESULTS We developed the Hi-C-based 3D Gene Domain analysis Tool (Hi-GDT) to identify fine-scale local chromatin contact domains in plants, with a particular focus on gene borders. Hi-GDT successfully identifies local contact domains, including single-gene and multigene domains, with high reproducibility. Hi-GDT can also be used to discover local contact domains that are differentially organized in association with differences in gene expression between tissue types, genotypes, or in response to environmental stimuli. CONCLUSIONS Hi-GDT is a valuable tool for identifying genes regulated by dynamic 3D conformational changes, expanding our understanding of the structural and functional relevance of local 3D chromatin organization in plants. Hi-GDT is publicly available at https://github.com/CDL-HongwooLee/Hi-GDT.
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Affiliation(s)
- Hongwoo Lee
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea
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7
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Su XM, Yuan DY, Liu N, Zhang ZC, Yang M, Li L, Chen S, Zhou Y, He XJ. ALFIN-like proteins link histone H3K4me3 to H2A ubiquitination and coordinate diverse chromatin modifications in Arabidopsis. MOLECULAR PLANT 2025; 18:130-150. [PMID: 39668562 DOI: 10.1016/j.molp.2024.12.007] [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: 07/10/2024] [Revised: 11/15/2024] [Accepted: 12/08/2024] [Indexed: 12/14/2024]
Abstract
Trimethylation of histone H3K4 (H3K4me3) is widely distributed at numerous actively transcribed protein-coding genes throughout the genome. However, the interplay between H3K4me3 and other chromatin modifications in plants remains poorly understood. In this study, we show that the Arabidopsis thaliana ALFIN-LIKE (AL) proteins contain a C-terminal PHD finger capable of binding to H3K4me3 and a PHD-associated AL (PAL) domain that interacts with components of the Polycomb repressive complex 1, thereby facilitating H2A ubiquitination (H2Aub) at H3K4me3-enriched genes throughout the genome. Furthermore, we demonstrate that loss of function of SDG2, encoding a key histone H3K4 methyltransferase, leads to a reduction in H3K4me3 level, which subsequently causes a genome-wide decrease in H2Aub, revealing a strong association between H3K4me3 and H2Aub. Finally, we discover that the PAL domain of AL proteins interacts with various other chromatin-related proteins or complexes, including those involved in regulating H2A.Z deposition, H3K27me3 demethylation, histone deacetylation, and chromatin accessibility. Our genome-wide analysis suggests that the AL proteins play a crucial role in coordinating H3K4me3 with multiple other chromatin modifications across the genome.
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Affiliation(s)
- Xiao-Min Su
- College of Life Sciences, Beijing Normal University, Beijing, 100875, China; National Institute of Biological Sciences, Beijing 102206, China
| | - Dan-Yang Yuan
- National Institute of Biological Sciences, Beijing 102206, China
| | - Na Liu
- National Institute of Biological Sciences, Beijing 102206, China
| | - Zhao-Chen Zhang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Minqi Yang
- 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
| | - Lin Li
- National Institute of Biological Sciences, Beijing 102206, China
| | - She Chen
- National Institute of Biological Sciences, Beijing 102206, 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
| | - Xin-Jian He
- College of Life Sciences, Beijing Normal University, Beijing, 100875, China; National Institute of Biological Sciences, Beijing 102206, China; Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 10084, China.
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8
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Wang D, Xiao S, Shu J, Luo L, Yang M, Calonje M, He H, Song B, Zhou Y. Promoter capture Hi-C identifies promoter-related loops and fountain structures in Arabidopsis. Genome Biol 2024; 25:324. [PMID: 39741350 DOI: 10.1186/s13059-024-03465-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Accepted: 12/19/2024] [Indexed: 01/02/2025] Open
Abstract
BACKGROUND Promoters serve as key elements in the regulation of gene transcription. In mammals, loop interactions between promoters and enhancers increase the complexity of the promoter-based regulatory networks. However, the identification of enhancer-promoter or promoter-related loops in Arabidopsis remains incomplete. RESULTS Here, we use promoter capture Hi-C to identify promoter-related loops in Arabidopsis, which shows that gene body, proximal promoter, and intergenic regions can interact with promoters, potentially functioning as distal regulatory elements or enhancers. We find that promoter-related loops mainly repress gene transcription and are associated with ordered chromatin structures, such as topologically associating domains and fountains-chromatin structures not previously identified in Arabidopsis. Cohesin binds to the center of fountains and is involved in their formation. Moreover, fountain strength is positively correlated with the number of promoter-related loops, and the maintenance of these loops is linked to H3K4me3. In atxr3 mutants, which lack the major H3K4me3 methyltransferases in Arabidopsis, the number of promoter-related loops at fountains is reduced, leading to upregulation of fountain-regulated genes. CONCLUSIONS We identify promoter-related loops associated with ordered chromatin structures and reveal the molecular mechanisms involved in fountain formation and maintenance.
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Affiliation(s)
- Dingyue Wang
- 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
| | - Suxin Xiao
- 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
| | - Jiayue Shu
- 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
| | - Lingxiao Luo
- 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
| | - Minqi Yang
- 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
| | - Myriam Calonje
- Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC), Avenida Américo Vespucio 49, 41092, Seville, Spain
| | - Hang He
- 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
| | - Baoxing Song
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261325, Shandong, 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.
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9
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Shu J, Sun L, Wang D, Yin X, Yang M, Yang Z, Gao Z, He Y, Calonje M, Lai J, Deng XW, He H, Zhou Y. EMF1 functions as a 3D chromatin modulator in Arabidopsis. Mol Cell 2024; 84:4729-4739.e6. [PMID: 39566504 DOI: 10.1016/j.molcel.2024.10.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 08/30/2024] [Accepted: 10/24/2024] [Indexed: 11/22/2024]
Abstract
It is well known that genome organizers, like mammalian CCCTC-binding factor (CTCF) or Drosophila architectural proteins CP190 and BEAF-32, contribute to the three-dimensional (3D) organization of the genome and ensure normal gene transcription. However, bona fide genome organizers have not been identified in plants. Here, we show that EMBRYONIC FLOWER1 (EMF1) functions as a genome modulator in Arabidopsis. EMF1 interacts with the cohesin component SISTER CHROMATIN COHESION3 (SCC3), and both proteins are enriched at compartment domain (CD) boundaries. Accordingly, emf1 and scc3 show a strength decrease at the CD boundary in which these proteins colocalize. EMF1 maintains CD boundary strength, either independently or in cooperation with histone modifications. Moreover, EMF1 is required to maintain gene-resolution interactions and to block long-range aberrant chromatin loops. These data unveil a key role of EMF1 in regulating 3D chromatin structure.
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Affiliation(s)
- Jiayue Shu
- 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
| | - Linhua Sun
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Dingyue Wang
- 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
| | - Xiaochang Yin
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
| | - Minqi Yang
- 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
| | - Zhijia Yang
- State Key Laboratory of Plant Physiology and Biochemistry & National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100183, China
| | - Zheng Gao
- 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
| | - Yuehui He
- 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; Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang 261325, China
| | - Myriam Calonje
- Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC), Avenida Américo Vespucio 49, Seville 41092, Spain
| | - Jinsheng Lai
- State Key Laboratory of Plant Physiology and Biochemistry & National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100183, China
| | - Xing Wang Deng
- 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; Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang 261325, China
| | - Hang He
- 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; Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang 261325, 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.
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10
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Yang T, Wang D, Luo L, Yin X, Song Z, Yang M, Zhou Y. PWOs repress gene transcription by regulating chromatin structures in Arabidopsis. Nucleic Acids Res 2024; 52:12918-12929. [PMID: 39526374 PMCID: PMC11602166 DOI: 10.1093/nar/gkae958] [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: 04/26/2024] [Accepted: 10/10/2024] [Indexed: 11/16/2024] Open
Abstract
PWWP-DOMAIN INTERACTOR OF POLYCOMBS (PWO) family proteins play a vital role in regulating plant development. However, the molecular mechanisms of how PWOs regulate chromatin structure is elusive. Our data show that the PWO1 binding sites are enriched with positive modifications but exclusive with H3K27me3. Moreover, PWO1 binds to the H3K27me3-enriched compartment domain (H3K27me3-CD) boundary regions, and functions to maintain the boundary strength. Meanwhile, we found that PWOs and Polycomb repressive complex 2 (PRC2) function parallelly in maintaining H3K27me3-CDs' structure. Loss of either PWOs or PRC2 leads to H3K27me3-CD strength reduction, B to A compartment switching as well as the H3K27me3-CD relocating away from the nuclear periphery. Additionally, PWOs and lamin-like proteins collaborate to regulate multiple chromatin structures to repress gene transcription within H3K27me3-CDs. We conclude that PWOs maintain H3K27me3-CDs' repressive state and regulate their spatial position in the nucleus.
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Affiliation(s)
- Tingting Yang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, No.5 Yiheyuan Road, Haidian District, Beijing 100871, China
| | - Dingyue Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, No.5 Yiheyuan Road, Haidian District, Beijing 100871, China
| | - Lingxiao Luo
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, No.5 Yiheyuan Road, Haidian District, Beijing 100871, China
| | - Xiaochang Yin
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, No.5 Yiheyuan Road, Haidian District, Beijing 100871, China
| | - Zhihan Song
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, No.5 Yiheyuan Road, Haidian District, Beijing 100871, China
| | - Minqi Yang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, No.5 Yiheyuan Road, Haidian District, Beijing 100871, 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, No.5 Yiheyuan Road, Haidian District, Beijing 100871, China
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11
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Liu P, Vigneau J, Craig RJ, Barrera-Redondo J, Avdievich E, Martinho C, Borg M, Haas FB, Liu C, Coelho SM. 3D chromatin maps of a brown alga reveal U/V sex chromosome spatial organization. Nat Commun 2024; 15:9590. [PMID: 39505852 PMCID: PMC11541908 DOI: 10.1038/s41467-024-53453-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 10/08/2024] [Indexed: 11/08/2024] Open
Abstract
Nuclear three dimensional (3D) folding of chromatin structure has been linked to gene expression regulation and correct developmental programs, but little is known about the 3D architecture of sex chromosomes within the nucleus, and how that impacts their role in sex determination. Here, we determine the sex-specific 3D organization of the model brown alga Ectocarpus chromosomes at 2 kb resolution, by mapping long-range chromosomal interactions using Hi-C coupled with Oxford Nanopore long reads. We report that Ectocarpus interphase chromatin exhibits a non-Rabl conformation, with strong contacts among telomeres and among centromeres, which feature centromere-specific LTR retrotransposons. The Ectocarpus chromosomes do not contain large local interactive domains that resemble TADs described in animals, but their 3D genome organization is largely shaped by post-translational modifications of histone proteins. We show that the sex determining region (SDR) within the U and V chromosomes are insulated and span the centromeres and we link sex-specific chromatin dynamics and gene expression levels to the 3D chromatin structure of the U and V chromosomes. Finally, we uncover the unique conformation of a large genomic region on chromosome 6 harboring an endogenous viral element, providing insights regarding the impact of a latent giant dsDNA virus on the host genome's 3D chromosomal folding.
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Affiliation(s)
- Pengfei Liu
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Jeromine Vigneau
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Rory J Craig
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Josué Barrera-Redondo
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Elena Avdievich
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Claudia Martinho
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
- School of Life Sciences, Division of Plant Sciences, University of Dundee, At James Hutton Institute, Errol Road, Invergowrie, Dundee, UK
| | - Michael Borg
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Fabian B Haas
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Chang Liu
- Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Susana M Coelho
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany.
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12
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Göbel AM, Zhou S, Wang Z, Tzourtzou S, Himmelbach A, Zheng S, Pradillo M, Liu C, Jiang H. Mutations of PDS5 genes enhance TAD-like domain formation Arabidopsis thaliana. Nat Commun 2024; 15:9308. [PMID: 39468060 PMCID: PMC11519323 DOI: 10.1038/s41467-024-53760-x] [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: 08/09/2024] [Accepted: 10/22/2024] [Indexed: 10/30/2024] Open
Abstract
In eukaryotes, topologically associating domains (TADs) organize the genome into functional compartments. While TAD-like structures are common in mammals and many plants, they are challenging to detect in Arabidopsis thaliana. Here, we demonstrate that Arabidopsis PDS5 proteins play a negative role in TAD-like domain formation. Through Hi-C analysis, we show that mutations in PDS5 genes lead to the widespread emergence of enhanced TAD-like domains throughout the Arabidopsis genome, excluding pericentromeric regions. These domains exhibit increased chromatin insulation and enhanced chromatin interactions, without significant changes in gene expression or histone modifications. Our results suggest that PDS5 proteins are key regulators of genome architecture, influencing 3D chromatin organization independently of transcriptional activity. This study provides insights into the unique chromatin structure of Arabidopsis and the broader mechanisms governing plant genome folding.
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Affiliation(s)
- Anna-Maria Göbel
- Department of Epigenetics, Institute of Biology, University of Hohenheim, Garbenstrasse 30, Stuttgart, Germany
| | - Sida Zhou
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, Potsdam-Golm, Germany
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Zhidan Wang
- Department of Epigenetics, Institute of Biology, University of Hohenheim, Garbenstrasse 30, Stuttgart, Germany
| | - Sofia Tzourtzou
- Department of Epigenetics, Institute of Biology, University of Hohenheim, Garbenstrasse 30, Stuttgart, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Shiwei Zheng
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, Potsdam-Golm, Germany
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Mónica Pradillo
- Departamento de Genética, Fisiología y Microbiología, Facultad de Ciencias Biológicas, Universidad Complutense, Madrid, Spain
| | - Chang Liu
- Department of Epigenetics, Institute of Biology, University of Hohenheim, Garbenstrasse 30, Stuttgart, Germany.
| | - Hua Jiang
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, Potsdam-Golm, Germany.
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany.
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.
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13
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Li Z, Sun L, Xu X, Liu Y, He H, Deng XW. Light control of three-dimensional chromatin organization in soybean. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:2596-2611. [PMID: 38762905 PMCID: PMC11331798 DOI: 10.1111/pbi.14372] [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: 10/08/2023] [Revised: 03/24/2024] [Accepted: 04/24/2024] [Indexed: 05/21/2024]
Abstract
Higher-order chromatin structure is critical for regulation of gene expression. In plants, light profoundly affects the morphogenesis of emerging seedlings as well as global gene expression to ensure optimal adaptation to environmental conditions. However, the changes and functional significance of chromatin organization in response to light during seedling development are not well documented. We constructed Hi-C contact maps for the cotyledon, apical hook and hypocotyl of soybean subjected to dark and light conditions. The resulting high-resolution Hi-C contact maps identified chromosome territories, A/B compartments, A/B sub-compartments, TADs (Topologically Associated Domains) and chromatin loops in each organ. We observed increased chromatin compaction under light and we found that domains that switched from B sub-compartments in darkness to A sub-compartments under light contained genes that were activated during photomorphogenesis. At the local scale, we identified a group of TADs constructed by gene clusters consisting of different numbers of Small Auxin-Upregulated RNAs (SAURs), which exhibited strict co-expression in the hook and hypocotyl in response to light stimulation. In the hypocotyl, RNA polymerase II (RNAPII) regulated the transcription of a SAURs cluster under light via TAD condensation. Our results suggest that the 3D genome is involved in the regulation of light-related gene expression in a tissue-specific manner.
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Affiliation(s)
- Zhu Li
- National Key Laboratory of Wheat ImprovementPeking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at WeifangShandongChina
- School of Plant Science and Food SecurityTel Aviv UniversityTel AvivIsrael
| | - Linhua Sun
- National Key Laboratory of Wheat ImprovementPeking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at WeifangShandongChina
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene ResearchPeking UniversityBeijingChina
| | - Xiao Xu
- National Key Laboratory of Wheat ImprovementPeking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at WeifangShandongChina
| | - Yutong Liu
- National Key Laboratory of Wheat ImprovementPeking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at WeifangShandongChina
| | - Hang He
- National Key Laboratory of Wheat ImprovementPeking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at WeifangShandongChina
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene ResearchPeking UniversityBeijingChina
| | - Xing Wang Deng
- National Key Laboratory of Wheat ImprovementPeking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at WeifangShandongChina
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene ResearchPeking UniversityBeijingChina
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14
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Go D, Lu B, Alizadeh M, Gazzarrini S, Song L. Voice from both sides: a molecular dialogue between transcriptional activators and repressors in seed-to-seedling transition and crop adaptation. FRONTIERS IN PLANT SCIENCE 2024; 15:1416216. [PMID: 39166233 PMCID: PMC11333834 DOI: 10.3389/fpls.2024.1416216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 06/20/2024] [Indexed: 08/22/2024]
Abstract
High-quality seeds provide valuable nutrients to human society and ensure successful seedling establishment. During maturation, seeds accumulate storage compounds that are required to sustain seedling growth during germination. This review focuses on the epigenetic repression of the embryonic and seed maturation programs in seedlings. We begin with an extensive overview of mutants affecting these processes, illustrating the roles of core proteins and accessory components in the epigenetic machinery by comparing mutants at both phenotypic and molecular levels. We highlight how omics assays help uncover target-specific functional specialization and coordination among various epigenetic mechanisms. Furthermore, we provide an in-depth discussion on the Seed dormancy 4 (Sdr4) transcriptional corepressor family, comparing and contrasting their regulation of seed germination in the dicotyledonous species Arabidopsis and two monocotyledonous crops, rice and wheat. Finally, we compare the similarities in the activation and repression of the embryonic and seed maturation programs through a shared set of cis-regulatory elements and discuss the challenges in applying knowledge largely gained in model species to crops.
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Affiliation(s)
- Dongeun Go
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Bailan Lu
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Milad Alizadeh
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Sonia Gazzarrini
- Department of Biological Science, University of Toronto Scarborough, Toronto, ON, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Liang Song
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
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15
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Baile F, Calonje M. Dynamics of polycomb group marks in Arabidopsis. CURRENT OPINION IN PLANT BIOLOGY 2024; 80:102553. [PMID: 38776572 DOI: 10.1016/j.pbi.2024.102553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/08/2024] [Accepted: 05/02/2024] [Indexed: 05/25/2024]
Abstract
Polycomb Group (PcG) histone-modifying system is key in maintaining gene repression, providing a mitotically heritable cellular memory. Nevertheless, to allow plants to transition through distinct transcriptional programs during development or to respond to external cues, PcG-mediated repression requires reversibility. Several data suggest that the dynamics of PcG marks may vary considerably in different cell contexts; however, how PcG marks are established, maintained, or removed in each case is far from clear. In this review, we survey the knowns and unknowns of the molecular mechanisms underlying the maintenance or turnover of PcG marks in different cell stages.
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Affiliation(s)
- Fernando Baile
- Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC-US), Avenida Américo Vespucio 49, 41092, Seville, Spain
| | - Myriam Calonje
- Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC-US), Avenida Américo Vespucio 49, 41092, Seville, Spain.
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16
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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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17
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Sun L, Zhou J, Xu X, Liu Y, Ma N, Liu Y, Nie W, Zou L, Deng XW, He H. Mapping nucleosome-resolution chromatin organization and enhancer-promoter loops in plants using Micro-C-XL. Nat Commun 2024; 15:35. [PMID: 38167349 PMCID: PMC10762229 DOI: 10.1038/s41467-023-44347-z] [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: 02/17/2023] [Accepted: 12/10/2023] [Indexed: 01/05/2024] Open
Abstract
Although chromatin organizations in plants have been dissected at the scales of compartments and topologically associating domain (TAD)-like domains, there remains a gap in resolving fine-scale structures. Here, we use Micro-C-XL, a high-throughput chromosome conformation capture (Hi-C)-based technology that involves micrococcal nuclease (instead of restriction enzymes) and long cross-linkers, to dissect single nucleosome-resolution chromatin organization in Arabidopsis. Insulation analysis reveals more than 14,000 boundaries, which mostly include chromatin accessibility, epigenetic modifications, and transcription factors. Micro-C-XL reveals associations between RNA Pols and local chromatin organizations, suggesting that gene transcription substantially contributes to the establishment of local chromatin domains. By perturbing Pol II both genetically and chemically at the gene level, we confirm its function in regulating chromatin organization. Visible loops and stripes are assigned to super-enhancers and their targeted genes, thus providing direct insights for the identification and mechanistic analysis of distal CREs and their working modes in plants. We further investigate possible factors regulating these chromatin loops. Subsequently, we expand Micro-C-XL to soybean and rice. In summary, we use Micro-C-XL for analyses of plants, which reveal fine-scale chromatin organization and enhancer-promoter loops and provide insights regarding three-dimensional genomes in plants.
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Affiliation(s)
- Linhua Sun
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, 261000, China
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Jingru Zhou
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, 261000, China
| | - Xiao Xu
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, 261000, China
| | - Yi Liu
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Ni Ma
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, 261000, China
- PKU-Tsinghua-NIBS Graduate Program, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Yutong Liu
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, 261000, China
| | - Wenchao Nie
- Wuhan Frasergen Bioinformatics Co., Ltd., Wuhan, 430075, China
| | - Ling Zou
- Wuhan Frasergen Bioinformatics Co., Ltd., Wuhan, 430075, China
| | - Xing Wang Deng
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, 261000, China.
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China.
| | - Hang He
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, 261000, China.
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China.
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Deng L, Zhou Q, Zhou J, Zhang Q, Jia Z, Zhu G, Cheng S, Cheng L, Yin C, Yang C, Shen J, Nie J, Zhu JK, Li G, Zhao L. 3D organization of regulatory elements for transcriptional regulation in Arabidopsis. Genome Biol 2023; 24:181. [PMID: 37550699 PMCID: PMC10405511 DOI: 10.1186/s13059-023-03018-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 07/20/2023] [Indexed: 08/09/2023] Open
Abstract
BACKGROUND Although spatial organization of compartments and topologically associating domains at large scale is relatively well studied, the spatial organization of regulatory elements at fine scale is poorly understood in plants. RESULTS Here we perform high-resolution chromatin interaction analysis using paired-end tag sequencing approach. We map chromatin interactions tethered with RNA polymerase II and associated with heterochromatic, transcriptionally active, and Polycomb-repressive histone modifications in Arabidopsis. Analysis of the regulatory repertoire shows that distal active cis-regulatory elements are linked to their target genes through long-range chromatin interactions with increased expression of the target genes, while poised cis-regulatory elements are linked to their target genes through long-range chromatin interactions with depressed expression of the target genes. Furthermore, we demonstrate that transcription factor MYC2 is critical for chromatin spatial organization, and propose that MYC2 occupancy and MYC2-mediated chromatin interactions coordinately facilitate transcription within the framework of 3D chromatin architecture. Analysis of functionally related gene-defined chromatin connectivity networks reveals that genes implicated in flowering-time control are functionally compartmentalized into separate subdomains via their spatial activity in the leaf or shoot apical meristem, linking active mark- or Polycomb-repressive mark-associated chromatin conformation to coordinated gene expression. CONCLUSION The results reveal that the regulation of gene transcription in Arabidopsis is not only by linear juxtaposition, but also by long-range chromatin interactions. Our study uncovers the fine scale genome organization of Arabidopsis and the potential roles of such organization in orchestrating transcription and development.
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Affiliation(s)
- Li Deng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qiangwei Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Agricultural Bioinformatics Key Laboratory of Hubei Province and Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jie Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qing Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhibo Jia
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guangfeng Zhu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Sheng Cheng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Agricultural Bioinformatics Key Laboratory of Hubei Province and Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lulu Cheng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Caijun Yin
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chao Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Junwei Nie
- Vazyme Biotech Co., Ltd., Nanjing, 210000, China
| | - Jian-Kang Zhu
- Institute of Advanced Biotechnology and School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.
- Center for Advanced Bioindustry Technologies, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
- Agricultural Bioinformatics Key Laboratory of Hubei Province and Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Lun Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
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Sun L, Cao Y, Li Z, Liu Y, Yin X, Deng XW, He H, Qian W. Conserved H3K27me3-associated chromatin looping mediates physical interactions of gene clusters in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:1966-1982. [PMID: 37154484 DOI: 10.1111/jipb.13502] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/26/2023] [Accepted: 05/06/2023] [Indexed: 05/10/2023]
Abstract
Higher-order chromatin organization is essential for transcriptional regulation, genome stability maintenance, and other genome functions. Increasing evidence has revealed significant differences in 3D chromatin organization between plants and animals. However, the extent, pattern, and rules of chromatin organization in plants are still unclear. In this study, we systematically identified and characterized long-range chromatin loops in the Arabidopsis 3D genome. We identified hundreds of long-range cis chromatin loops and found their anchor regions are closely associated with H3K27me3 epigenetic modifications. Furthermore, we demonstrated that these chromatin loops are dependent on Polycomb group (PcG) proteins, suggesting that the Polycomb repressive complex 2 (PRC2) complex is essential for establishing and maintaining these novel loops. Although most of these PcG-medicated chromatin loops are stable, many of these loops are tissue-specific or dynamically regulated by different treatments. Interestingly, tandemly arrayed gene clusters and metabolic gene clusters are enriched in anchor regions. Long-range H3K27me3-marked chromatin interactions are associated with the coregulation of specific gene clusters. Finally, we also identified H3K27me3-associated chromatin loops associated with gene clusters in Oryza sativa and Glycine max, indicating that these long-range chromatin loops are conserved in plants. Our results provide novel insights into genome evolution and transcriptional coregulation in plants.
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Affiliation(s)
- Linhua Sun
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
| | - Yuxin Cao
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
| | - Zhu Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China
- School of Plant Science and Food Security, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Yi Liu
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
| | - Xiaochang Yin
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
| | - Xing Wang Deng
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
| | - Hang He
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
| | - Weiqiang Qian
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
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