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Jiao W, Lu K, Wen M, Mao J, Ni Z, Chen ZJ, Wang X, Song Q, Yuan J. Ploidy variation induces butterfly effect on chromatin topology in wheat. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:2450-2463. [PMID: 39003593 DOI: 10.1111/tpj.16932] [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: 11/30/2023] [Revised: 06/19/2024] [Accepted: 07/03/2024] [Indexed: 07/15/2024]
Abstract
Polyploidy is a prominent driver of plant diversification, accompanied with dramatic chromosomal rearrangement and epigenetic changes that affect gene expression. How chromatin interactions within and between subgenomes adapt to ploidy transition remains poorly understood. We generate open chromatin interaction maps for natural hexaploid wheat (AABBDD), extracted tetraploid wheat (AABB), diploid wheat progenitor Aegilops tauschii (DD) and resynthesized hexaploid wheat (RHW, AABBDD). Thousands of intra- and interchromosomal loops are de novo established or disappeared in AB subgenomes after separation of D subgenome, in which 37-95% of novel loops are lost again in RHW after merger of D genome. Interestingly, more than half of novel loops are formed by cascade reactions that are triggered by disruption of chromatin interaction between AB and D subgenomes. The interaction repressed genes in RHW relative to DD are expression suppressed, resulting in more balanced expression of the three homoeologs in RHW. The interaction levels of cascade anchors are decreased step-by-step. Leading single nucleotide polymorphisms of yield- and plant architecture-related quantitative trait locus are significantly enriched in cascade anchors. The expression of 116 genes interacted with these anchors are significantly correlated with the corresponding traits. Our findings reveal trans-regulation of intrachromosomal loops by interchromosomal interactions during genome merger and separation in polyploid species.
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Affiliation(s)
- Wu Jiao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Kening Lu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Mingxing Wen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Junrong Mao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (MOE)/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Z Jeffrey Chen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, 78712, Texas, USA
| | - Xiue Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, 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, Jiangsu, China
| | - Jingya Yuan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
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Polyploidy and Myc Proto-Oncogenes Promote Stress Adaptation via Epigenetic Plasticity and Gene Regulatory Network Rewiring. Int J Mol Sci 2022; 23:ijms23179691. [PMID: 36077092 PMCID: PMC9456078 DOI: 10.3390/ijms23179691] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
Polyploid cells demonstrate biological plasticity and stress adaptation in evolution; development; and pathologies, including cardiovascular diseases, neurodegeneration, and cancer. The nature of ploidy-related advantages is still not completely understood. Here, we summarize the literature on molecular mechanisms underlying ploidy-related adaptive features. Polyploidy can regulate gene expression via chromatin opening, reawakening ancient evolutionary programs of embryonality. Chromatin opening switches on genes with bivalent chromatin domains that promote adaptation via rapid induction in response to signals of stress or morphogenesis. Therefore, stress-associated polyploidy can activate Myc proto-oncogenes, which further promote chromatin opening. Moreover, Myc proto-oncogenes can trigger polyploidization de novo and accelerate genome accumulation in already polyploid cells. As a result of these cooperative effects, polyploidy can increase the ability of cells to search for adaptive states of cellular programs through gene regulatory network rewiring. This ability is manifested in epigenetic plasticity associated with traits of stemness, unicellularity, flexible energy metabolism, and a complex system of DNA damage protection, combining primitive error-prone unicellular repair pathways, advanced error-free multicellular repair pathways, and DNA damage-buffering ability. These three features can be considered important components of the increased adaptability of polyploid cells. The evidence presented here contribute to the understanding of the nature of stress resistance associated with ploidy and may be useful in the development of new methods for the prevention and treatment of cardiovascular and oncological diseases.
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Parteka LM, Mariath JEA, Vanzela ALL, Silvério A. Nuclear variations and tapetum polyploidy related to pollen grain development in Passiflora L. (Passifloraceae). Cell Biol Int 2021; 46:462-474. [PMID: 34931383 DOI: 10.1002/cbin.11748] [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: 09/20/2021] [Revised: 11/25/2021] [Accepted: 12/12/2021] [Indexed: 11/09/2022]
Abstract
Tapetal cells comprise an anther tissue fundamental to pollen grain development. They are associated with endoreduplication events, which culminate in polyploid and multinucleated cells, high metabolic activity, and different organelle arrangements to support all the development of the pollen grains. Passiflora species present a secretory tapetum, with diversity in the number and size of nuclei. Tapetal cells undergo numerous changes in a short period of development when compared to the plant's life span. To improve our knowledge of tapetum development, tests assessing ploidy levels, anatomy, cytochemistry, transmission electron microscopy, flow cytometry, as well as conventional and molecular cytogenetics were used in Passiflora actinia and P. elegans. The current data show striking differences in nuclear organisation during tapetal cell development, including mono to quadrinucleate cells, and ploidy levels from 2n to 32n. One of the most peculiar features was the atypical behaviour of the ER, which accumulated in the cell border, similar to a 'cER', as well as large dictyosomes. This endomembrane configuration may be related to the tapetum nutritional network and secretion of compounds at the end of meiosis. Another atypical feature of the ER was the formation of an invagination to establish 'binucleated' polyploid cells. This membrane projection appears when the nuclei form two lobes, as well as when it organises a nucleoplasmic reticulum. These data demonstrate that there are important ultrastructural changes in tapetal cells, including organelle arrangements, ploidy levels, and nuclear activity, common to P. actinia and P. elegans, but different from the plant model A. thaliana. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Letícia M Parteka
- Programa de Pós-Graduação em Biologia Evolutiva, Universidade Estadual do Centro-Oeste-UNICENTRO, Guarapuava, PR, Brazil.,Laboratório de Citogenética e Diversidade de Plantas, Universidade Estadual de Londrina-UEL, Londrina, PR, Brazil.,Laboratório de Botânica Estrutural, Universidade Estadual do Centro-Oeste-UNICENTRO, Guarapuava, PR, Brazil
| | - Jorge E A Mariath
- Laboratório de Anatomia Vegetal-LAVeg, Universidade Federal do Rio Grande do Sul-UFRGS, Porto Alegre, RS, Brazil
| | - André L L Vanzela
- Laboratório de Citogenética e Diversidade de Plantas, Universidade Estadual de Londrina-UEL, Londrina, PR, Brazil
| | - Adriano Silvério
- Programa de Pós-Graduação em Biologia Evolutiva, Universidade Estadual do Centro-Oeste-UNICENTRO, Guarapuava, PR, Brazil.,Laboratório de Botânica Estrutural, Universidade Estadual do Centro-Oeste-UNICENTRO, Guarapuava, PR, Brazil
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Shimotohno A, Aki SS, Takahashi N, Umeda M. Regulation of the Plant Cell Cycle in Response to Hormones and the Environment. ANNUAL REVIEW OF PLANT BIOLOGY 2021; 72:273-296. [PMID: 33689401 DOI: 10.1146/annurev-arplant-080720-103739] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Developmental and environmental signals converge on cell cycle machinery to achieve proper and flexible organogenesis under changing environments. Studies on the plant cell cycle began 30 years ago, and accumulated research has revealed many links between internal and external factors and the cell cycle. In this review, we focus on how phytohormones and environmental signals regulate the cell cycle to enable plants to cope with a fluctuating environment. After introducing key cell cycle regulators, we first discuss how phytohormones and their synergy are important for regulating cell cycle progression and how environmental factors positively and negatively affect cell division. We then focus on the well-studied example of stress-induced G2 arrest and view the current model from an evolutionary perspective. Finally, we discuss the mechanisms controlling the transition from the mitotic cycle to the endocycle, which greatly contributes to cell enlargement and resultant organ growth in plants.
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Affiliation(s)
- Akie Shimotohno
- Department of Biological Science, The University of Tokyo, Tokyo 113-0033, Japan
- Current affiliation: Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya 464-8601, Japan;
| | - Shiori S Aki
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara 630-0192, Japan; , ,
| | - Naoki Takahashi
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara 630-0192, Japan; , ,
| | - Masaaki Umeda
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara 630-0192, Japan; , ,
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Bente H, Foerster AM, Lettner N, Mittelsten Scheid O. Polyploidy-associated paramutation in Arabidopsis is determined by small RNAs, temperature, and allele structure. PLoS Genet 2021; 17:e1009444. [PMID: 33690630 PMCID: PMC7978347 DOI: 10.1371/journal.pgen.1009444] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 03/19/2021] [Accepted: 02/24/2021] [Indexed: 11/18/2022] Open
Abstract
Paramutation is a form of non-Mendelian inheritance in which the expression of a paramutable allele changes when it encounters a paramutagenic allele. This change in expression of the paramutable alleles is stably inherited even after segregation of both alleles. While the discovery of paramutation and studies of its underlying mechanism were made with alleles that change plant pigmentation, paramutation-like phenomena are known to modulate the expression of other traits and in other eukaryotes, and many cases have probably gone undetected. It is likely that epigenetic mechanisms are responsible for the phenomenon, as paramutation forms epialleles, genes with identical sequences but different expression states. This could account for the intergenerational inheritance of the paramutated allele, providing profound evidence that triggered epigenetic changes can be maintained over generations. Here, we use a case of paramutation that affects a transgenic selection reporter gene in tetraploid Arabidopsis thaliana. Our data suggest that different types of small RNA are derived from paramutable and paramutagenic epialleles. In addition, deletion of a repeat within the epiallele changes its paramutability. Further, the temperature during the growth of the epiallelic hybrids determines the degree and timing of the allelic interaction. The data further make it plausible why paramutation in this system becomes evident only in the segregating F2 population of tetraploid plants containing both epialleles. In summary, the results support a model for polyploidy-associated paramutation, with similarities as well as distinctions from other cases of paramutation.
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Affiliation(s)
- Heinrich Bente
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Andrea M. Foerster
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Nicole Lettner
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Ortrun Mittelsten Scheid
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
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Doyle JJ, Coate JE. Autopolyploidy: an epigenetic macromutation. AMERICAN JOURNAL OF BOTANY 2020; 107:1097-1100. [PMID: 32737992 DOI: 10.1002/ajb2.1513] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 05/05/2020] [Indexed: 05/28/2023]
Affiliation(s)
- Jeff J Doyle
- School of Integrative Plant Science, Plant Breeding & Genetics and Plant Biology Sections, Cornell University, Ithaca, NY, 14853, USA
| | - Jeremy E Coate
- Department of Biology, Reed College, Portland, OR, 97202, USA
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Robinson DO, Coate JE, Singh A, Hong L, Bush M, Doyle JJ, Roeder AHK. Ploidy and Size at Multiple Scales in the Arabidopsis Sepal. THE PLANT CELL 2018; 30:2308-2329. [PMID: 30143539 PMCID: PMC6241276 DOI: 10.1105/tpc.18.00344] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 08/10/2018] [Accepted: 08/22/2018] [Indexed: 05/02/2023]
Abstract
Ploidy and size phenomena are observed to be correlated across several biological scales, from subcellular to organismal. Two kinds of ploidy change can affect plants. Whole-genome multiplication increases ploidy in whole plants and is broadly associated with increases in cell and organism size. Endoreduplication increases ploidy in individual cells. Ploidy increase is strongly correlated with increased cell size and nuclear volume. Here, we investigate scaling relationships between ploidy and size by simultaneously quantifying nuclear size, cell size, and organ size in sepals from an isogenic series of diploid, tetraploid, and octoploid Arabidopsis thaliana plants, each of which contains an internal endopolyploidy series. We find that pavement cell size and transcriptome size increase linearly with whole-organism ploidy, but organ area increases more modestly due to a compensatory decrease in cell number. We observe that cell size and nuclear size are maintained at a constant ratio; the value of this constant is similar in diploid and tetraploid plants and slightly lower in octoploid plants. However, cell size is maintained in a mutant with reduced nuclear size, indicating that cell size is scaled to cell ploidy rather than to nuclear size. These results shed light on how size is regulated in plants and how cells and organisms of differing sizes are generated by ploidy change.
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Affiliation(s)
- Dana O Robinson
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853
- School of Integrative Plant Science, Section of Plant Biology, Cornell University, Ithaca, New York 14853
| | - Jeremy E Coate
- Department of Biology, Reed College, Portland, Oregon 97202
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, Biomedical Engineering, University of Delaware, Newark, Delaware 19716
| | - Lilan Hong
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853
- School of Integrative Plant Science, Section of Plant Biology, Cornell University, Ithaca, New York 14853
| | - Max Bush
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Jeff J Doyle
- School of Integrative Plant Science, Section of Plant Biology, Cornell University, Ithaca, New York 14853
- School of Integrative Plant Science, Section of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14853
| | - Adrienne H K Roeder
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853
- School of Integrative Plant Science, Section of Plant Biology, Cornell University, Ithaca, New York 14853
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Dong Q, Li N, Li X, Yuan Z, Xie D, Wang X, Li J, Yu Y, Wang J, Ding B, Zhang Z, Li C, Bian Y, Zhang A, Wu Y, Liu B, Gong L. Genome-wide Hi-C analysis reveals extensive hierarchical chromatin interactions in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 94:1141-1156. [PMID: 29660196 DOI: 10.1111/tpj.13925] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 03/27/2018] [Accepted: 04/04/2018] [Indexed: 05/23/2023]
Abstract
The non-random spatial packing of chromosomes in the nucleus plays a critical role in orchestrating gene expression and genome function. Here, we present a Hi-C analysis of the chromatin interaction patterns in rice (Oryza sativa L.) at hierarchical architectural levels. We confirm that rice chromosomes occupy their own territories with certain preferential inter-chromosomal associations. Moderate compartment delimitation and extensive TADs (Topologically Associated Domains) were determined to be associated with heterogeneous genomic compositions and epigenetic marks in the rice genome. We found subtle features including chromatin loops, gene loops, and off-/near-diagonal intensive interaction regions. Gene chromatin loops associated with H3K27me3 could be positively involved in gene expression. In addition to insulated enhancing effects for neighbor gene expression, the identified rice gene loops could bi-directionally (+/-) affect the expression of looped genes themselves. Finally, web-interleaved off-diagonal IHIs/KEEs (Interactive Heterochromatic Islands or KNOT ENGAGED ELEMENTs) could trap transposable elements (TEs) via the enrichment of silencing epigenetic marks. In parallel, the near-diagonal FIREs (Frequently Interacting Regions) could positively affect the expression of involved genes. Our results suggest that the chromatin packing pattern in rice is generally similar to that in Arabidopsis thaliana but with clear differences at specific structural levels. We conclude that genomic composition, epigenetic modification, and transcriptional activity could act in combination to shape global and local chromatin packing in rice. Our results confirm recent observations in rice and A. thaliana but also provide additional insights into the patterns and features of chromatin organization in higher plants.
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Affiliation(s)
- Qianli Dong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Ning Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Xiaochong Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Zan Yuan
- Annoroad Gene Technology Co., Ltd, Beijing, 100176, China
| | - Dejian Xie
- Annoroad Gene Technology Co., Ltd, Beijing, 100176, China
| | - Xiaofei Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Jianing Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Yanan Yu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Jinbin Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Baoxu Ding
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Zhibin Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Changping Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Yao Bian
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Ai Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Ying Wu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
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