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Pachamuthu K, Simon M, Borges F. Targeted suppression of siRNA biogenesis in Arabidopsis pollen promotes triploid seed viability. Nat Commun 2024; 15:4612. [PMID: 38816386 PMCID: PMC11139921 DOI: 10.1038/s41467-024-48950-6] [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: 01/05/2024] [Accepted: 05/14/2024] [Indexed: 06/01/2024] Open
Abstract
In plants, small-interfering RNAs (siRNAs) mediate epigenetic silencing via the RNA-directed DNA methylation (RdDM) pathway, which is particularly prominent during reproduction and seed development. However, there is limited understanding of the origins and dynamics of reproductive siRNAs acting in different cellular and developmental contexts. Here, we used the RNaseIII-like protein RTL1 to suppress siRNA biogenesis in Arabidopsis pollen, and found distinct siRNA subsets produced during pollen development. We demonstrate that RTL1 expression in the late microspore and vegetative cell strongly impairs epigenetic silencing, and resembles RdDM mutants in their ability to bypass interploidy hybridization barriers in the seed. However, germline-specific RTL1 expression did not impact transgenerational inheritance of triploid seed lethality. These results reveal the existence of multiple siRNA subsets accumulated in mature pollen, and suggest that mobile siRNAs involved in the triploid block are produced in germline precursor cells after meiosis, or in the vegetative cell during pollen mitosis.
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Affiliation(s)
- Kannan Pachamuthu
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Matthieu Simon
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Filipe Borges
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France.
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2
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Dew-Budd KJ, Chow HT, Kendall T, David BC, Rozelle JA, Mosher RA, Beilstein MA. Mating system is associated with seed phenotypes upon loss of RNA-directed DNA methylation in Brassicaceae. PLANT PHYSIOLOGY 2024; 194:2136-2148. [PMID: 37987565 DOI: 10.1093/plphys/kiad622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 10/03/2023] [Accepted: 10/23/2023] [Indexed: 11/22/2023]
Abstract
In plants, de novo DNA methylation is guided by 24-nt short interfering (si)RNAs in a process called RNA-directed DNA methylation (RdDM). Primarily targeted at transposons, RdDM causes transcriptional silencing and can indirectly influence expression of neighboring genes. During reproduction, a small number of siRNA loci are dramatically upregulated in the maternally derived seed coat, suggesting that RdDM might have a special function during reproduction. However, the developmental consequence of RdDM has been difficult to dissect because disruption of RdDM does not result in overt phenotypes in Arabidopsis (Arabidopsis thaliana), where the pathway has been most thoroughly studied. In contrast, Brassica rapa mutants lacking RdDM have a severe seed production defect, which is determined by the maternal sporophytic genotype. To explore the factors that underlie the different phenotypes of these species, we produced RdDM mutations in 3 additional members of the Brassicaceae family: Camelina sativa, Capsella rubella, and Capsella grandiflora. Among these 3 species, only mutations in the obligate outcrosser, C. grandiflora, displayed a seed production defect similar to Brassica rapa mutants, suggesting that mating system is a key determinant for reproductive phenotypes in RdDM mutants.
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Affiliation(s)
- Kelly J Dew-Budd
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Hiu Tung Chow
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Timmy Kendall
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Brandon C David
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - James A Rozelle
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Rebecca A Mosher
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Mark A Beilstein
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
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3
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Mahmood T, He S, Abdullah M, Sajjad M, Jia Y, Ahmar S, Fu G, Chen B, Du X. Epigenetic insight into floral transition and seed development in plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 339:111926. [PMID: 37984609 DOI: 10.1016/j.plantsci.2023.111926] [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: 08/12/2023] [Revised: 10/20/2023] [Accepted: 11/14/2023] [Indexed: 11/22/2023]
Abstract
Seasonal changes are crucial in shifting the developmental stages from the vegetative phase to the reproductive phase in plants, enabling them to flower under optimal conditions. Plants grown at different latitudes sense and interpret these seasonal variations, such as changes in day length (photoperiod) and exposure to cold winter temperatures (vernalization). These environmental factors influence the expression of various genes related to flowering. Plants have evolved to stimulate a rapid response to environmental conditions through genetic and epigenetic mechanisms. Multiple epigenetic regulation systems have emerged in plants to interpret environmental signals. During the transition to the flowering phase, changes in gene expression are facilitated by chromatin remodeling and small RNAs interference, particularly in annual and perennial plants. Key flowering regulators, such as FLOWERING LOCUS C (FLC) and FLOWERING LOCUS T (FT), interact with various factors and undergo chromatin remodeling in response to seasonal cues. The Polycomb silencing complex (PRC) controls the expression of flowering-related genes in photoperiodic flowering regulation. Under vernalization-dependent flowering, FLC acts as a potent flowering suppressor by downregulating the gene expression of various flower-promoting genes. Eventually, PRCs are critically involved in the regulation of FLC and FT locus interacting with several key genes in photoperiod and vernalization. Subsequently, PRCs also regulate Epigenetical events during gametogenesis and seed development as a driving force. Furthermore, DNA methylation in the context of CHG, CG, and CHH methylation plays a critical role in embryogenesis. DNA glycosylase DME (DEMETER) is responsible for demethylation during seed development. Thus, the review briefly discusses flowering regulation through light signaling, day length variation, temperature variation and seed development in plants.
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Affiliation(s)
- Tahir Mahmood
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang (CAAS), Anyang 455000, China; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Shoupu He
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang (CAAS), Anyang 455000, China
| | - Muhammad Abdullah
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Muhammad Sajjad
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang (CAAS), Anyang 455000, China
| | - Yinhua Jia
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang (CAAS), Anyang 455000, China
| | - Sunny Ahmar
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Jagiellonska 28, 40-032 Katowice, Poland
| | - Guoyong Fu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang (CAAS), Anyang 455000, China
| | - Baojun Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang (CAAS), Anyang 455000, China
| | - Xiongming Du
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang (CAAS), Anyang 455000, China.
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4
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Vaucheret H, Voinnet O. The plant siRNA landscape. THE PLANT CELL 2024; 36:246-275. [PMID: 37772967 PMCID: PMC10827316 DOI: 10.1093/plcell/koad253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 09/12/2023] [Accepted: 09/28/2023] [Indexed: 09/30/2023]
Abstract
Whereas micro (mi)RNAs are considered the clean, noble side of the small RNA world, small interfering (si)RNAs are often seen as a noisy set of molecules whose barbarian acronyms reflect a large diversity of often elusive origins and functions. Twenty-five years after their discovery in plants, however, new classes of siRNAs are still being identified, sometimes in discrete tissues or at particular developmental stages, making the plant siRNA world substantially more complex and subtle than originally anticipated. Focusing primarily on the model Arabidopsis, we review here the plant siRNA landscape, including transposable elements (TE)-derived siRNAs, a vast array of non-TE-derived endogenous siRNAs, as well as exogenous siRNAs produced in response to invading nucleic acids such as viruses or transgenes. We primarily emphasize the extraordinary sophistication and diversity of their biogenesis and, secondarily, the variety of their known or presumed functions, including via non-cell autonomous activities, in the sporophyte, gametophyte, and shortly after fertilization.
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Affiliation(s)
- Hervé Vaucheret
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Olivier Voinnet
- Department of Biology, Swiss Federal Institute of Technology (ETH-Zurich), 8092 Zürich, Switzerland
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5
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Kirov I. Toward Transgene-Free Transposon-Mediated Biological Mutagenesis for Plant Breeding. Int J Mol Sci 2023; 24:17054. [PMID: 38069377 PMCID: PMC10706983 DOI: 10.3390/ijms242317054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/20/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
Genetic diversity is a key factor for plant breeding. The birth of novel genic and genomic variants is also crucial for plant adaptation in nature. Therefore, the genomes of almost all living organisms possess natural mutagenic mechanisms. Transposable elements (TEs) are a major mutagenic force driving genetic diversity in wild plants and modern crops. The relatively rare TE transposition activity during the thousand-year crop domestication process has led to the phenotypic diversity of many cultivated species. The utilization of TE mutagenesis by artificial and transient acceleration of their activity in a controlled mode is an attractive foundation for a novel type of mutagenesis called TE-mediated biological mutagenesis. Here, I focus on TEs as mutagenic sources for plant breeding and discuss existing and emerging transgene-free approaches for TE activation in plants. Furthermore, I also review the non-randomness of TE insertions in a plant genome and the molecular and epigenetic factors involved in shaping TE insertion preferences. Additionally, I discuss the molecular mechanisms that prevent TE transpositions in germline plant cells (e.g., meiocytes, pollen, egg and embryo cells, and shoot apical meristem), thereby reducing the chances of TE insertion inheritance. Knowledge of these mechanisms can expand the TE activation toolbox using novel gene targeting approaches. Finally, the challenges and future perspectives of plant populations with induced novel TE insertions (iTE plant collections) are discussed.
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Affiliation(s)
- Ilya Kirov
- All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia;
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
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6
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Pachamuthu K, Borges F. Epigenetic control of transposons during plant reproduction: From meiosis to hybrid seeds. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102419. [PMID: 37480640 DOI: 10.1016/j.pbi.2023.102419] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/23/2023] [Accepted: 06/20/2023] [Indexed: 07/24/2023]
Abstract
The regulation of transposable elements (TEs) requires overlapping epigenetic modifications that must be reinforced every cell division and generation. In plants, this is achieved by multiple pathways including small RNAs, DNA methylation, and repressive histone marks that act together to control TE expression and activity throughout the entire life cycle. However, transient TE activation is observed during reproductive transitions as a result of epigenome reprogramming, thus providing windows of opportunity for TE proliferation and epigenetic novelty. Ultimately, these events may originate complex TE-driven transcriptional networks or cell-to-cell communication strategies via mobile small RNAs. In this review, we discuss recent findings and current understanding of TE regulation during sexual plant reproduction, and its implications for fertility, early seed development, and epigenetic inheritance.
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Affiliation(s)
- Kannan Pachamuthu
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France. https://twitter.com/@KannanPachamut1
| | - Filipe Borges
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France.
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7
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Shu J, Yin X, Liu Y, Mi Y, Zhang B, Zhang A, Guo H, Dong J. MBD3 Regulates Male Germ Cell Division and Sperm Fertility in Arabidopsis thaliana. PLANTS (BASEL, SWITZERLAND) 2023; 12:2654. [PMID: 37514268 PMCID: PMC10384339 DOI: 10.3390/plants12142654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/03/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023]
Abstract
DNA methylation plays important roles through the methyl-CpG-binding domain (MBD) to realize epigenetic modifications. Thirteen AtMBD proteins have been identified from the Arabidopsis thaliana genome, but the functions of some members are unclear. AtMBD3 was found to be highly expressed in pollen and seeds and it preferably binds methylated CG, CHG, and unmethylated DNA sequences. Then, two mutant alleles at the AtMBD3 locus were obtained in order to further explore its function using CRISPR/Cas9. When compared with 92.17% mature pollen production in the wild type, significantly lower percentages of 84.31% and 78.91% were observed in the mbd3-1 and mbd3-2 mutants, respectively. About 16-21% of pollen from the mbd3 mutants suffered a collapse in reproductive transmission, whereas the other pollen was found to be normal. After pollination, about 16% and 24% of mbd3-1 and mbd3-2 mutant seeds underwent early or late abortion, respectively. Among all the late abortion seeds in mbd3-2 plants, 25% of the abnormal seeds were at the globular stage, 31.25% were at the transition stage, and 43.75% were at the heart stage. A transcriptome analysis of the seeds found 950 upregulated genes and 1128 downregulated genes between wild type and mbd3-2 mutants. Some transcriptional factors involved in embryo development were selected to be expressed, and we found significant differences between wild type and mbd3 mutants, such as WOXs, CUC1, AIB4, and RGL3. Furthermore, we found a gene that is specifically expressed in pollen, named PBL6. PBL6 was found to directly interact with AtMBD3. Our results provide insights into the function of AtMBD3 in plants, especially in sperm fertility.
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Affiliation(s)
- Jia Shu
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Xiaochang Yin
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Yannan Liu
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Yingjie Mi
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Bin Zhang
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Aoyuan Zhang
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Hongbo Guo
- College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China
| | - Juane Dong
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
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8
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Manavella PA, Godoy Herz MA, Kornblihtt AR, Sorenson R, Sieburth LE, Nakaminami K, Seki M, Ding Y, Sun Q, Kang H, Ariel FD, Crespi M, Giudicatti AJ, Cai Q, Jin H, Feng X, Qi Y, Pikaard CS. Beyond transcription: compelling open questions in plant RNA biology. THE PLANT CELL 2023; 35:1626-1653. [PMID: 36477566 PMCID: PMC10226580 DOI: 10.1093/plcell/koac346] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/14/2022] [Accepted: 12/06/2022] [Indexed: 05/30/2023]
Abstract
The study of RNAs has become one of the most influential research fields in contemporary biology and biomedicine. In the last few years, new sequencing technologies have produced an explosion of new and exciting discoveries in the field but have also given rise to many open questions. Defining these questions, together with old, long-standing gaps in our knowledge, is the spirit of this article. The breadth of topics within RNA biology research is vast, and every aspect of the biology of these molecules contains countless exciting open questions. Here, we asked 12 groups to discuss their most compelling question among some plant RNA biology topics. The following vignettes cover RNA alternative splicing; RNA dynamics; RNA translation; RNA structures; R-loops; epitranscriptomics; long non-coding RNAs; small RNA production and their functions in crops; small RNAs during gametogenesis and in cross-kingdom RNA interference; and RNA-directed DNA methylation. In each section, we will present the current state-of-the-art in plant RNA biology research before asking the questions that will surely motivate future discoveries in the field. We hope this article will spark a debate about the future perspective on RNA biology and provoke novel reflections in the reader.
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Affiliation(s)
- Pablo A Manavella
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe 3000, Argentina
| | - Micaela A Godoy Herz
- Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Universidad de Buenos Aires (UBA), Buenos Aires C1428EHA, Argentina
| | - Alberto R Kornblihtt
- Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Universidad de Buenos Aires (UBA), Buenos Aires C1428EHA, Argentina
| | - Reed Sorenson
- School of Biological Sciences, University of UtahSalt Lake City 84112, USA
| | - Leslie E Sieburth
- School of Biological Sciences, University of UtahSalt Lake City 84112, USA
| | - Kentaro Nakaminami
- Center for Sustainable Resource Science, RIKEN, Kanagawa 230-0045, Japan
| | - Motoaki Seki
- Center for Sustainable Resource Science, RIKEN, Kanagawa 230-0045, Japan
- Cluster for Pioneering Research, RIKEN, Saitama 351-0198, Japan
- Kihara Institute for Biological Research, Yokohama City University, Kanagawa 244-0813, Japan
| | - Yiliang Ding
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Qianwen Sun
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Hunseung Kang
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea
| | - Federico D Ariel
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe 3000, Argentina
| | - Martin Crespi
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Evry, Université Paris-Saclay, Bâtiment 630, Orsay 91405, France
- Institute of Plant Sciences Paris-Saclay IPS2, Université de Paris, Bâtiment 630, Orsay 91405, France
| | - Axel J Giudicatti
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe 3000, Argentina
| | - Qiang Cai
- State Key Laboratory of Hybrid Rice, College of Life Science, Wuhan University, Wuhan 430072, China
| | - Hailing Jin
- Department of Microbiology and Plant Pathology and Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, California 92507, USA
| | - Xiaoqi Feng
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Yijun Qi
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Craig S Pikaard
- Howard Hughes Medical Institute, Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA
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9
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Chow HT, Mosher RA. Small RNA-mediated DNA methylation during plant reproduction. THE PLANT CELL 2023; 35:1787-1800. [PMID: 36651080 DOI: 10.1093/plcell/koad010] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 01/11/2023] [Accepted: 01/11/2023] [Indexed: 05/30/2023]
Abstract
Reproductive tissues are a rich source of small RNAs, including several classes of short interfering (si)RNAs that are restricted to this stage of development. In addition to RNA polymerase IV-dependent 24-nt siRNAs that trigger canonical RNA-directed DNA methylation, abundant reproductive-specific siRNAs are produced from companion cells adjacent to the developing germ line or zygote and may move intercellularly before inducing methylation. In some cases, these siRNAs are produced via non-canonical biosynthesis mechanisms or from sequences with little similarity to transposons. While the precise role of these siRNAs and the methylation they trigger is unclear, they have been implicated in specifying a single megaspore mother cell, silencing transposons in the male germ line, mediating parental dosage conflict to ensure proper endosperm development, hypermethylation of mature embryos, and trans-chromosomal methylation in hybrids. In this review, we summarize the current knowledge of reproductive siRNAs, including their biosynthesis, transport, and function.
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Affiliation(s)
- Hiu Tung Chow
- The School of Plant Sciences, The University of Arizona, Tucson, Arizona 85721-0036, USA
| | - Rebecca A Mosher
- The School of Plant Sciences, The University of Arizona, Tucson, Arizona 85721-0036, USA
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10
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Hou Q, Zhang T, Qi Y, Dong Z, Wan X. Epigenetic Dynamics and Regulation of Plant Male Reproduction. Int J Mol Sci 2022; 23:ijms231810420. [PMID: 36142333 PMCID: PMC9499625 DOI: 10.3390/ijms231810420] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 08/30/2022] [Accepted: 09/05/2022] [Indexed: 11/16/2022] Open
Abstract
Flowering plant male germlines develop within anthers and undergo epigenetic reprogramming with dynamic changes in DNA methylation, chromatin modifications, and small RNAs. Profiling the epigenetic status using different technologies has substantially accumulated information on specific types of cells at different stages of male reproduction. Many epigenetically related genes involved in plant gametophyte development have been identified, and the mutation of these genes often leads to male sterility. Here, we review the recent progress on dynamic epigenetic changes during pollen mother cell differentiation, microsporogenesis, microgametogenesis, and tapetal cell development. The reported epigenetic variations between male fertile and sterile lines are summarized. We also summarize the epigenetic regulation-associated male sterility genes and discuss how epigenetic mechanisms in plant male reproduction can be further revealed.
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11
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Chakraborty T, Trujillo JT, Kendall T, Mosher RA. A null allele of the pol IV second subunit impacts stature and reproductive development in Oryza sativa. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:748-755. [PMID: 35635763 DOI: 10.1111/tpj.15848] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
All eukaryotes possess three DNA-dependent RNA polymerases, Pols I-III, while land plants possess two additional polymerases, Pol IV and Pol V. Derived through duplication of Pol II subunits, Pol IV produces 24-nt short interfering RNAs that interact with Pol V transcripts to target de novo DNA methylation and silence transcription of transposons. Members of the grass family encode additional duplicated subunits of Pol IV and V, raising questions regarding the function of each paralog. In this study, we identify a null allele of the putative Pol IV second subunit, NRPD2, and demonstrate that NRPD2 is the sole subunit functioning with NRPD1 in small RNA production and CHH methylation in leaves. Homozygous nrpd2 mutants have neither gametophytic defects nor embryo lethality, although adult plants are dwarf and sterile.
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Affiliation(s)
- Tania Chakraborty
- School of Plant Sciences, University of Arizona, Tucson, Arizona, 85721, USA
| | - Joshua T Trujillo
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Timmy Kendall
- School of Plant Sciences, University of Arizona, Tucson, Arizona, 85721, USA
| | - Rebecca A Mosher
- School of Plant Sciences, University of Arizona, Tucson, Arizona, 85721, USA
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12
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Wang L, Xu D, Zeng L, Yang DL. The Rise and Fall of Billionaire siRNAs during Reproductive Development in Rice. PLANTS (BASEL, SWITZERLAND) 2022; 11:1957. [PMID: 35956435 PMCID: PMC9370656 DOI: 10.3390/plants11151957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/15/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
RNA polymerase IV-dependent siRNAs, usually 24 nt in length, function in the RNA-directed DNA methylation that is responsible for de novo methylation in plants. We analyzed 24 nt siRNAs in inflorescences and found that among the 20,200 24 nt siRNA clusters, the top 0.81% highly expressed clusters accounted for more than 68% of the 24 nt siRNA reads in inflorescences. We named the highly expressed siRNAs as billionaire siRNAs (bill-siRNAs) and the less-expressed siRNAs as pauper siRNAs (pau-siRNAs). The bill-siRNAs in inflorescences are mainly derived from the ovary. Female gametes produced more bill-siRNAs than male gametes. In embryos and seedlings developed from fertilized egg cells, the bill-siRNAs from gametes disappeared. The endosperm, which develops from the fertilized central cell, also contained no bill-siRNAs from gametes but did contain newly and highly expressed siRNAs produced in different regions. In contrast, bill-siRNAs from the ovaries were maintained in the seed coat. The biosynthesis of bill-siRNAs in various tissues and cells is dependent on OsRDR2 (RNA-dependent RNA polymerase 2) and Pol IV (DNA-dependent RNA polymerase IV). Similar to the pau-siRNAs, the first base of bill-siRNAs is enriched at adenine, and bill-siRNAs can direct DNA methylation in various tissues.
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Affiliation(s)
- Lili Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China; (L.W.); (D.X.)
| | - Dachao Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China; (L.W.); (D.X.)
| | - Longjun Zeng
- Yichun Academy of Sciences, Yichun 336000, China;
| | - Dong-Lei Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China; (L.W.); (D.X.)
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13
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RNA Pol IV induces antagonistic parent-of-origin effects on Arabidopsis endosperm. PLoS Biol 2022; 20:e3001602. [PMID: 35389984 PMCID: PMC9017945 DOI: 10.1371/journal.pbio.3001602] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 04/19/2022] [Accepted: 03/11/2022] [Indexed: 12/14/2022] Open
Abstract
Gene expression in endosperm-a seed tissue that mediates transfer of maternal resources to offspring-is under complex epigenetic control. We show here that plant-specific RNA polymerase IV (Pol IV) mediates parental control of endosperm gene expression. Pol IV is required for the production of small interfering RNAs that typically direct DNA methylation. We compared small RNAs (sRNAs), DNA methylation, and mRNAs in Arabidopsis thaliana endosperm from heterozygotes produced by reciprocally crossing wild-type (WT) plants to Pol IV mutants. We find that maternally and paternally acting Pol IV induce distinct effects on endosperm. Loss of maternal or paternal Pol IV impacts sRNAs and DNA methylation at different genomic sites. Strikingly, maternally and paternally acting Pol IV have antagonistic impacts on gene expression at some loci, divergently promoting or repressing endosperm gene expression. Antagonistic parent-of-origin effects have only rarely been described and are consistent with a gene regulatory system evolving under parental conflict.
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14
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Oliver C, Annacondia ML, Wang Z, Jullien PE, Slotkin RK, Köhler C, Martinez G. The miRNome function transitions from regulating developmental genes to transposable elements during pollen maturation. THE PLANT CELL 2022; 34:784-801. [PMID: 34755870 PMCID: PMC8824631 DOI: 10.1093/plcell/koab280] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 11/04/2021] [Indexed: 06/13/2023]
Abstract
Animal and plant microRNAs (miRNAs) are essential for the spatio-temporal regulation of development. Together with this role, plant miRNAs have been proposed to target transposable elements (TEs) and stimulate the production of epigenetically active small interfering RNAs. This activity is evident in the plant male gamete containing structure, the male gametophyte or pollen grain. How the dual role of plant miRNAs, regulating both genes and TEs, is integrated during pollen development and which mRNAs are regulated by miRNAs in this cell type at a genome-wide scale are unknown. Here, we provide a detailed analysis of miRNA dynamics and activity during pollen development in Arabidopsis thaliana using small RNA and degradome parallel analysis of RNA end high-throughput sequencing. Furthermore, we uncover miRNAs loaded into the two main active Argonaute (AGO) proteins in the uninuclear and mature pollen grain, AGO1 and AGO5. Our results indicate that the developmental progression from microspore to mature pollen grain is characterized by a transition from miRNAs targeting developmental genes to miRNAs regulating TE activity.
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Affiliation(s)
- Cecilia Oliver
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden
| | - Maria Luz Annacondia
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden
| | - Zhenxing Wang
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden
- College of Horticulture and State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs and Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, Nanjing Agricultural University, Nanjing 210095, China
| | - Pauline E Jullien
- Institute of Plant Sciences, University of Bern, Bern 3013, Switzerland
| | - R Keith Slotkin
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
- Division of Biological Sciences, University of Missouri Columbia, Columbia, Missouri 65201, USA
| | - Claudia Köhler
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
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15
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Li C, Gent JI, Xu H, Fu H, Russell SD, Sundaresan V. Resetting of the 24-nt siRNA landscape in rice zygotes. Genome Res 2022; 32:309-323. [PMID: 34949668 PMCID: PMC8805726 DOI: 10.1101/gr.275981.121] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 12/19/2021] [Indexed: 11/24/2022]
Abstract
The zygote, a totipotent stem cell, is crucial to the life cycle of sexually reproducing organisms. It is produced by the fusion of two differentiated cells-the egg and sperm, which in plants have radically different siRNA transcriptomes from each other and from multicellular embryos. Owing to technical challenges, the epigenetic changes that accompany the transition from differentiated gametes to totipotent zygote are poorly understood. Because siRNAs serve as both regulators and outputs of the epigenome, we characterized small RNA transcriptomes of zygotes from rice. Zygote small RNAs exhibit extensive maternal carryover and an apparent lack of paternal contribution, indicated by absence of sperm signature siRNAs. Zygote formation is accompanied by widespread redistribution of 24-nt siRNAs relative to gametes, such that ∼70% of the zygote siRNA loci do not overlap any egg cell siRNA loci. Newly detected siRNA loci in zygote are gene-proximal and not associated with centromeric heterochromatin, similar to canonical siRNAs, in sharp contrast to gametic siRNA loci that are gene-distal and heterochromatic. In addition, zygote but not egg siRNA loci are associated with high DNA methylation in the mature embryo. Thus, the zygote begins transitioning before the first embryonic division to an siRNA profile that is associated with future RdDM in embryogenesis. These findings indicate that, in addition to changes in gene expression, the transition to totipotency in the plant zygote is accompanied by resetting of the epigenetic reprogramming that occurred during gamete formation.
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Affiliation(s)
- Chenxin Li
- Department of Plant Biology, University of California, Davis, California 95616, USA
| | - Jonathan I Gent
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Hengping Xu
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma 73019, USA
| | - Hong Fu
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma 73019, USA
| | - Scott D Russell
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma 73019, USA
| | - Venkatesan Sundaresan
- Department of Plant Biology, University of California, Davis, California 95616, USA
- Department of Plant Sciences, University of California, Davis, California 95616, USA
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16
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Liang W, Li J, Sun L, Liu Y, Lan Z, Qian W. Deciphering the synergistic and redundant roles of CG and non-CG DNA methylation in plant development and transposable element silencing. THE NEW PHYTOLOGIST 2022; 233:722-737. [PMID: 34655488 PMCID: PMC9298111 DOI: 10.1111/nph.17804] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 10/11/2021] [Indexed: 05/10/2023]
Abstract
DNA methylation plays key roles in transposable element (TE) silencing and gene expression regulation. DNA methylation occurs at CG, CHG and CHH sequence contexts in plants. However, the synergistic and redundant roles of CG and non-CG methylation are poorly understood. By introducing CRISPR/Cas9-induced met1 mutation into the ddcc (drm1 drm2 cmt2 cmt3) mutant, we attempted to knock out all five DNA methyltransferases in Arabidopsis and then investigate the synergistic and redundant roles of CG and non-CG DNA methylation. We found that the homozygous ddcc met1 quintuple mutants are embryonically lethal, although met1 and ddcc mutants only display some developmental abnormalities. Unexpectedly, the ddcc met1 quintuple mutations only reduce transmission through the male gametophytes. The ddcc met1+/- mutants show apparent size divergence, which is not associated with difference in DNA methylation patterns, but associated with the difference in the levels of DNA damage. Finally, we show that a group of TEs are specifically activated in the ddcc met1+/- mutants. This work reveals that CG and non-CG DNA methylation synergistically and redundantly regulate plant reproductive development, vegetative development and TE silencing in Arabidopsis. Our findings provide insights into the roles of DNA methylation in plant development.
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Affiliation(s)
- Wenjie Liang
- State Key Laboratory of Protein and Plant Gene ResearchPeking‐Tsinghua Center for Life SciencesSchool of Life SciencesPeking UniversityBeijing100871China
| | - Jinchao Li
- State Key Laboratory of Protein and Plant Gene ResearchPeking‐Tsinghua Center for Life SciencesSchool of Life SciencesPeking UniversityBeijing100871China
- School of Advanced Agricultural SciencesPeking UniversityBeijing100871China
| | - Linhua Sun
- School of Advanced Agricultural SciencesPeking UniversityBeijing100871China
| | - Yi Liu
- State Key Laboratory of Protein and Plant Gene ResearchPeking‐Tsinghua Center for Life SciencesSchool of Life SciencesPeking UniversityBeijing100871China
| | - Zijun Lan
- State Key Laboratory of Protein and Plant Gene ResearchPeking‐Tsinghua Center for Life SciencesSchool of Life SciencesPeking UniversityBeijing100871China
| | - Weiqiang Qian
- State Key Laboratory of Protein and Plant Gene ResearchPeking‐Tsinghua Center for Life SciencesSchool of Life SciencesPeking UniversityBeijing100871China
- School of Advanced Agricultural SciencesPeking UniversityBeijing100871China
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17
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Vigneau J, Borg M. The epigenetic origin of life history transitions in plants and algae. PLANT REPRODUCTION 2021; 34:267-285. [PMID: 34236522 PMCID: PMC8566409 DOI: 10.1007/s00497-021-00422-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/14/2021] [Indexed: 05/17/2023]
Abstract
Plants and algae have a complex life history that transitions between distinct life forms called the sporophyte and the gametophyte. This phenomenon-called the alternation of generations-has fascinated botanists and phycologists for over 170 years. Despite the mesmerizing array of life histories described in plants and algae, we are only now beginning to learn about the molecular mechanisms controlling them and how they evolved. Epigenetic silencing plays an essential role in regulating gene expression during multicellular development in eukaryotes, raising questions about its impact on the life history strategy of plants and algae. Here, we trace the origin and function of epigenetic mechanisms across the plant kingdom, from unicellular green algae through to angiosperms, and attempt to reconstruct the evolutionary steps that influenced life history transitions during plant evolution. Central to this evolutionary scenario is the adaption of epigenetic silencing from a mechanism of genome defense to the repression and control of alternating generations. We extend our discussion beyond the green lineage and highlight the peculiar case of the brown algae. Unlike their unicellular diatom relatives, brown algae lack epigenetic silencing pathways common to animals and plants yet display complex life histories, hinting at the emergence of novel life history controls during stramenopile evolution.
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Affiliation(s)
- Jérômine Vigneau
- Department of Algal Development and Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Michael Borg
- Department of Algal Development and Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany.
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18
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Goodman K, Paez-Valencia J, Pennington J, Sonntag A, Ding X, Lee HN, Ahlquist PG, Molina I, Otegui MS. ESCRT components ISTL1 andLIP5 are required for tapetal function and pollen viability. THE PLANT CELL 2021; 33:2850-2868. [PMID: 34125207 PMCID: PMC8408459 DOI: 10.1093/plcell/koab132] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 05/07/2021] [Indexed: 05/03/2023]
Abstract
Pollen wall assembly is crucial for pollen development and plant fertility. The durable biopolymer sporopollenin and the constituents of the tryphine coat are delivered to developing pollen grains by the highly coordinated secretory activity of the surrounding tapetal cells. The role of membrane trafficking in this process, however, is largely unknown. In this study, we used Arabidopsis thaliana to characterize the role of two late-acting endosomal sorting complex required for transport (ESCRT) components, ISTL1 and LIP5, in tapetal function. Plants lacking ISTL1 and LIP5 form pollen with aberrant exine patterns, leading to partial pollen lethality. We found that ISTL1 and LIP5 are required for exocytosis of plasma membrane and secreted proteins in the tapetal cells at the free microspore stage, contributing to pollen wall development and tryphine deposition. Whereas the ESCRT machinery is well known for its role in endosomal trafficking, the function of ISTL1 and LIP5 in exocytosis is not a typical ESCRT function. The istl1 lip5 double mutants also show reduced intralumenal vesicle concatenation in multivesicular endosomes in both tapetal cells and developing pollen grains as well as morphological defects in early endosomes/trans-Golgi networks, suggesting that late ESCRT components function in the early endosomal pathway and exocytosis.
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Affiliation(s)
- Kaija Goodman
- Department of Botany, University of Wisconsin-Madison, Wisconsin 53706, USA
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Julio Paez-Valencia
- Department of Botany, University of Wisconsin-Madison, Wisconsin 53706, USA
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Janice Pennington
- Department of Botany, University of Wisconsin-Madison, Wisconsin 53706, USA
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Annika Sonntag
- Department of Biology, Algoma University, Ontario P6A 2G4, Canada
| | - Xinxin Ding
- Department of Botany, University of Wisconsin-Madison, Wisconsin 53706, USA
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Han Nim Lee
- Department of Botany, University of Wisconsin-Madison, Wisconsin 53706, USA
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Paul G. Ahlquist
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Department of Oncology and Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
- Morgridge Institute for Research, Madison, Wisconsin 53706, USA
| | - Isabel Molina
- Department of Biology, Algoma University, Ontario P6A 2G4, Canada
| | - Marisa S. Otegui
- Department of Botany, University of Wisconsin-Madison, Wisconsin 53706, USA
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Author for Correspondence:
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19
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Dziegielewski W, Ziolkowski PA. License to Regulate: Noncoding RNA Special Agents in Plant Meiosis and Reproduction. FRONTIERS IN PLANT SCIENCE 2021; 12:662185. [PMID: 34489987 PMCID: PMC8418119 DOI: 10.3389/fpls.2021.662185] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 06/07/2021] [Indexed: 06/13/2023]
Abstract
The complexity of the subcellular processes that take place during meiosis requires a significant remodeling of cellular metabolism and dynamic changes in the organization of chromosomes and the cytoskeleton. Recently, investigations of meiotic transcriptomes have revealed additional noncoding RNA factors (ncRNAs) that directly or indirectly influence the course of meiosis. Plant meiosis is the point at which almost all known noncoding RNA-dependent regulatory pathways meet to influence diverse processes related to cell functioning and division. ncRNAs have been shown to prevent transposon reactivation, create germline-specific DNA methylation patterns, and affect the expression of meiosis-specific genes. They can also influence chromosome-level processes, including the stimulation of chromosome condensation, the definition of centromeric chromatin, and perhaps even the regulation of meiotic recombination. In many cases, our understanding of the mechanisms underlying these processes remains limited. In this review, we will examine how the different functions of each type of ncRNA have been adopted in plants, devoting attention to both well-studied examples and other possible functions about which we can only speculate for now. We will also briefly discuss the most important challenges in the investigation of ncRNAs in plant meiosis.
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Affiliation(s)
| | - Piotr A. Ziolkowski
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
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20
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Pokhrel S, Huang K, Bélanger S, Zhan J, Caplan JL, Kramer EM, Meyers BC. Pre-meiotic 21-nucleotide reproductive phasiRNAs emerged in seed plants and diversified in flowering plants. Nat Commun 2021; 12:4941. [PMID: 34400639 PMCID: PMC8368212 DOI: 10.1038/s41467-021-25128-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 07/24/2021] [Indexed: 02/07/2023] Open
Abstract
Plant small RNAs are important regulatory elements that fine-tune gene expression and maintain genome integrity by silencing transposons. Reproductive organs of monocots produce abundant phased, small interfering RNAs (phasiRNAs). The 21-nt reproductive phasiRNAs triggered by miR2118 are highly enriched in pre-meiotic anthers, and have been found in multiple eudicot species, in contrast with prior reports of monocot specificity. The 24-nt reproductive phasiRNAs are triggered by miR2275, and are highly enriched during meiosis in many angiosperms. Here, we report the widespread presence of the 21-nt reproductive phasiRNA pathway in eudicots including canonical and non-canonical microRNA (miRNA) triggers of this pathway. In eudicots, these 21-nt phasiRNAs are enriched in pre-meiotic stages, a spatiotemporal distribution consistent with that of monocots and suggesting a role in anther development. Although this pathway is apparently absent in well-studied eudicot families including the Brassicaceae, Solanaceae and Fabaceae, our work in eudicots supports an earlier singular finding in spruce, a gymnosperm, indicating that the pathway of 21-nt reproductive phasiRNAs emerged in seed plants and was lost in some lineages.
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Affiliation(s)
- Suresh Pokhrel
- grid.34424.350000 0004 0466 6352Donald Danforth Plant Science Center, Saint Louis, MO USA ,grid.134936.a0000 0001 2162 3504Division of Plant Sciences, University of Missouri-Columbia, Columbia, MO USA
| | - Kun Huang
- grid.33489.350000 0001 0454 4791Bio-Imaging Center, Delaware Biotechnology Institute, University of Delaware, Newark, DE USA
| | - Sébastien Bélanger
- grid.34424.350000 0004 0466 6352Donald Danforth Plant Science Center, Saint Louis, MO USA
| | - Junpeng Zhan
- grid.34424.350000 0004 0466 6352Donald Danforth Plant Science Center, Saint Louis, MO USA ,grid.263817.9Department of Biology and Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, Guangdong China
| | - Jeffrey L. Caplan
- grid.33489.350000 0001 0454 4791Bio-Imaging Center, Delaware Biotechnology Institute, University of Delaware, Newark, DE USA
| | - Elena M. Kramer
- grid.38142.3c000000041936754XDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA USA
| | - Blake C. Meyers
- grid.34424.350000 0004 0466 6352Donald Danforth Plant Science Center, Saint Louis, MO USA ,grid.134936.a0000 0001 2162 3504Division of Plant Sciences, University of Missouri-Columbia, Columbia, MO USA
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21
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The effect of RNA polymerase V on 24-nt siRNA accumulation depends on DNA methylation contexts and histone modifications in rice. Proc Natl Acad Sci U S A 2021; 118:2100709118. [PMID: 34290143 DOI: 10.1073/pnas.2100709118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
RNA-directed DNA methylation (RdDM) functions in de novo methylation in CG, CHG, and CHH contexts. Here, we performed map-based cloning of OsNRPE1, which encodes the largest subunit of RNA polymerase V (Pol V), a key regulator of gene silencing and reproductive development in rice. We found that rice Pol V is required for CHH methylation on RdDM loci by transcribing long noncoding RNAs. Pol V influences the accumulation of 24-nucleotide small interfering RNAs (24-nt siRNAs) in a locus-specific manner. Biosynthesis of 24-nt siRNAs on loci with high CHH methylation levels and low CG and CHG methylation levels tends to depend on Pol V. In contrast, low methylation levels in the CHH context and high methylation levels in CG and CHG contexts predisposes 24-nt siRNA accumulation to be independent of Pol V. H3K9me1 and H3K9me2 tend to be enriched on Pol V-independent 24-nt siRNA loci, whereas various active histone modifications are enriched on Pol V-dependent 24-nt siRNA loci. DNA methylation is required for 24-nt siRNAs biosynthesis on Pol V-dependent loci but not on Pol V-independent loci. Our results reveal the function of rice Pol V for long noncoding RNA production, DNA methylation, 24-nt siRNA accumulation, and reproductive development.
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22
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Abstract
Plants have an extraordinary diversity of transcription machineries, including five nuclear DNA-dependent RNA polymerases. Four of these enzymes are dedicated to the production of long noncoding RNAs (lncRNAs), which are ribonucleic acids with functions independent of their protein-coding potential. lncRNAs display a broad range of lengths and structures, but they are distinct from the small RNA guides of RNA interference (RNAi) pathways. lncRNAs frequently serve as structural, catalytic, or regulatory molecules for gene expression. They can affect all elements of genes, including promoters, untranslated regions, exons, introns, and terminators, controlling gene expression at various levels, including modifying chromatin accessibility, transcription, splicing, and translation. Certain lncRNAs protect genome integrity, while others respond to environmental cues like temperature, drought, nutrients, and pathogens. In this review, we explain the challenge of defining lncRNAs, introduce the machineries responsible for their production, and organize this knowledge by viewing the functions of lncRNAs throughout the structure of a typical plant gene.
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Affiliation(s)
- Andrzej T Wierzbicki
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA;
| | - Todd Blevins
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, F-67084 Strasbourg, France;
| | - Szymon Swiezewski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland;
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23
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Ono A, Kinoshita T. Epigenetics and plant reproduction: Multiple steps for responsibly handling succession. CURRENT OPINION IN PLANT BIOLOGY 2021; 61:102032. [PMID: 33744743 DOI: 10.1016/j.pbi.2021.102032] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 01/31/2021] [Accepted: 02/10/2021] [Indexed: 05/02/2023]
Abstract
Although flowering plants and mammals have distinct life cycles and developmental programs, epigenetic information in both plant and mammalian cells is faithfully inherited across mitotic cell division. In mammals, epigenetic reprograming is a prominent process that is re-established in the zygote and germ line during early development. By contrast, plants do not produce germ cells until later in development. This difference, along with the many examples of the transmission of stable epialleles in plants, suggests that epigenetic reprograming in plants and mammals occurs via distinct mechanisms. In this review, we highlight recent advances in genome-wide epigenetic analyses in plants. These analyses provide insight into dynamic epigenetic regulation in plants and reveal unique processes that maintain genome integrity during plant sexual reproduction.
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Affiliation(s)
- Akemi Ono
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, Totsuka, Yokohama, Kanagawa, 244-0813, Japan.
| | - Tetsu Kinoshita
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, Totsuka, Yokohama, Kanagawa, 244-0813, Japan.
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24
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Florez-Rueda AM, Fiscalini F, Roth M, Grossniklaus U, Städler T. Endosperm and Seed Transcriptomes Reveal Possible Roles for Small RNA Pathways in Wild Tomato Hybrid Seed Failure. Genome Biol Evol 2021; 13:6278300. [PMID: 34009298 PMCID: PMC8358227 DOI: 10.1093/gbe/evab107] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2021] [Indexed: 01/10/2023] Open
Abstract
Crosses between the wild tomato species Solanum peruvianum and Solanum chilense result in hybrid seed failure (HSF), characterized by endosperm misdevelopment and embryo arrest. We previously showed that genomic imprinting, the parent-of-origin–dependent expression of alleles, is perturbed in the hybrid endosperm, with many of the normally paternally expressed genes losing their imprinted status. Here, we report transcriptome-based analyses of gene and small RNA (sRNA) expression levels. We identified 2,295 genes and 387 sRNA clusters as differentially expressed when comparing reciprocal hybrid seed to seeds and endosperms from the two within-species crosses. Our analyses uncovered a pattern of overdominance in endosperm gene expression in both hybrid cross directions, in marked contrast to the patterns of sRNA expression in whole seeds. Intriguingly, patterns of increased gene expression resemble the previously reported increased maternal expression proportions in hybrid endosperms. We identified physical clusters of sRNAs; differentially expressed sRNAs exhibit reduced transcript abundance in hybrid seeds of both cross directions. Moreover, sRNAs map to genes coding for key proteins involved in epigenetic regulation of gene expression, suggesting a regulatory feedback mechanism. We describe examples of genes that appear to be targets of sRNA-mediated gene silencing; in these cases, reduced sRNA abundance is concomitant with increased gene expression in hybrid seeds. Our analyses also show that S. peruvianum dominance impacts gene and sRNA expression in hybrid seeds. Overall, our study indicates roles for sRNA-mediated epigenetic regulation in HSF between closely related wild tomato species.
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Affiliation(s)
- Ana Marcela Florez-Rueda
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, 8008 Zurich, Switzerland.,Institute of Integrative Biology & Zurich-Basel Plant Science Center, ETH Zurich, 8092 Zurich, Switzerland
| | - Flurin Fiscalini
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, 8008 Zurich, Switzerland
| | - Morgane Roth
- Institute of Integrative Biology & Zurich-Basel Plant Science Center, ETH Zurich, 8092 Zurich, Switzerland
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, 8008 Zurich, Switzerland
| | - Thomas Städler
- Institute of Integrative Biology & Zurich-Basel Plant Science Center, ETH Zurich, 8092 Zurich, Switzerland
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25
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Wang Z, Butel N, Santos-González J, Simon L, Wärdig C, Köhler C. Transgenerational effect of mutants in the RNA-directed DNA methylation pathway on the triploid block in Arabidopsis. Genome Biol 2021; 22:141. [PMID: 33957942 PMCID: PMC8101200 DOI: 10.1186/s13059-021-02359-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 04/22/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Hybridization of plants that differ in number of chromosome sets (ploidy) frequently causes endosperm failure and seed arrest, a phenomenon referred to as triploid block. In Arabidopsis, loss of function of NRPD1, encoding the largest subunit of the plant-specific RNA polymerase IV (Pol IV), can suppress the triploid block. Pol IV generates short RNAs required to guide de novo methylation in the RNA-directed DNA methylation (RdDM) pathway. Recent work suggests that suppression of the triploid block by mutants in RdDM components differs, depending on whether the diploid pollen is derived from tetraploid plants or from the omission in second division 1 (osd1) mutant. This study aims to understand this difference. RESULTS In this study, we find that the ability of mutants in the RdDM pathway to suppress the triploid block depends on their degree of inbreeding. While first homozygous generation mutants in RdDM components NRPD1, RDR2, NRPE1, and DRM2 have weak or no ability to rescue the triploid block, they are able to suppress the triploid block with successive generations of inbreeding. Inbreeding of nrpd1 was connected with a transgenerational loss of non-CG DNA methylation on sites jointly regulated by CHROMOMETHYLASES 2 and 3. CONCLUSIONS Our data reveal that loss of RdDM function differs in its effect in early and late generations, which has important implications when interpreting the effect of RdDM mutants.
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Affiliation(s)
- Zhenxing Wang
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007 Uppsala, Sweden
- Present address: College of Horticulture, Nanjing Agricultural University and State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing, 210095 China
| | - Nicolas Butel
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007 Uppsala, Sweden
| | - Juan Santos-González
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007 Uppsala, Sweden
| | - Lauriane Simon
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007 Uppsala, Sweden
| | - Cecilia Wärdig
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007 Uppsala, Sweden
| | - Claudia Köhler
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007 Uppsala, Sweden
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
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26
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Liu S, de Jonge J, Trejo‐Arellano MS, Santos‐González J, Köhler C, Hennig L. Role of H1 and DNA methylation in selective regulation of transposable elements during heat stress. THE NEW PHYTOLOGIST 2021; 229:2238-2250. [PMID: 33091182 PMCID: PMC7894476 DOI: 10.1111/nph.17018] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/09/2020] [Indexed: 05/03/2023]
Abstract
Heat-stressed Arabidopsis plants release heterochromatin-associated transposable element (TE) silencing, yet it is not accompanied by major reductions of epigenetic repressive modifications. In this study, we explored the functional role of histone H1 in repressing heterochromatic TEs in response to heat stress. We generated and analyzed RNA and bisulfite-sequencing data of wild-type and h1 mutant seedlings before and after heat stress. Loss of H1 caused activation of pericentromeric Gypsy elements upon heat treatment, despite these elements remaining highly methylated. By contrast, nonpericentromeric Copia elements became activated concomitantly with loss of DNA methylation. The same Copia elements became activated in heat-treated chromomethylase 2 (cmt2) mutants, indicating that H1 represses Copia elements through maintaining DNA methylation under heat. We discovered that H1 is required for TE repression in response to heat stress, but its functional role differs depending on TE location. Strikingly, H1-deficient plants treated with the DNA methyltransferase inhibitor zebularine were highly tolerant to heat stress, suggesting that both H1 and DNA methylation redundantly suppress the plant response to heat stress.
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Affiliation(s)
- Shujing Liu
- Department of Plant BiologySwedish University of Agricultural Sciences and Linnean Center for Plant BiologyUppsala75007Sweden
| | - Jennifer de Jonge
- Department of Plant BiologySwedish University of Agricultural Sciences and Linnean Center for Plant BiologyUppsala75007Sweden
| | - Minerva S. Trejo‐Arellano
- Department of Plant BiologySwedish University of Agricultural Sciences and Linnean Center for Plant BiologyUppsala75007Sweden
| | - Juan Santos‐González
- Department of Plant BiologySwedish University of Agricultural Sciences and Linnean Center for Plant BiologyUppsala75007Sweden
| | - Claudia Köhler
- Department of Plant BiologySwedish University of Agricultural Sciences and Linnean Center for Plant BiologyUppsala75007Sweden
| | - Lars Hennig
- Department of Plant BiologySwedish University of Agricultural Sciences and Linnean Center for Plant BiologyUppsala75007Sweden
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27
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Palomar VM, Garciarrubio A, Garay-Arroyo A, Martínez-Martínez C, Rosas-Bringas O, Reyes JL, Covarrubias AA. The canonical RdDM pathway mediates the control of seed germination timing under salinity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:691-707. [PMID: 33131171 DOI: 10.1111/tpj.15064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 09/11/2020] [Accepted: 10/26/2020] [Indexed: 06/11/2023]
Abstract
Plants respond to adverse environmental cues by adjusting a wide variety of processes through highly regulated mechanisms to maintain plant homeostasis for survival. As a result of the sessile nature of plants, their response, adjustment and adaptation to the changing environment is intimately coordinated with their developmental programs through the crosstalk of regulatory networks. Germination is a critical process in the plant life cycle, and thus plants have evolved various strategies to control the timing of germination according to their local environment. The mechanisms involved in these adjustment responses are largely unknown, however. Here, we report that mutations in core elements of canonical RNA-directed DNA methylation (RdDM) affect the germination and post-germination growth of Arabidopsis seeds grown under salinity stress. Transcriptomic and whole-genome bisulfite sequencing (WGBS) analyses support the involvement of this pathway in the control of germination timing and post-germination growth under salinity stress by preventing the transcriptional activation of genes implicated in these processes. Subsequent transcriptional effects on genes that function in relation to these developmental events support this conclusion.
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Affiliation(s)
- Víctor Miguel Palomar
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apdo. Postal 510-3, Cuernavaca, Mor. C.P, 62250, Mexico
| | - Alejandro Garciarrubio
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apdo. Postal 510-3, Cuernavaca, Mor. C.P, 62250, Mexico
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior S/N anexo Jardín Botánico Exterior, Ciudad Universitaria, Ciudad de México, C.P. 04500, México
| | - Coral Martínez-Martínez
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apdo. Postal 510-3, Cuernavaca, Mor. C.P, 62250, Mexico
| | - Omar Rosas-Bringas
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apdo. Postal 510-3, Cuernavaca, Mor. C.P, 62250, Mexico
| | - José L Reyes
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apdo. Postal 510-3, Cuernavaca, Mor. C.P, 62250, Mexico
| | - Alejandra A Covarrubias
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apdo. Postal 510-3, Cuernavaca, Mor. C.P, 62250, Mexico
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28
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Borg M, Papareddy RK, Dombey R, Axelsson E, Nodine MD, Twell D, Berger F. Epigenetic reprogramming rewires transcription during the alternation of generations in Arabidopsis. eLife 2021; 10:e61894. [PMID: 33491647 PMCID: PMC7920552 DOI: 10.7554/elife.61894] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 01/25/2021] [Indexed: 12/18/2022] Open
Abstract
Alternation between morphologically distinct haploid and diploid life forms is a defining feature of most plant and algal life cycles, yet the underlying molecular mechanisms that govern these transitions remain unclear. Here, we explore the dynamic relationship between chromatin accessibility and epigenetic modifications during life form transitions in Arabidopsis. The diploid-to-haploid life form transition is governed by the loss of H3K9me2 and DNA demethylation of transposon-associated cis-regulatory elements. This event is associated with dramatic changes in chromatin accessibility and transcriptional reprogramming. In contrast, the global loss of H3K27me3 in the haploid form shapes a chromatin accessibility landscape that is poised to re-initiate the transition back to diploid life after fertilisation. Hence, distinct epigenetic reprogramming events rewire transcription through major reorganisation of the regulatory epigenome to guide the alternation of generations in flowering plants.
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Affiliation(s)
- Michael Borg
- Gregor Mendel Institute (GMI), Austrian Academy of SciencesViennaAustria
| | | | - Rodolphe Dombey
- Gregor Mendel Institute (GMI), Austrian Academy of SciencesViennaAustria
| | - Elin Axelsson
- Gregor Mendel Institute (GMI), Austrian Academy of SciencesViennaAustria
| | - Michael D Nodine
- Gregor Mendel Institute (GMI), Austrian Academy of SciencesViennaAustria
| | - David Twell
- Gregor Mendel Institute (GMI), Austrian Academy of SciencesViennaAustria
- Department of Genetics, University of LeicesterLeicesterUnited Kingdom
| | - Frédéric Berger
- Gregor Mendel Institute (GMI), Austrian Academy of SciencesViennaAustria
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29
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DNA methylation mutants in Physcomitrella patens elucidate individual roles of CG and non-CG methylation in genome regulation. Proc Natl Acad Sci U S A 2020; 117:33700-33710. [PMID: 33376225 DOI: 10.1073/pnas.2011361117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Cytosine (DNA) methylation in plants regulates the expression of genes and transposons. While methylation in plant genomes occurs at CG, CHG, and CHH sequence contexts, the comparative roles of the individual methylation contexts remain elusive. Here, we present Physcomitrella patens as the second plant system, besides Arabidopsis thaliana, with viable mutants with an essentially complete loss of methylation in the CG and non-CG contexts. In contrast to A. thaliana, P. patens has more robust CHH methylation, similar CG and CHG methylation levels, and minimal cross-talk between CG and non-CG methylation, making it possible to study context-specific effects independently. Our data found CHH methylation to act in redundancy with symmetric methylation in silencing transposons and to regulate the expression of CG/CHG-depleted transposons. Specific elimination of CG methylation did not dysregulate transposons or genes. In contrast, exclusive removal of non-CG methylation massively up-regulated transposons and genes. In addition, comparing two exclusively but equally CG- or CHG-methylated genomes, we show that CHG methylation acts as a greater transcriptional regulator than CG methylation. These results disentangle the transcriptional roles of CG and non-CG, as well as symmetric and asymmetric methylation in a plant genome, and point to the crucial role of non-CG methylation in genome regulation.
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30
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Borges F, Donoghue MTA, LeBlanc C, Wear EE, Tanurdžić M, Berube B, Brooks A, Thompson WF, Hanley-Bowdoin L, Martienssen RA. Loss of Small-RNA-Directed DNA Methylation in the Plant Cell Cycle Promotes Germline Reprogramming and Somaclonal Variation. Curr Biol 2020; 31:591-600.e4. [PMID: 33275892 DOI: 10.1016/j.cub.2020.10.098] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/24/2020] [Accepted: 10/30/2020] [Indexed: 02/07/2023]
Abstract
5-methyl cytosine is widespread in plant genomes in both CG and non-CG contexts. During replication, hemi-methylation on parental DNA strands guides symmetric CG methylation on nascent strands, but non-CG methylation requires modified histones and small RNA guides. Here, we used immortalized Arabidopsis cell suspensions to sort replicating nuclei and determine genome-wide cytosine methylation dynamics during the plant cell cycle. We find that symmetric mCG and mCHG are selectively retained in actively dividing cells in culture, whereas mCHH is depleted. mCG becomes transiently asymmetric during S phase but is rapidly restored in G2, whereas mCHG remains asymmetric throughout the cell cycle. Hundreds of loci gain ectopic CHG methylation, as well as 24-nt small interfering RNAs (siRNAs) and histone H3 lysine dimethylation (H3K9me2), without gaining CHH methylation. This suggests that spontaneous epialleles that arise in plant cell cultures are stably maintained by siRNA and H3K9me2 independent of the canonical RNA-directed DNA methylation (RdDM) pathway. In contrast, loci that fail to produce siRNA may be targeted for demethylation when the cell cycle arrests. Comparative analysis with methylomes of various tissues and cell types suggests that loss of small-RNA-directed non-CG methylation during DNA replication promotes germline reprogramming and epigenetic variation in plants propagated as clones.
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Affiliation(s)
- Filipe Borges
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
| | - Mark T A Donoghue
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Chantal LeBlanc
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Emily E Wear
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Milos Tanurdžić
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Benjamin Berube
- Cold Spring Harbor Laboratory School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Ashley Brooks
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - William F Thompson
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Linda Hanley-Bowdoin
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Robert A Martienssen
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
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31
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Rymen B, Ferrafiat L, Blevins T. Non-coding RNA polymerases that silence transposable elements and reprogram gene expression in plants. Transcription 2020; 11:172-191. [PMID: 33180661 PMCID: PMC7714444 DOI: 10.1080/21541264.2020.1825906] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Multisubunit RNA polymerase (Pol) complexes are the core machinery for gene expression in eukaryotes. The enzymes Pol I, Pol II and Pol III transcribe distinct subsets of nuclear genes. This family of nuclear RNA polymerases expanded in terrestrial plants by the duplication of Pol II subunit genes. Two Pol II-related enzymes, Pol IV and Pol V, are highly specialized in the production of regulatory, non-coding RNAs. Pol IV and Pol V are the central players of RNA-directed DNA methylation (RdDM), an RNA interference pathway that represses transposable elements (TEs) and selected genes. Genetic and biochemical analyses of Pol IV/V subunits are now revealing how these enzymes evolved from ancestral Pol II to sustain non-coding RNA biogenesis in silent chromatin. Intriguingly, Pol IV-RdDM regulates genes that influence flowering time, reproductive development, stress responses and plant–pathogen interactions. Pol IV target genes vary among closely related taxa, indicating that these regulatory circuits are often species-specific. Data from crops like maize, rice, tomato and Brassicarapa suggest that dynamic repositioning of TEs, accompanied by Pol IV targeting to TE-proximal genes, leads to the reprogramming of plant gene expression over short evolutionary timescales.
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Affiliation(s)
- Bart Rymen
- Institut de biologie moléculaire des plantes, Université de Strasbourg , Strasbourg, France
| | - Laura Ferrafiat
- Institut de biologie moléculaire des plantes, Université de Strasbourg , Strasbourg, France
| | - Todd Blevins
- Institut de biologie moléculaire des plantes, Université de Strasbourg , Strasbourg, France
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32
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Mimulus sRNAs Are Wound Responsive and Associated with Transgenerationally Plastic Genes but Rarely Both. Int J Mol Sci 2020; 21:ijms21207552. [PMID: 33066159 PMCID: PMC7589798 DOI: 10.3390/ijms21207552] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/07/2020] [Accepted: 10/10/2020] [Indexed: 12/25/2022] Open
Abstract
Organisms alter development in response to environmental cues. Recent studies demonstrate that they can transmit this plasticity to progeny. While the phenotypic and transcriptomic evidence for this “transgenerational plasticity” has accumulated, genetic and developmental mechanisms remain unclear. Plant defenses, gene expression and DNA methylation are modified as an outcome of parental wounding in Mimulus guttatus. Here, we sequenced M. guttatus small RNAs (sRNA) to test their possible role in mediating transgenerational plasticity. We sequenced sRNA populations of leaf-wounded and control plants at 1 h and 72 h after damage and from progeny of wounded and control parents. This allowed us to test three components of an a priori model of sRNA mediated transgenerational plasticity—(1) A subset of sRNAs will be differentially expressed in response to wounding, (2) these will be associated with previously identified differentially expressed genes and differentially methylated regions and (3) changes in sRNA abundance in wounded plants will be predictive of sRNA abundance, DNA methylation, and/or gene expression shifts in the following generation. Supporting (1) and (2), we found significantly different sRNA abundances in wounded leaves; the majority were associated with tRNA fragments (tRFs) rather than small-interfering RNAs (siRNA). However, siRNAs responding to leaf wounding point to Jasmonic Acid mediated responses in this system. We found that different sRNA classes were associated with regions of the genome previously found to be differentially expressed or methylated in progeny of wounded plants. Evidence for (3) was mixed. We found that non-dicer sRNAs with increased abundance in response to wounding tended to be nearby genes with decreased expression in the next generation. Counter to expectations, we did not find that siRNA responses to wounding were associated with gene expression or methylation changes in the next generation and within plant and transgenerational sRNA plasticity were negatively correlated.
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33
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Zhang S, Wu XQ, Xie HT, Zhao SS, Wu JG. Multifaceted roles of RNA polymerase IV in plant growth and development. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5725-5732. [PMID: 32969476 PMCID: PMC7541909 DOI: 10.1093/jxb/eraa346] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We discuss the latest findings on RNA polymerase IV (Pol IV) in plant growth and development, providing new insights and expanding on new ideas for further, more in-depth research on Pol IV.
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Affiliation(s)
- Shuai Zhang
- Vector-borne Virus Research Center, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Province Key Laboratory of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiao-Qing Wu
- Vector-borne Virus Research Center, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Province Key Laboratory of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hui-Ting Xie
- Vector-borne Virus Research Center, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Province Key Laboratory of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shan-Shan Zhao
- Vector-borne Virus Research Center, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Province Key Laboratory of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jian-Guo Wu
- Vector-borne Virus Research Center, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Province Key Laboratory of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
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34
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Liu Y, Teng C, Xia R, Meyers BC. PhasiRNAs in Plants: Their Biogenesis, Genic Sources, and Roles in Stress Responses, Development, and Reproduction. THE PLANT CELL 2020; 32:3059-3080. [PMID: 32817252 PMCID: PMC7534485 DOI: 10.1105/tpc.20.00335] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/29/2020] [Accepted: 08/14/2020] [Indexed: 05/08/2023]
Abstract
Phased secondary small interfering RNAs (phasiRNAs) constitute a major category of small RNAs in plants, but most of their functions are still poorly defined. Some phasiRNAs, known as trans-acting siRNAs, are known to target complementary mRNAs for degradation and to function in development. However, the targets or biological roles of other phasiRNAs remain speculative. New insights into phasiRNA biogenesis, their conservation, and their variation across the flowering plants continue to emerge due to the increased availability of plant genomic sequences, deeper and more sophisticated sequencing approaches, and improvements in computational biology and biochemical/molecular/genetic analyses. In this review, we survey recent progress in phasiRNA biology, with a particular focus on two classes associated with male reproduction: 21-nucleotide (accumulate early in anther ontogeny) and 24-nucloetide (produced in somatic cells during meiosis) phasiRNAs. We describe phasiRNA biogenesis, function, and evolution and define the unanswered questions that represent topics for future research.
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Affiliation(s)
- Yuanlong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong 510640, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510640, China
- College of Horticulture, South China Agricultural University, Guangzhou 510640, Guangdong, China
| | - Chong Teng
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
| | - Rui Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong 510640, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510640, China
- College of Horticulture, South China Agricultural University, Guangzhou 510640, Guangdong, China
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
- Division of Plant Sciences, University of Missouri-Columbia, Columbia, Missouri 65211
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35
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Small RNA Function in Plants: From Chromatin to the Next Generation. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2020; 84:133-140. [PMID: 32518093 DOI: 10.1101/sqb.2019.84.040394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Small RNA molecules can target a particular virus, gene, or transposable element (TE) with a high degree of specificity. Their ability to move from cell to cell and recognize targets in trans also allows building networks capable of regulating a large number of related targets at once. In the case of epigenetic silencing, small RNA may use the widespread distribution of TEs in eukaryotic genomes to coordinate many loci across developmental and generational time. Here, we discuss the intriguing role of plant small RNA in targeting transposons and repeats in pollen and seeds. Epigenetic reprogramming in the germline and early seed development provides a mechanism to control genome dosage, imprinted gene expression, and incompatible hybridizations via the "triploid block."
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36
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Zhan J. Pol IV Function is Differentially Essential within the Brassicaceae. THE PLANT CELL 2020; 32:791-792. [PMID: 32024690 PMCID: PMC7145460 DOI: 10.1105/tpc.20.00086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Affiliation(s)
- Junpeng Zhan
- Donald Danforth Plant Science CenterSt. Louis, MissouriDepartment of Biology and Institute of Plant and Food ScienceSouthern University of Science and TechnologyShenzhen, Guangdong, China
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