1
|
Xu D, Zeng L, Wang L, Yang DL. Rice requires a chromatin remodeler for Polymerase IV-small interfering RNA production and genomic immunity. Plant Physiol 2024; 194:2149-2164. [PMID: 37992039 DOI: 10.1093/plphys/kiad624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/19/2023] [Accepted: 10/19/2023] [Indexed: 11/24/2023]
Abstract
Transgenes are often spontaneously silenced, which hinders the application of genetic modifications to crop breeding. While gene silencing has been extensively studied in Arabidopsis (Arabidopsis thaliana), the molecular mechanism of transgene silencing remains elusive in crop plants. We used rice (Oryza sativa) plants silenced for a 35S::OsGA2ox1 (Gibberellin 2-oxidase 1) transgene to isolate five elements mountain (fem) mutants showing restoration of transgene expression. In this study, we isolated multiple fem2 mutants defective in a homolog of Required to Maintain Repression 1 (RMR1) of maize (Zea mays) and CLASSY (CLSY) of Arabidopsis. In addition to failing to maintain transgene silencing, as occurs in fem3, in which mutation occurs in NUCLEAR RNA POLYMERASE E1 (OsNRPE1), the fem2 mutant failed to establish transgene silencing of 35S::OsGA2ox1. Mutation in FEM2 eliminated all RNA POLYMERASE IV (Pol-IV)-FEM1/OsRDR2 (RNA-DEPENDENT RNA POLYMERASE 2)-dependent small interfering RNAs (siRNAs), reduced DNA methylation on genome-wide scale in rice seedlings, caused pleiotropic developmental defects, and increased disease resistance. Simultaneous mutation in 2 FEM2 homologous genes, FEM2-Like 1 (FEL1) and FEL2, however, did not affect DNA methylation and rice development and disease resistance. The predominant expression of FEM2 over FEL1 and FEL2 in various tissues was likely caused by epigenetic states. Overexpression of FEL1 but not FEL2 partially rescued hypomethylation of fem2, indicating that FEL1 maintains the cryptic function. In summary, FEM2 is essential for establishing and maintaining gene silencing; moreover, FEM2 is solely required for Pol IV-FEM1 siRNA biosynthesis and de novo DNA methylation.
Collapse
Affiliation(s)
- Dachao Xu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Longjun Zeng
- Institute of Crop Sciences, Yichun Academy of Sciences, Yichun, 336000 Jiangxi, China
| | - Lili Wang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Dong-Lei Yang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| |
Collapse
|
2
|
Xie G, Du X, Hu H, Du J. Molecular mechanisms of the RNA polymerases in plant RNA-directed DNA methylation. Trends Biochem Sci 2024; 49:247-256. [PMID: 38072749 DOI: 10.1016/j.tibs.2023.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 11/16/2023] [Accepted: 11/21/2023] [Indexed: 03/10/2024]
Abstract
In plants, two atypical DNA-dependent RNA polymerases, RNA polymerase IV (Pol IV) and Pol V, and an RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) together produce noncoding RNAs (ncRNAs) to guide the plant-specific RNA-directed DNA methylation (RdDM). Although both Pol IV and Pol V have evolved from the canonical Pol II, they have adapted to different roles in RdDM. The mechanisms of their adaptation are key to understanding plant DNA methylation and the divergent evolution of polymerases. In this review, we summarize insights that have emerged from recent structural studies of Pol IV, Pol V, and RDR2 and discuss their structural features critical for efficient ncRNA production in RdDM.
Collapse
Affiliation(s)
- Guohui Xie
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xuan Du
- Department of Biochemistry and Molecular Biology, International Cancer Center, Shenzhen University Medical School, Shenzhen 518060, China
| | - Hongmiao Hu
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Jiamu Du
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China; Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen 518055, China.
| |
Collapse
|
3
|
Cao W, Yang L, Zhuang M, Lv H, Wang Y, Zhang Y, Ji J. Plant non-coding RNAs: The new frontier for the regulation of plant development and adaptation to stress. Plant Physiol Biochem 2024; 208:108435. [PMID: 38402798 DOI: 10.1016/j.plaphy.2024.108435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 02/07/2024] [Accepted: 02/11/2024] [Indexed: 02/27/2024]
Abstract
Most plant transcriptomes constitute functional non-coding RNAs (ncRNAs) that lack the ability to encode proteins. In recent years, more research has demonstrated that ncRNAs play important regulatory roles in almost all plant biological processes by modulating gene expression. Thus, it is important to study the biogenesis and function of ncRNAs, particularly in plant growth and development and stress tolerance. In this review, we systematically explore the process of formation and regulatory mechanisms of ncRNAs, particularly those of microRNAs (miRNAs), small interfering RNAs (siRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs). Additionally, we provide a comprehensive overview of the recent advancements in ncRNAs research, including their regulation of plant growth and development (seed germination, root growth, leaf morphogenesis, floral development, and fruit and seed development) and responses to abiotic and biotic stress (drought, heat, cold, salinity, pathogens and insects). We also discuss research challenges and provide recommendations to advance the understanding of the roles of ncRNAs in agronomic applications.
Collapse
Affiliation(s)
- Wenxue Cao
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs/Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No. 12 ZhongGuanCun South St., Beijing 100081, China
| | - Limei Yang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs/Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No. 12 ZhongGuanCun South St., Beijing 100081, China
| | - Mu Zhuang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs/Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No. 12 ZhongGuanCun South St., Beijing 100081, China
| | - Honghao Lv
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs/Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No. 12 ZhongGuanCun South St., Beijing 100081, China
| | - Yong Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs/Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No. 12 ZhongGuanCun South St., Beijing 100081, China
| | - Yangyong Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs/Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No. 12 ZhongGuanCun South St., Beijing 100081, China.
| | - Jialei Ji
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs/Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No. 12 ZhongGuanCun South St., Beijing 100081, China.
| |
Collapse
|
4
|
Singh VK, Ahmed S, Saini DK, Gahlaut V, Chauhan S, Khandare K, Kumar A, Sharma PK, Kumar J. Manipulating epigenetic diversity in crop plants: Techniques, challenges and opportunities. Biochim Biophys Acta Gen Subj 2024; 1868:130544. [PMID: 38104668 DOI: 10.1016/j.bbagen.2023.130544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/04/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
Epigenetic modifications act as conductors of inheritable alterations in gene expression, all while keeping the DNA sequence intact, thereby playing a pivotal role in shaping plant growth and development. This review article presents an overview of techniques employed to investigate and manipulate epigenetic diversity in crop plants, focusing on both naturally occurring and artificially induced epialleles. The significance of epigenetic modifications in facilitating adaptive responses is explored through the examination of how various biotic and abiotic stresses impact them. Further, environmental chemicals are explored for their role in inducing epigenetic changes, particularly focusing on inhibitors of DNA methylation like 5-AzaC and zebularine, as well as inhibitors of histone deacetylation including trichostatin A and sodium butyrate. The review delves into various approaches for generating epialleles, including tissue culture techniques, mutagenesis, and grafting, elucidating their potential to induce heritable epigenetic modifications in plants. In addition, the ground breaking CRISPR/Cas is emphasized for its accuracy in targeting specific epigenetic changes. This presents a potent tools for deciphering the intricacies of epigenetic mechanisms. Furthermore, the intricate relationship between epigenetic modifications and non-coding RNA expression, including siRNAs and miRNAs, is investigated. The emerging role of exo-RNAi in epigenetic regulation is also introduced, unveiling its promising potential for future applications. The article concludes by addressing the opportunities and challenges presented by these techniques, emphasizing their implications for crop improvement. Conclusively, this extensive review provides valuable insights into the intricate realm of epigenetic changes, illuminating their significance in phenotypic plasticity and their potential in advancing crop improvement.
Collapse
Affiliation(s)
| | - Shoeb Ahmed
- Ch. Charan Singh University, Meerut 250004, India
| | - Dinesh Kumar Saini
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, United States
| | - Vijay Gahlaut
- University Centre for Research and Development, Chandigarh University, Mohali 140413, Punjab, India
| | | | - Kiran Khandare
- Center of Innovative and Applied Bioprocessing, Mohali 140308, Punjab, India
| | - Ashutosh Kumar
- Center of Innovative and Applied Bioprocessing, Mohali 140308, Punjab, India
| | - Pradeep Kumar Sharma
- Ch. Charan Singh University, Meerut 250004, India; Maharaja Suhel Dev State University, Azamgarh 276404, U.P., India
| | - Jitendra Kumar
- National Agri-Food Biotechnology Institute, Sector-81, Mohali 140306, Punjab, India.
| |
Collapse
|
5
|
Sidorenko LV, Chandler VL, Wang X, Peterson T. Transcribed enhancer sequences are required for maize p1 paramutation. Genetics 2024; 226:iyad178. [PMID: 38169343 PMCID: PMC10763531 DOI: 10.1093/genetics/iyad178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 08/27/2023] [Indexed: 01/05/2024] Open
Abstract
Paramutation is a transfer of heritable silencing states between interacting endogenous alleles or between endogenous alleles and homologous transgenes. Prior results demonstrated that paramutation occurs at the P1-rr (red pericarp and red cob) allele of the maize p1 (pericarp color 1) gene when exposed to a transgene containing a 1.2-kb enhancer fragment (P1.2) of P1-rr. The paramutable P1-rr allele undergoes transcriptional silencing resulting in a paramutant light-pigmented P1-rr' state. To define more precisely the sequences required to elicit paramutation, the P1.2 fragment was further subdivided, and the fragments transformed into maize plants and crossed with P1-rr. Analysis of the progeny plants showed that the sequences required for paramutation are located within a ∼600-bp segment of P1.2 and that this segment overlaps with a previously identified enhancer that is present in 4 direct repeats in P1-rr. The paramutagenic segment is transcribed in both the expressed P1-rr and the silenced P1-rr'. Transcription is sensitive to α-amanitin, indicating that RNA polymerase II mediates most of the transcription of this sequence. Although transcription within the paramutagenic sequence was similar in all tested genotypes, small RNAs were more abundant in the silenced P1-rr' epiallele relative to the expressed P1-rr allele. In agreement with prior results indicating the association of RNA-mediated DNA methylation in p1 paramutation, DNA blot analyses detected increased cytosine methylation of the paramutant P1-rr' sequences homologous to the transgenic P1.2 subfragments. Together these results demonstrate that the P1-rr enhancer repeats mediate p1 paramutation.
Collapse
Affiliation(s)
- Lyudmila V Sidorenko
- Department of Plant Sciences, The University of Arizona, Tucson, AZ 85721, USA
- Corteva Agriscience, 7300 NW 62nd Ave, Johnston, IA 50131, USA
| | - Vicki L Chandler
- Department of Plant Sciences, The University of Arizona, Tucson, AZ 85721, USA
- Minerva University, 14 Mint Plaza, Suite 300, San Francisco, CA 94103, USA
| | - Xiujuan Wang
- Corteva Agriscience, 7300 NW 62nd Ave, Johnston, IA 50131, USA
- Department of Genetics, Development, and Cellular Biology, Department of Agronomy, Iowa State University, Ames, IA 50010, USA
| | - Thomas Peterson
- Department of Genetics, Development, and Cellular Biology, Department of Agronomy, Iowa State University, Ames, IA 50010, USA
| |
Collapse
|
6
|
Felgines L, Rymen B, Martins LM, Xu G, Matteoli C, Himber C, Zhou M, Eis J, Coruh C, Böhrer M, Kuhn L, Chicher J, Pandey V, Hammann P, Wohlschlegel J, Waltz F, Law JA, Blevins T. CLSY docking to Pol IV requires a conserved domain critical for small RNA biogenesis and transposon silencing. bioRxiv 2023:2023.12.26.573199. [PMID: 38234754 PMCID: PMC10793415 DOI: 10.1101/2023.12.26.573199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Eukaryotes must balance the need for gene transcription by RNA polymerase II (Pol II) against the danger of mutations caused by transposable element (TE) proliferation. In plants, these gene expression and TE silencing activities are divided between different RNA polymerases. Specifically, RNA polymerase IV (Pol IV), which evolved from Pol II, transcribes TEs to generate small interfering RNAs (siRNAs) that guide DNA methylation and block TE transcription by Pol II. While the Pol IV complex is recruited to TEs via SNF2-like CLASSY (CLSY) proteins, how Pol IV partners with the CLSYs remains unknown. Here we identified a conserved CYC-YPMF motif that is specific to Pol IV and is positioned on the complex exterior. Furthermore, we found that this motif is essential for the co-purification of all four CLSYs with Pol IV, but that only one CLSY is present in any given Pol IV complex. These findings support a "one CLSY per Pol IV" model where the CYC-YPMF motif acts as a CLSY-docking site. Indeed, mutations in and around this motif phenocopy pol iv null mutants. Together, these findings provide structural and functional insights into a critical protein feature that distinguishes Pol IV from other RNA polymerases, allowing it to promote genome stability by targeting TEs for silencing.
Collapse
|
7
|
Yang DL, Huang K, Deng D, Zeng Y, Wang Z, Zhang Y. DNA-dependent RNA polymerases in plants. Plant Cell 2023; 35:3641-3661. [PMID: 37453082 PMCID: PMC10533338 DOI: 10.1093/plcell/koad195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 06/09/2023] [Accepted: 05/29/2023] [Indexed: 07/18/2023]
Abstract
DNA-dependent RNA polymerases (Pols) transfer the genetic information stored in genomic DNA to RNA in all organisms. In eukaryotes, the typical products of nuclear Pol I, Pol II, and Pol III are ribosomal RNAs, mRNAs, and transfer RNAs, respectively. Intriguingly, plants possess two additional Pols, Pol IV and Pol V, which produce small RNAs and long noncoding RNAs, respectively, mainly for silencing transposable elements. The five plant Pols share some subunits, but their distinct functions stem from unique subunits that interact with specific regulatory factors in their transcription cycles. Here, we summarize recent advances in our understanding of plant nucleus-localized Pols, including their evolution, function, structures, and transcription cycles.
Collapse
Affiliation(s)
- Dong-Lei Yang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Kun Huang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Deyin Deng
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Lin’an, Hangzhou 311300, China
| | - Yuan Zeng
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Zhenxing Wang
- College of Horticulture, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Yu Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| |
Collapse
|
8
|
Zhang HW, Huang K, Gu ZX, Wu XX, Wang JW, Zhang Y. A cryo-EM structure of KTF1-bound polymerase V transcription elongation complex. Nat Commun 2023; 14:3118. [PMID: 37253723 DOI: 10.1038/s41467-023-38619-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/10/2023] [Indexed: 06/01/2023] Open
Abstract
De novo DNA methylation in plants relies on transcription of RNA polymerase V (Pol V) along with KTF1, which produce long non-coding RNAs for recruitment and assembly of the DNA methylation machinery. Here, we report a cryo-EM structure of the Pol V transcription elongation complex bound to KTF1. The structure reveals the conformation of the structural motifs in the active site of Pol V that accounts for its inferior RNA-extension ability. The structure also reveals structural features of Pol V that prevent it from interacting with the transcription factors of Pol II and Pol IV. The KOW5 domain of KTF1 binds near the RNA exit channel of Pol V providing a scaffold for the proposed recruitment of Argonaute proteins to initiate the assembly of the DNA methylation machinery. The structure provides insight into the Pol V transcription elongation process and the role of KTF1 during Pol V transcription-coupled DNA methylation.
Collapse
Affiliation(s)
- Hong-Wei Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kun Huang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhan-Xi Gu
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao-Xian Wu
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yu Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
| |
Collapse
|
9
|
Marquardt S, Petrillo E, Manavella PA. Cotranscriptional RNA processing and modification in plants. Plant Cell 2023; 35:1654-1670. [PMID: 36259932 PMCID: PMC10226594 DOI: 10.1093/plcell/koac309] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/14/2022] [Indexed: 05/30/2023]
Abstract
The activities of RNA polymerases shape the epigenetic landscape of genomes with profound consequences for genome integrity and gene expression. A fundamental event during the regulation of eukaryotic gene expression is the coordination between transcription and RNA processing. Most primary RNAs mature through various RNA processing and modification events to become fully functional. While pioneering results positioned RNA maturation steps after transcription ends, the coupling between the maturation of diverse RNA species and their transcription is becoming increasingly evident in plants. In this review, we discuss recent advances in our understanding of the crosstalk between RNA Polymerase II, IV, and V transcription and nascent RNA processing of both coding and noncoding RNAs.
Collapse
Affiliation(s)
- Sebastian Marquardt
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg, Denmark
| | - Ezequiel Petrillo
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-CONICET-UBA), Buenos Aires, C1428EHA, Argentina
| | - 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
| |
Collapse
|
10
|
Abstract
Robust plant immune systems are fine-tuned by both protein-coding genes and non-coding RNAs. Long non-coding RNAs (lncRNAs) refer to RNAs with a length of more than 200 nt and usually do not have protein-coding function and do not belong to any other well-known non-coding RNA types. The non-protein-coding, low expression, and non-conservative characteristics of lncRNAs restrict their recognition. Although studies of lncRNAs in plants are in the early stage, emerging studies have shown that plants employ lncRNAs to regulate plant immunity. Moreover, in response to stresses, numerous lncRNAs are differentially expressed, which manifests the actions of low-expressed lncRNAs and makes plant-microbe/insect interactions a convenient system to study the functions of lncRNAs. Here, we summarize the current advances in plant lncRNAs, discuss their regulatory effects in different stages of plant immunity, and highlight their roles in diverse plant-microbe/insect interactions. These insights will not only strengthen our understanding of the roles and actions of lncRNAs in plant-microbe/insect interactions but also provide novel insight into plant immune responses and a basis for further research in this field.
Collapse
Affiliation(s)
- Juan Huang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Wenling Zhou
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoming Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
- HainanYazhou Bay Seed Lab, Sanya, China
| | - Yi Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| |
Collapse
|
11
|
Abstract
In addition to the conserved RNA polymerases I to III (Pols I to III) in eukaryotes, two atypical polymerases, Pols IV and V, specifically produce noncoding RNA in the RNA-directed DNA methylation pathway in plants. Here, we report on the structures of cauliflower Pol V in the free and elongation conformations. A conserved tyrosine residue of NRPE2 stacks with a double-stranded DNA branch of the transcription bubble to potentially attenuate elongation by inducing transcription stalling. The nontemplate DNA strand is captured by NRPE2 to enhance backtracking, thereby increasing 3'-5' cleavage, which likely underpins Pol V's high fidelity. The structures also illuminate the mechanism of Pol V transcription stalling and enhanced backtracking, which may be important for Pol V's retention on chromatin to serve its function in tethering downstream factors for RNA-directed DNA methylation.
Collapse
Affiliation(s)
- Guohui Xie
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xuan Du
- Department of Biochemistry and Molecular Biology, International Cancer Center, Shenzhen University Medical School, Shenzhen 518060, China
| | - Hongmiao Hu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Sisi Li
- Department of Biochemistry and Molecular Biology, International Cancer Center, Shenzhen University Medical School, Shenzhen 518060, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Steven E Jacobsen
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA
- Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Jiamu Du
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| |
Collapse
|
12
|
Wang F, Huang HY, Huang J, Singh J, Pikaard CS. Enzymatic reactions of AGO4 in RNA-directed DNA methylation: siRNA duplex loading, passenger strand elimination, target RNA slicing, and sliced target retention. Genes Dev 2023; 37:103-118. [PMID: 36746605 PMCID: PMC10069450 DOI: 10.1101/gad.350240.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 01/13/2023] [Indexed: 02/08/2023]
Abstract
RNA-directed DNA methylation in plants is guided by 24-nt siRNAs generated in parallel with 23-nt RNAs of unknown function. We show that 23-nt RNAs function as passenger strands during 24-nt siRNA incorporation into AGO4. The 23-nt RNAs are then sliced into 11- and 12-nt fragments, with 12-nt fragments remaining associated with AGO4. Slicing recapitulated with recombinant AGO4 and synthetic RNAs reveals that siRNAs of 21-24 nt, with any 5'-terminal nucleotide, can guide slicing, with sliced RNAs then retained by AGO4. In vivo, RdDM target locus RNAs that copurify with AGO4 also display a sequence signature of slicing. Comparing plants expressing slicing-competent versus slicing-defective AGO4 shows that slicing elevates cytosine methylation levels at virtually all RdDM loci. We propose that siRNA passenger strand elimination and AGO4 tethering to sliced target RNAs are distinct modes by which AGO4 slicing enhances RNA-directed DNA methylation.
Collapse
Affiliation(s)
- Feng Wang
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA
- Howard Hughes Medical Institute, Indiana University, Bloomington, Indiana 47405, USA
| | - Hsiao-Yun Huang
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Jie Huang
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Jasleen Singh
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Craig S Pikaard
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA;
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA
- Howard Hughes Medical Institute, Indiana University, Bloomington, Indiana 47405, USA
| |
Collapse
|
13
|
Akinmusola RY, Wilkins CA, Doughty J. DDM1-Mediated TE Silencing in Plants. Plants (Basel) 2023; 12:437. [PMID: 36771522 PMCID: PMC9919755 DOI: 10.3390/plants12030437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/05/2023] [Accepted: 01/09/2023] [Indexed: 06/18/2023]
Abstract
Epigenetic modifications are indispensable for regulating gene bodies and TE silencing. DECREASE IN DNA METHYLATION 1 (DDM1) is a chromatin remodeller involved in histone modifications and DNA methylation. Apart from maintaining the epigenome, DDM1 also maintains key plant traits such as flowering time and heterosis. The role of DDM1 in epigenetic regulation is best characterised in plants, especially arabidopsis, rice, maize and tomato. The epigenetic changes induced by DDM1 establish the stable inheritance of many plant traits for at least eight generations, yet DDM1 does not methylate protein-coding genes. The DDM1 TE silencing mechanism is distinct and has evolved independently of other silencing pathways. Unlike the RNA-directed DNA Methylation (RdDM) pathway, DDM1 does not depend on siRNAs to enforce the heterochromatic state of TEs. Here, we review DDM1 TE silencing activity in the RdDM and non-RdDM contexts. The DDM1 TE silencing machinery is strongly associated with the histone linker H1 and histone H2A.W. While the linker histone H1 excludes the RdDM factors from methylating the heterochromatin, the histone H2A.W variant prevents TE mobility. The DDM1-H2A.W strategy alone silences nearly all the mobile TEs in the arabidopsis genome. Thus, the DDM1-directed TE silencing essentially preserves heterochromatic features and abolishes mobile threats to genome stability.
Collapse
|
14
|
Jing X, Xu L, Huai X, Zhang H, Zhao F, Qiao Y. Genome-Wide Identification and Characterization of Argonaute, Dicer-like and RNA-Dependent RNA Polymerase Gene Families and Their Expression Analyses in Fragaria spp. Genes (Basel) 2023; 14:genes14010121. [PMID: 36672862 PMCID: PMC9859564 DOI: 10.3390/genes14010121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/19/2022] [Accepted: 12/29/2022] [Indexed: 01/04/2023] Open
Abstract
In the growth and development of plants, some non-coding small RNAs (sRNAs) not only mediate RNA interference at the post-transcriptional level, but also play an important regulatory role in chromatin modification at the transcriptional level. In these processes, the protein factors Argonaute (AGO), Dicer-like (DCL), and RNA-dependent RNA polymerase (RDR) play very important roles in the synthesis of sRNAs respectively. Though they have been identified in many plants, the information about these gene families in strawberry was poorly understood. In this study, using a genome-wide analysis and a phylogenetic approach, 13 AGO, six DCL, and nine RDR genes were identified in diploid strawberry Fragaria vesca. We also identified 33 AGO, 18 DCL, and 28 RDR genes in octoploid strawberry Fragaria × ananassa, studied the expression patterns of these genes in various tissues and developmental stages of strawberry, and researched the response of these genes to some hormones, finding that almost all genes respond to the five hormone stresses. This study is the first report of a genome-wide analysis of AGO, DCL, and RDR gene families in Fragaria spp., in which we provide basic genomic information and expression patterns for these genes. Additionally, this study provides a basis for further research on the functions of these genes and some evidence for the evolution between diploid and octoploid strawberries.
Collapse
Affiliation(s)
- Xiaotong Jing
- Laboratory of Fruit Crop Biotechnology, College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China
| | - Linlin Xu
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Xinjia Huai
- Laboratory of Fruit Crop Biotechnology, College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China
| | - Hong Zhang
- Laboratory of Fruit Crop Biotechnology, College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China
| | - Fengli Zhao
- Laboratory of Fruit Crop Biotechnology, College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China
| | - Yushan Qiao
- Laboratory of Fruit Crop Biotechnology, College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
- Correspondence:
| |
Collapse
|
15
|
Wang Z, Zheng H, Huang J, Yang G, Yan K, Zhang S, Wu C, Zheng C. DEMETHYLATION REGULATOR 1 regulates DNA demethylation of the nuclear and mitochondrial genomes. J Integr Plant Biol 2022; 64:2344-2360. [PMID: 36223079 DOI: 10.1111/jipb.13386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Active DNA demethylation effectively modulates gene expression during plant development and in response to stress. However, little is known about the upstream regulatory factors that regulate DNA demethylation. We determined that the demethylation regulator 1 (demr1) mutant exhibits a distinct DNA methylation profile at selected loci queried by methylation-sensitive polymerase chain reaction and globally based on whole-genome bisulfite sequencing. Notably, the transcript levels of the DNA demethylase gene REPRESSOR OF SILENCING 1 (ROS1) were lower in the demr1 mutant. We established that DEMR1 directly binds to the ROS1 promoter in vivo and in vitro, and the methylation level in the DNA methylation monitoring sequence of ROS1 promoter decreased by 60% in the demr1 mutant. About 40% of the hyper-differentially methylated regions (DMRs) in the demr1 mutant were shared with the ros1-4 mutant. Genetic analysis indicated that DEMR1 acts upstream of ROS1 to positively regulate abscisic acid (ABA) signaling during seed germination and seedling establishment stages. Surprisingly, the loss of DEMR1 function also caused a rise in methylation levels of the mitochondrial genome, impaired mitochondrial structure and an early flowering phenotype. Together, our results show that DEMR1 is a novel regulator of DNA demethylation of both the nuclear and mitochondrial genomes in response to ABA and plant development in Arabidopsis.
Collapse
Affiliation(s)
- Zhen Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Hao Zheng
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
- National Institute of Biological Sciences (NIBS), Beijing, 102206, China
| | - Jinguang Huang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Guodong Yang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Kang Yan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Shizhong Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Changai Wu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Chengchao Zheng
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| |
Collapse
|
16
|
Leichter SM, Du J, Zhong X. Structure and Mechanism of Plant DNA Methyltransferases. Adv Exp Med Biol 2022; 1389:137-57. [PMID: 36350509 DOI: 10.1007/978-3-031-11454-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
DNA methylation is an important epigenetic mark conserved in eukaryotes from fungi to animals and plants, where it plays a crucial role in regulating gene expression and transposon silencing. Once the methylation mark is established by de novo DNA methyltransferases, specific regulatory mechanisms are required to maintain the methylation state during chromatin replication, both during meiosis and mitosis. Plant DNA methylation is found in three contexts; CG, CHG, and CHH (H = A, T, C), which are established and maintained by a unique set of DNA methyltransferases and are regulated by plant-specific pathways. DNA methylation in plants is often associated with other epigenetic modifications, such as noncoding RNA and histone modifications. This chapter focuses on the structure, function, and regulatory mechanism of plant DNA methyltransferases and their crosstalk with other epigenetic pathways.
Collapse
|
17
|
Jagić M, Vuk T, Škiljaica A, Markulin L, Vičić Bočkor V, Tokić M, Miškec K, Razdorov G, Habazin S, Šoštar M, Weber I, Bauer N, Leljak Levanić D. BPM1 regulates RdDM-mediated DNA methylation via a cullin 3 independent mechanism. Plant Cell Rep 2022; 41:2139-2157. [PMID: 36066603 DOI: 10.1007/s00299-022-02911-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
BPM1 interacts with components of the DDR complex and stimulates DNA methylation at CHH sites, suggesting its involvement in the RdDM methylation pathway. The best-known function of MATH-BTB proteins, including Arabidopsis BPM proteins, is their role as substrate-specific adaptors of CUL3-based E3 ligases in the ubiquitin-proteasome pathway. This paper reports a new CUL3-independent role of BPM1 in RNA-directed DNA methylation (RdDM). Using quantitative and qualitative Y2H, pull down, microscale thermophoresis and FRET-FLIM, we demonstrate that BPM1 interacts with DMS3 and RDM1, components of the chromatin remodeling DDR complex involved in the recruitment of the RdDM methylation machinery. All three proteins colocalized predominantly in the nucleus. The MATH domain, which specifically binds proteins destined for degradation, was not essential for interactions with DMS3 and RDM1. In plants overexpressing BPM1, endogenous DMS3 protein levels were stable, indicating that BPM1 does not induce proteasomal degradation. In RDM1-overexpressing plants, RDM1 was not ubiquitinated. Together, these results suggest that BPM1 does not mediate the degradation of DMS3 and RDM1. Additionally, overexpression of BPM1 caused increased global methylation levels as well as CHH methylation in promoters of two RdDM-regulated genes, FWA and CML41. Overall, BPM1 seems to have a stimulating effect on RdDM activity, and this role appears to be unrelated to its known function as a Cul3-based E3 ligase adaptor.
Collapse
Affiliation(s)
- Mateja Jagić
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Tamara Vuk
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Andreja Škiljaica
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Lucija Markulin
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Vedrana Vičić Bočkor
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Mirta Tokić
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Karlo Miškec
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | | | | | - Marko Šoštar
- Division of Molecular Biology, Institute Ruđer Bošković, Zagreb, Croatia
| | - Igor Weber
- Division of Molecular Biology, Institute Ruđer Bošković, Zagreb, Croatia
| | - Nataša Bauer
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Dunja Leljak Levanić
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia.
| |
Collapse
|
18
|
Niu C, Jiang L, Cao F, Liu C, Guo J, Zhang Z, Yue Q, Hou N, Liu Z, Li X, Tahir MM, He J, Li Z, Li C, Ma F, Guan Q. Methylation of a MITE insertion in the MdRFNR1-1 promoter is positively associated with its allelic expression in apple in response to drought stress. Plant Cell 2022; 34:3983-4006. [PMID: 35897144 PMCID: PMC9520589 DOI: 10.1093/plcell/koac220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Miniature inverted-repeat transposable elements (MITEs) are widely distributed in the plant genome and can be methylated. However, whether DNA methylation of MITEs is associated with induced allelic expression and drought tolerance is unclear. Here, we identified the drought-inducible MdRFNR1 (root-type ferredoxin-NADP+ oxidoreductase) gene in apple (Malus domestica). MdRFNR1 plays a positive role in drought tolerance by regulating the redox system, including increasing NADP+ accumulation and catalase and peroxidase activities and decreasing NADPH levels. Sequence analysis identified a MITE insertion (MITE-MdRF1) in the promoter of MdRFNR1-1 but not the MdRFNR1-2 allele. MdRFNR1-1 but not MdRFNR1-2 expression was significantly induced by drought stress, which was positively associated with the MITE-MdRF1 insertion and its DNA methylation. The methylated MITE-MdRF1 is recognized by the transcriptional anti-silencing factors MdSUVH1 and MdSUVH3, which recruit the DNAJ domain-containing proteins MdDNAJ1, MdDNAJ2, and MdDNAJ5, thereby activating MdRFNR1-1 expression under drought stress. Finally, we showed that MdSUVH1 and MdDNAJ1 are positive regulators of drought tolerance. These findings illustrate the molecular roles of methylated MITE-MdRF1 (which is recognized by the MdSUVH-MdDNAJ complex) in induced MdRFNR1-1 expression as well as the drought response of apple and shed light on the molecular mechanisms of natural variation in perennial trees.
Collapse
Affiliation(s)
| | | | | | - Chen Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Junxing Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Zitong Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Qianyu Yue
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Nan Hou
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Zeyuan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Xuewei Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
- College of Life Science, Northwest A&F University, Yangling 712100, China
| | - Muhammad Mobeen Tahir
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Jieqiang He
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Zhongxing Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Chao Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | | |
Collapse
|
19
|
Wang M, He L, Chen B, Wang Y, Wang L, Zhou W, Zhang T, Cao L, Zhang P, Xie L, Zhang Q. Transgenerationally Transmitted DNA Demethylation of a Spontaneous Epialleles Using CRISPR/dCas9-TET1cd Targeted Epigenetic Editing in Arabidopsis. Int J Mol Sci 2022; 23:ijms231810492. [PMID: 36142407 PMCID: PMC9504898 DOI: 10.3390/ijms231810492] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/30/2022] [Accepted: 09/07/2022] [Indexed: 11/24/2022] Open
Abstract
CRISPR/dCas9 is an important DNA modification tool in which a disarmed Cas9 protein with no nuclease activity is fused with a specific DNA modifying enzyme. A previous study reported that overexpression of the TET1 catalytic domain (TET1cd) reduces genome-wide methylation in Arabidopsis. A spontaneous naturally occurring methylation region (NMR19-4) was identified in the promoter region of the PPH (Pheophytin Pheophorbide Hydrolase) gene, which encodes an enzyme that can degrade chlorophyll and accelerate leaf senescence. The methylation status of NMR19-4 is associated with PPH expression and leaf senescence in Arabidopsis natural accessions. In this study, we show that the CRISPR/dCas9-TET1cd system can be used to target the methylation of hypermethylated NMR19-4 region to reduce the level of methylation, thereby increasing the expression of PPH and accelerating leaf senescence. Furthermore, hybridization between transgenic demethylated plants and hypermethylated ecotypes showed that the demethylation status of edited NMR19-4, along with the enhanced PPH expression and accelerated leaf senescence, showed Mendelian inheritance in F1 and F2 progeny, indicating that spontaneous epialleles are stably transmitted trans-generationally after demethylation editing. Our results provide a rational approach for future editing of spontaneously mutated epialleles and provide insights into the epigenetic mechanisms that control plant leaf senescence.
Collapse
Affiliation(s)
- Min Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Li He
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Bowei Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Yanwei Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Lishan Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Wei Zhou
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Tianxu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
| | - Lesheng Cao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Peng Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Linan Xie
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Qingzhu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Correspondence:
| |
Collapse
|
20
|
Du X, Yang Z, Ariza AJF, Wang Q, Xie G, Li S, Du J. Structure of plant RNA-DEPENDENT RNA POLYMERASE 2, an enzyme involved in small interfering RNA production. Plant Cell 2022; 34:2140-2149. [PMID: 35188193 PMCID: PMC9134047 DOI: 10.1093/plcell/koac067] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/10/2022] [Indexed: 06/14/2023]
Abstract
In plants, the biogenesis of small interfering RNA (siRNA) requires a family of RNA-dependent RNA polymerases that convert single-stranded RNA (ssRNA) into double-stranded RNA (dsRNA), which is subsequently cleaved into defined lengths by Dicer endonucleases. Here, we determined the structure of maize (Zea mays) RNA-DEPENDENT RNA POLYMERASE 2 (ZmRDR2) in the closed and open conformations. The core catalytic region of ZmRDR2 possesses the canonical DNA-dependent RNA polymerase (DdRP) catalytic sites, pointing to a shared RNA production mechanism between DdRPs and plant RDR-family proteins. Apo-ZmRDR2 adopts a highly compact structure, representing an inactive closed conformation. By contrast, adding RNA induced a significant conformational change in the ZmRDR2 Head domain that opened the RNA binding tunnel, suggesting this is an active elongation conformation of ZmRDR2. Overall, our structural studies trapped both the active and inactive conformations of ZmRDR2, providing insights into the molecular mechanism of dsRNA synthesis during plant siRNA production.
Collapse
Affiliation(s)
| | | | - Alfredo Jose Florez Ariza
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, USA
- Biophysics Graduate Group, University of California, Berkeley, California 94720, USA
| | - Qian Wang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Guohui Xie
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Sisi Li
- Department of Biochemistry and Molecular Biology, International Cancer Center, Shenzhen University Health Science Center, Shenzhen 518060, China
| | | |
Collapse
|
21
|
Kumari P, Khan S, Wani IA, Gupta R, Verma S, Alam P, Alaklabi A. Unravelling the Role of Epigenetic Modifications in Development and Reproduction of Angiosperms: A Critical Appraisal. Front Genet 2022; 13:819941. [PMID: 35664328 PMCID: PMC9157814 DOI: 10.3389/fgene.2022.819941] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/14/2022] [Indexed: 12/28/2022] Open
Abstract
Epigenetics are the heritable changes in gene expression patterns which occur without altering DNA sequence. These changes are reversible and do not change the sequence of the DNA but can alter the way in which the DNA sequences are read. Epigenetic modifications are induced by DNA methylation, histone modification, and RNA-mediated mechanisms which alter the gene expression, primarily at the transcriptional level. Such alterations do control genome activity through transcriptional silencing of transposable elements thereby contributing toward genome stability. Plants being sessile in nature are highly susceptible to the extremes of changing environmental conditions. This increases the likelihood of epigenetic modifications within the composite network of genes that affect the developmental changes of a plant species. Genetic and epigenetic reprogramming enhances the growth and development, imparts phenotypic plasticity, and also ensures flowering under stress conditions without changing the genotype for several generations. Epigenetic modifications hold an immense significance during the development of male and female gametophytes, fertilization, embryogenesis, fruit formation, and seed germination. In this review, we focus on the mechanism of epigenetic modifications and their dynamic role in maintaining the genomic integrity during plant development and reproduction.
Collapse
Affiliation(s)
- Priyanka Kumari
- Conservation and Molecular Biology Lab., Department of Botany, Baba Ghulam Shah Badshah University, Rajouri, India
| | - Sajid Khan
- Conservation and Molecular Biology Lab., Department of Botany, Baba Ghulam Shah Badshah University, Rajouri, India
| | - Ishfaq Ahmad Wani
- Conservation and Molecular Biology Lab., Department of Botany, Baba Ghulam Shah Badshah University, Rajouri, India
| | - Renu Gupta
- Division of Soil Sciences & Agricultural Chemistry, Faculty of Agriculture Sher e Kashmir University of Agricultural Sciences and Technology, Chatha, India
| | - Susheel Verma
- Department of Botany, University of Jammu, Jammu, India
- *Correspondence: Susheel Verma,
| | - Pravej Alam
- Department of Biology, College of Science and Humanities, Prince Sattam bin Abdulaziz University (PSAU), Alkharj, Saudi Arabia
| | - Abdullah Alaklabi
- Department of Biology, College of Science, University of Bisha, Bisha, Saudi Arabia
| |
Collapse
|
22
|
Chen S, Liu W, Naganuma M, Tomari Y, Iwakawa HO. Functional specialization of monocot DCL3 and DCL5 proteins through the evolution of the PAZ domain. Nucleic Acids Res 2022; 50:4669-4684. [PMID: 35380679 PMCID: PMC9071481 DOI: 10.1093/nar/gkac223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 03/18/2022] [Accepted: 03/23/2022] [Indexed: 11/13/2022] Open
Abstract
Monocot DICER-LIKE3 (DCL3) and DCL5 produce distinct 24-nt small interfering RNAs (siRNAs), heterochromatic siRNAs (hc-siRNAs) and phased secondary siRNAs (phasiRNAs), respectively. The former small RNAs are linked to silencing of transposable elements and heterochromatic repeats, and the latter to reproductive processes. It is assumed that these DCLs evolved from an ancient ‘eudicot-type’ DCL3 ancestor, which may have produced both types of siRNAs. However, how functional differentiation was achieved after gene duplication remains elusive. Here, we find that monocot DCL3 and DCL5 exhibit biochemically distinct preferences for 5′ phosphates and 3′ overhangs, consistent with the structural properties of their in vivo double-stranded RNA substrates. Importantly, these distinct substrate specificities are determined by the PAZ domains of DCL3 and DCL5, which have accumulated mutations during the course of evolution. These data explain the mechanism by which these DCLs cleave their cognate substrates from a fixed end, ensuring the production of functional siRNAs. Our study also indicates how plants have diversified and optimized RNA silencing mechanisms during evolution.
Collapse
Affiliation(s)
- Shirui Chen
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Wei Liu
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Masahiro Naganuma
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Yukihide Tomari
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Hiro-Oki Iwakawa
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| |
Collapse
|
23
|
Gutschker S, Corral JM, Schmiedl A, Ludewig F, Koch W, Fiedler-Wiechers K, Czarnecki O, Harms K, Keller I, Martins Rodrigues C, Pommerrenig B, Neuhaus HE, Zierer W, Sonnewald U, Müdsam C. Multi-omics data integration reveals link between epigenetic modifications and gene expression in sugar beet (Beta vulgaris subsp. vulgaris) in response to cold. BMC Genomics 2022; 23:144. [PMID: 35176993 DOI: 10.1186/s12864-022-08312-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/13/2022] [Indexed: 12/19/2022] Open
Abstract
Background DNA methylation is thought to influence the expression of genes, especially in response to changing environmental conditions and developmental changes. Sugar beet (Beta vulgaris ssp. vulgaris), and other biennial or perennial plants are inevitably exposed to fluctuating temperatures throughout their lifecycle and might even require such stimulus to acquire floral competence. Therefore, plants such as beets, need to fine-tune their epigenetic makeup to ensure phenotypic plasticity towards changing environmental conditions while at the same time steering essential developmental processes. Different crop species may show opposing reactions towards the same abiotic stress, or, vice versa, identical species may respond differently depending on the specific kind of stress. Results In this study, we investigated common effects of cold treatment on genome-wide DNA methylation and gene expression of two Beta vulgaris accessions via multi-omics data analysis. Cold exposure resulted in a pronounced reduction of DNA methylation levels, which particularly affected methylation in CHH context (and to a lesser extent CHG) and was accompanied by transcriptional downregulation of the chromomethyltransferase CMT2 and strong upregulation of several genes mediating active DNA demethylation. Conclusion Integration of methylomic and transcriptomic data revealed that, rather than methylation having directly influenced expression, epigenetic modifications correlated with changes in expression of known players involved in DNA (de)methylation. In particular, cold triggered upregulation of genes putatively contributing to DNA demethylation via the ROS1 pathway. Our observations suggest that these transcriptional responses precede the cold-induced global DNA-hypomethylation in non-CpG, preparing beets for additional transcriptional alterations necessary for adapting to upcoming environmental changes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08312-2.
Collapse
|
24
|
Loffer A, Singh J, Fukudome A, Mishra V, Wang F, Pikaard CS. A DCL3 dicing code within Pol IV-RDR2 transcripts diversifies the siRNA pool guiding RNA-directed DNA methylation. eLife 2022; 11:e73260. [PMID: 35098919 PMCID: PMC8846587 DOI: 10.7554/elife.73260] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 01/28/2022] [Indexed: 11/26/2022] Open
Abstract
In plants, selfish genetic elements, including retrotransposons and DNA viruses, are transcriptionally silenced by RNA-directed DNA methylation. Guiding the process are short interfering RNAs (siRNAs) cut by DICER-LIKE 3 (DCL3) from double-stranded precursors of ~30 bp that are synthesized by NUCLEAR RNA POLYMERASE IV (Pol IV) and RNA-DEPENDENT RNA POLYMERASE 2 (RDR2). We show that Pol IV's choice of initiating nucleotide, RDR2's initiation 1-2 nt internal to Pol IV transcript ends and RDR2's terminal transferase activity collectively yield a code that influences which precursor end is diced and whether 24 or 23 nt siRNAs are produced. By diversifying the size, sequence, and strand specificity of siRNAs derived from a given precursor, alternative patterns of DCL3 dicing allow for maximal siRNA coverage at methylated target loci.
Collapse
Affiliation(s)
- Andrew Loffer
- Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University BloomingtonBloomingtonUnited States
| | - Jasleen Singh
- Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University BloomingtonBloomingtonUnited States
| | - Akihito Fukudome
- Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University BloomingtonBloomingtonUnited States
- Howard Hughes Medical Institute, Indiana UniversityBloomingtonUnited States
| | - Vibhor Mishra
- Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University BloomingtonBloomingtonUnited States
- Howard Hughes Medical Institute, Indiana UniversityBloomingtonUnited States
| | - Feng Wang
- Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University BloomingtonBloomingtonUnited States
- Howard Hughes Medical Institute, Indiana UniversityBloomingtonUnited States
| | - Craig S Pikaard
- Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University BloomingtonBloomingtonUnited States
- Howard Hughes Medical Institute, Indiana UniversityBloomingtonUnited States
| |
Collapse
|
25
|
Huang K, Wu XX, Fang CL, Xu ZG, Zhang HW, Gao J, Zhou CM, You LL, Gu ZX, Mu WH, Feng Y, Wang JW, Zhang Y. Pol IV and RDR2: A two-RNA-polymerase machine that produces double-stranded RNA. Science 2021; 374:1579-1586. [DOI: 10.1126/science.abj9184] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Kun Huang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao-Xian Wu
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Cheng-Li Fang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhou-Geng Xu
- University of Chinese Academy of Sciences, Beijing 100049, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Hong-Wei Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Gao
- University of Chinese Academy of Sciences, Beijing 100049, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Chuan-Miao Zhou
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Lin-Lin You
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhan-Xi Gu
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wen-Hui Mu
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Yu Feng
- Department of Biophysics, and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yu Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| |
Collapse
|
26
|
Fukudome A, Singh J, Mishra V, Reddem E, Martinez-Marquez F, Wenzel S, Yan R, Shiozaki M, Yu Z, Wang JCY, Takagi Y, Pikaard CS. Structure and RNA template requirements of Arabidopsis RNA-DEPENDENT RNA POLYMERASE 2. Proc Natl Acad Sci U S A 2021; 118:e2115899118. [PMID: 34903670 PMCID: PMC8713982 DOI: 10.1073/pnas.2115899118] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2021] [Indexed: 01/18/2023] Open
Abstract
RNA-dependent RNA polymerases play essential roles in RNA-mediated gene silencing in eukaryotes. In Arabidopsis, RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) physically interacts with DNA-dependent NUCLEAR RNA POLYMERASE IV (Pol IV) and their activities are tightly coupled, with Pol IV transcriptional arrest, induced by the nontemplate DNA strand, somehow enabling RDR2 to engage Pol IV transcripts and generate double-stranded RNAs. The double-stranded RNAs are then released from the Pol IV-RDR2 complex and diced into short-interfering RNAs that guide RNA-directed DNA methylation and silencing. Here we report the structure of full-length RDR2, at an overall resolution of 3.1 Å, determined by cryoelectron microscopy. The N-terminal region contains an RNA-recognition motif adjacent to a positively charged channel that leads to a catalytic center with striking structural homology to the catalytic centers of multisubunit DNA-dependent RNA polymerases. We show that RDR2 initiates 1 to 2 nt internal to the 3' ends of its templates and can transcribe the RNA of an RNA/DNA hybrid, provided that 9 or more nucleotides are unpaired at the RNA's 3' end. Using a nucleic acid configuration that mimics the arrangement of RNA and DNA strands upon Pol IV transcriptional arrest, we show that displacement of the RNA 3' end occurs as the DNA template and nontemplate strands reanneal, enabling RDR2 transcription. These results suggest a model in which Pol IV arrest and backtracking displaces the RNA 3' end as the DNA strands reanneal, allowing RDR2 to engage the RNA and synthesize the complementary strand.
Collapse
Affiliation(s)
- Akihito Fukudome
- HHMI, Indiana University, Bloomington, IN 47405
- Department of Biology, Indiana University, Bloomington, IN 47405
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405
| | - Jasleen Singh
- Department of Biology, Indiana University, Bloomington, IN 47405
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405
| | - Vibhor Mishra
- HHMI, Indiana University, Bloomington, IN 47405
- Department of Biology, Indiana University, Bloomington, IN 47405
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405
| | - Eswar Reddem
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 47405
| | - Francisco Martinez-Marquez
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 47405
| | - Sabine Wenzel
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 47405
| | - Rui Yan
- CryoEM Facility, Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147
| | - Momoko Shiozaki
- CryoEM Facility, Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147
| | - Zhiheng Yu
- CryoEM Facility, Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147
| | - Joseph Che-Yen Wang
- Indiana University Electron Microscopy Center, Indiana University, Bloomington, IN 47405
| | - Yuichiro Takagi
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 47405;
| | - Craig S Pikaard
- HHMI, Indiana University, Bloomington, IN 47405;
- Department of Biology, Indiana University, Bloomington, IN 47405
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405
| |
Collapse
|
27
|
Palo MZ, Zhu J, Mishanina TV, Landick R. Conserved Trigger Loop Histidine of RNA Polymerase II Functions as a Positional Catalyst Primarily through Steric Effects. Biochemistry 2021; 60:3323-3336. [PMID: 34705427 DOI: 10.1021/acs.biochem.1c00528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In all domains of life, multisubunit RNA polymerases (RNAPs) catalyze both the extension of mRNA transcripts by nucleotide addition and the hydrolysis of RNA, which enables proofreading by removal of misincorporated nucleotides. A highly conserved catalytic module within RNAPs called the trigger loop (TL) functions as the key controller of these activities. The TL is proposed to act as a positional catalyst of phosphoryl transfer and transcript cleavage via electrostatic and steric contacts with substrates in its folded helical form. The function of a near-universally conserved TL histidine that contacts NTP phosphates is of particular interest. Despite its exceptional conservation, substitutions of the TL His with Gln support efficient catalysis in bacterial and yeast RNAPs. Unlike bacterial TLs, which contain a nearby Arg, the TL His is the only acid-base catalyst candidate in the eukaryotic RNAPII TL. Nonetheless, replacement of the TL His with Leu is reported to support cell growth in yeast, suggesting that even hydrogen bonding and polarity at this position may be dispensable for efficient catalysis by RNAPII. To test how a TL His-to-Leu substitution affects the enzymatic functions of RNAPII, we compared its rates of nucleotide addition, pyrophosphorolysis, and RNA hydrolysis to those of the wild-type RNAPII enzyme. The His-to-Leu substitution slightly reduced rates of phosphoryl transfer with little if any effect on intrinsic transcript cleavage. These findings indicate that the highly conserved TL His is neither an obligate acid-base catalyst nor a polar contact for NTP phosphates but instead functions as a positional catalyst mainly through steric effects.
Collapse
Affiliation(s)
- Michael Z Palo
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Junqiao Zhu
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Tatiana V Mishanina
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.,Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| |
Collapse
|
28
|
Huang P, Huang H, Lin X, Liu P, Zhao L, Nie W, Zhu J, Lang Z. MSI4/FVE is required for accumulation of 24-nt siRNAs and DNA methylation at a subset of target regions of RNA-directed DNA methylation. Plant J 2021; 108:347-357. [PMID: 34314526 PMCID: PMC9292519 DOI: 10.1111/tpj.15441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 07/20/2021] [Indexed: 05/20/2023]
Abstract
DNA methylation is an important epigenetic mark. In plants, de novo DNA methylation occurs mainly through the RNA-directed DNA methylation (RdDM) pathway. Researchers have previously inferred that a flowering regulator, MULTICOPY SUPPRESSOR OF IRA1 4 (MSI4)/FVE, is involved in non-CG methylation at several RdDM targets, suggesting a role of FVE in RdDM. However, whether and how FVE affects RdDM genome-wide is not known. Here, we report that FVE is required for DNA methylation at thousands of RdDM target regions. In addition, dysfunction of FVE significantly reduces 24-nucleotide siRNA accumulation that is dependent on factors downstream in the RdDM pathway. By using chromatin immunoprecipitation and sequencing (ChIP-seq), we show that FVE directly binds to FVE-dependent 24-nucleotide siRNA cluster regions. Our results also indicate that FVE may function in RdDM by physically interacting with RDM15, a downstream factor in the RdDM pathway. Our study has therefore revealed that FVE, by associating with RDM15, directly regulates DNA methylation and siRNA accumulation at a subset of RdDM targets.
Collapse
Affiliation(s)
- Pei Huang
- Shanghai Center for Plant Stress BiologyNational Key Laboratory of Plant Molecular GeneticsCenter for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai201602China
- University of Chinese Academy of SciencesNo.19 Yuquan Road, Shijingshan DistrictBeijing100049China
| | - Huan Huang
- Shanghai Center for Plant Stress BiologyNational Key Laboratory of Plant Molecular GeneticsCenter for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai201602China
| | - Xueqiang Lin
- Shanghai Center for Plant Stress BiologyNational Key Laboratory of Plant Molecular GeneticsCenter for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai201602China
| | - Pan Liu
- Shanghai Center for Plant Stress BiologyNational Key Laboratory of Plant Molecular GeneticsCenter for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai201602China
| | - Lun Zhao
- Shanghai Center for Plant Stress BiologyNational Key Laboratory of Plant Molecular GeneticsCenter for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai201602China
- National Key Laboratory of Crop Genetic ImprovementNational Center of Rapeseed ImprovementHuazhong Agricultural UniversityWuhan430070China
| | - Wen‐Feng Nie
- Department of HorticultureCollege of Horticulture and Plant ProtectionYangzhou UniversityYangzhouJiangsu225009China
| | - Jian‐Kang Zhu
- Shanghai Center for Plant Stress BiologyNational Key Laboratory of Plant Molecular GeneticsCenter for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai201602China
| | - Zhaobo Lang
- Shanghai Center for Plant Stress BiologyNational Key Laboratory of Plant Molecular GeneticsCenter for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai201602China
| |
Collapse
|
29
|
Rothi MH, Tsuzuki M, Sethuraman S, Wierzbicki AT. Reinforcement of transcriptional silencing by a positive feedback between DNA methylation and non-coding transcription. Nucleic Acids Res 2021; 49:9799-9808. [PMID: 34469565 PMCID: PMC8464056 DOI: 10.1093/nar/gkab746] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 07/09/2021] [Accepted: 08/23/2021] [Indexed: 11/12/2022] Open
Abstract
Non-coding transcription is an important determinant of heterochromatin formation. In Arabidopsis thaliana a specialized RNA polymerase V (Pol V) transcribes pervasively and produces long non-coding RNAs. These transcripts work with small interfering RNA to facilitate locus-specific establishment of RNA-directed DNA methylation (RdDM). Subsequent maintenance of RdDM is associated with elevated levels of Pol V transcription. However, the impact of DNA methylation on Pol V transcription remained unresolved. We found that DNA methylation strongly enhances Pol V transcription. The level of Pol V transcription is reduced in mutants defective in RdDM components working downstream of Pol V, indicating that RdDM is maintained by a mutual reinforcement of DNA methylation and Pol V transcription. Pol V transcription is affected only on loci that lose DNA methylation in all sequence contexts in a particular mutant, including mutants lacking maintenance DNA methyltransferases, which suggests that RdDM works in a complex crosstalk with other silencing pathways.
Collapse
Affiliation(s)
- M Hafiz Rothi
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Masayuki Tsuzuki
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan
| | - Shriya Sethuraman
- Bioinformatics Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Andrzej T Wierzbicki
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| |
Collapse
|
30
|
El-Sappah AH, Yan K, Huang Q, Islam MM, Li Q, Wang Y, Khan MS, Zhao X, Mir RR, Li J, El-Tarabily KA, Abbas M. Comprehensive Mechanism of Gene Silencing and Its Role in Plant Growth and Development. Front Plant Sci 2021; 12:705249. [PMID: 34589097 PMCID: PMC8475493 DOI: 10.3389/fpls.2021.705249] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 08/10/2021] [Indexed: 05/19/2023]
Abstract
Gene silencing is a negative feedback mechanism that regulates gene expression to define cell fate and also regulates metabolism and gene expression throughout the life of an organism. In plants, gene silencing occurs via transcriptional gene silencing (TGS) and post-transcriptional gene silencing (PTGS). TGS obscures transcription via the methylation of 5' untranslated region (5'UTR), whereas PTGS causes the methylation of a coding region to result in transcript degradation. In this review, we summarized the history and molecular mechanisms of gene silencing and underlined its specific role in plant growth and crop production.
Collapse
Affiliation(s)
- Ahmed H. El-Sappah
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
- Key Laboratory of Sichuan Province for Refining Sichuan Tea, Yibin, China
| | - Kuan Yan
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Key Laboratory of Sichuan Province for Refining Sichuan Tea, Yibin, China
| | - Qiulan Huang
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Key Laboratory of Sichuan Province for Refining Sichuan Tea, Yibin, China
- College of Tea Science, Yibin University, Yibin, China
| | | | - Quanzi Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Yu Wang
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Key Laboratory of Sichuan Province for Refining Sichuan Tea, Yibin, China
| | - Muhammad Sarwar Khan
- Center of Agriculture Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Xianming Zhao
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Key Laboratory of Sichuan Province for Refining Sichuan Tea, Yibin, China
| | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Faculty of Agriculture (FoA), Sher-e-Kashmir University of Agricultural Sciences and Technology (SKUAST–K), Sopore, India
| | - Jia Li
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Key Laboratory of Sichuan Province for Refining Sichuan Tea, Yibin, China
| | - Khaled A. El-Tarabily
- Department of Biology, College of Science, United Arab Emirates University, Al-Ain, United Arab Emirates
- Harry Butler Institute, Murdoch University, Murdoch, WA, Australia
| | - Manzar Abbas
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Key Laboratory of Sichuan Province for Refining Sichuan Tea, Yibin, China
| |
Collapse
|
31
|
Dalakouras A, Vlachostergios D. Epigenetic approaches to crop breeding: current status and perspectives. J Exp Bot 2021; 72:5356-5371. [PMID: 34017985 DOI: 10.1093/jxb/erab227] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/18/2021] [Indexed: 05/10/2023]
Abstract
In order to tackle the cumulative adverse effects of global climate change, reduced farmland, and heightened needs of an ever-increasing world population, modern agriculture is in urgent search of solutions that can ensure world food security and sustainable development. Classical crop breeding is still a powerful method to obtain crops with valued agronomical traits, but its potential is gradually being compromised by the menacing decline of genetic variation. Resorting to the epigenome as a source of variation could serve as a promising alternative. Here, we discuss current status of epigenetics-mediated crop breeding (epibreeding), highlight its advances and limitations, outline currently available methodologies, and propose novel RNA-based strategies to modify the epigenome in a gene-specific and transgene-free manner.
Collapse
Affiliation(s)
- Athanasios Dalakouras
- Institute of Industrial and Forage Crops, HAO-DEMETER, 41335 Larissa, Greece
- Institute of Plant Breeding and Genetic Resources, HAO-DEMETER, 57001 Thessaloniki, Greece
| | | |
Collapse
|
32
|
Zheng K, Wang L, Zeng L, Xu D, Guo Z, Gao X, Yang DL. 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:e2100709118. [PMID: 34290143 DOI: 10.1073/pnas.2100709118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [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.
Collapse
|
33
|
Zhou JX, Du P, Liu ZW, Feng C, Cai XW, He XJ. FVE promotes RNA-directed DNA methylation by facilitating the association of RNA polymerase V with chromatin. Plant J 2021; 107:467-479. [PMID: 33942410 DOI: 10.1111/tpj.15302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/19/2021] [Accepted: 04/26/2021] [Indexed: 06/12/2023]
Abstract
Association of RNA polymerase V (Pol V) with chromatin is a critical step for RNA- directed DNA methylation (RdDM) in plants. Although the methylated DNA-binding proteins SUVH2 and SUVH9 and the chromatin remodeler-containing complex DRD1-DMS3-RDM1 are known to be required for the association of Pol V with chromatin, the molecular mechanisms underlying the association of Pol V with different chromatin environments remain largely unknown. Here we found that SUVH9 interacts with FVE, a homolog of the mammalian retinoblastoma-associated protein, which has been previously identified as a shared subunit of the histone deacetylase complex and the polycomb-type histone H3K27 trimethyltransferase complex. We demonstrated that FVE facilitates the association of Pol V with chromatin and thus contributes to DNA methylation at a substantial subset of RdDM target loci. Compared with FVE-independent RdDM target loci, FVE-dependent RdDM target loci are more abundant in gene-rich chromosome arms than in pericentromeric heterochromatin regions. This study contributes to our understanding of how the association of Pol V with chromatin is regulated in different chromatin environments.
Collapse
Affiliation(s)
- Jin-Xing Zhou
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Ping Du
- National Institute of Biological Sciences, Beijing, 102206, China
- College of Life Sciences, Beijing Normal University, Beijing, China
| | - Zhang-Wei Liu
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Chao Feng
- National Institute of Biological Sciences, Beijing, 102206, China
- College of Life Sciences, Beijing Normal University, Beijing, China
| | - Xue-Wei Cai
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing, 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 100084, China
| |
Collapse
|
34
|
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.
Collapse
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;
| |
Collapse
|
35
|
Zhao T, Mei H, Cao Z, Wang L, Tao X, Feng S, Fang L, Guan X. Absence of CG methylation alters the long noncoding transcriptome landscape in multiple species. FEBS Lett 2021; 595:1734-1747. [PMID: 33950520 DOI: 10.1002/1873-3468.14100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/31/2021] [Accepted: 04/21/2021] [Indexed: 11/12/2022]
Abstract
The noncoding regions throughout the genome are in large part comprised of transposable elements (TEs), some of which are functionalized with long intergenic noncoding RNAs (lincRNAs). DNA methylation is predominantly associated with TEs, but little is known about its contribution to the transcription of lincRNAs. Here, we examine the lincRNA profiles of DNA methylation-related mutants of five species, Arabidopsis, rice, tomato, maize, and mouse, to elucidate patterns in lincRNA regulation under altered DNA methylation status. Significant activation of lincRNAs was observed in the absence of CG DNA methylation rather than non-CG. Our study establishes a working model of the contribution of DNA methylation to regulation of the dynamic activity of lincRNA transcription.
Collapse
Affiliation(s)
- Ting Zhao
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Huan Mei
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Zeyi Cao
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Luyao Wang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.,College of Agriculture, Engineering Research Center of Ministry of Cotton Education, Xinjiang Agricultural University, Urumqi, China
| | - Xiaoyuan Tao
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Shouli Feng
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Lei Fang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Xueying Guan
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| |
Collapse
|
36
|
Liu W, Gallego-Bartolomé J, Zhou Y, Zhong Z, Wang M, Wongpalee SP, Gardiner J, Feng S, Kuo PH, Jacobsen SE. Ectopic targeting of CG DNA methylation in Arabidopsis with the bacterial SssI methyltransferase. Nat Commun 2021; 12:3130. [PMID: 34035251 PMCID: PMC8149686 DOI: 10.1038/s41467-021-23346-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Accepted: 03/30/2021] [Indexed: 01/03/2023] Open
Abstract
The ability to target epigenetic marks like DNA methylation to specific loci is important in both basic research and in crop plant engineering. However, heritability of targeted DNA methylation, how it impacts gene expression, and which epigenetic features are required for proper establishment are mostly unknown. Here, we show that targeting the CG-specific methyltransferase M.SssI with an artificial zinc finger protein can establish heritable CG methylation and silencing of a targeted locus in Arabidopsis. In addition, we observe highly heritable widespread ectopic CG methylation mainly over euchromatic regions. This hypermethylation shows little effect on transcription while it triggers a mild but significant reduction in the accumulation of H2A.Z and H3K27me3. Moreover, ectopic methylation occurs preferentially at less open chromatin that lacks positive histone marks. These results outline general principles of the heritability and interaction of CG methylation with other epigenomic features that should help guide future efforts to engineer epigenomes. The ability to target DNA methylation to specific loci is important for both basic and applied research. Here, the authors fuse CG-specific methyltransferase SssI with an artificial zinc finger protein for DNA methylation targeting and show the chromatin features favorable for efficient gain of methylation.
Collapse
Affiliation(s)
- Wanlu Liu
- Department of Orthopedic of the Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China. .,Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, Haining, China. .,Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA.
| | - Javier Gallego-Bartolomé
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA.,Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universidad Politécnica de Valencia, Valencia, Spain
| | - Yuxing Zhou
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, Haining, China
| | - Zhenhui Zhong
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Ming Wang
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Somsakul Pop Wongpalee
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA.,Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Jason Gardiner
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Suhua Feng
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA.,Eli & Edythe Broad Center of Regenerative Medicine & Stem Cell Research, University of California at Los Angeles, Los Angeles, CA, USA
| | - Peggy Hsuanyu Kuo
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Steven E Jacobsen
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA. .,Eli & Edythe Broad Center of Regenerative Medicine & Stem Cell Research, University of California at Los Angeles, Los Angeles, CA, USA. .,Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, CA, USA.
| |
Collapse
|
37
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
38
|
Krishnatreya DB, Baruah PM, Dowarah B, Chowrasia S, Mondal TK, Agarwala N. Genome-wide identification, evolutionary relationship and expression analysis of AGO, DCL and RDR family genes in tea. Sci Rep 2021; 11:8679. [PMID: 33883595 DOI: 10.1038/s41598-021-87991-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 04/07/2021] [Indexed: 12/05/2022] Open
Abstract
Three gene families in plants viz. Argonaute (AGOs), Dicer-like (DCLs) and RNA dependent RNA polymerase (RDRs) constitute the core components of small RNA mediated gene silencing machinery. The present study endeavours to identify members of these gene families in tea and to investigate their expression patterns in different tissues and various stress regimes. Using genome-wide analysis, we have identified 18 AGOs, 5 DCLs and 9 RDRs in tea, and analyzed their phylogenetic relationship with orthologs of Arabidopsis thaliana. Gene expression analysis revealed constitutive expression of CsAGO1 in all the studied tissues and stress conditions, whereas CsAGO10c showed most variable expression among all the genes. CsAGO10c gene was found to be upregulated in tissues undergoing high meristematic activity such as buds and roots, as well as in Exobasidium vexans infected samples. CsRDR2 and two paralogs of CsAGO4, which are known to participate in biogenesis of hc-siRNAs, showed similarities in their expression levels in most of the tea plant tissues. This report provides first ever insight into the important gene families involved in biogenesis of small RNAs in tea. The comprehensive knowledge of these small RNA biogenesis purveyors can be utilized for tea crop improvement aimed at stress tolerance and quality enhancement.
Collapse
|
39
|
Mishra V, Singh J, Wang F, Zhang Y, Fukudome A, Trinidad JC, Takagi Y, Pikaard CS. Assembly of a dsRNA synthesizing complex: RNA-DEPENDENT RNA POLYMERASE 2 contacts the largest subunit of NUCLEAR RNA POLYMERASE IV. Proc Natl Acad Sci U S A 2021; 118:e2019276118. [PMID: 33753485 DOI: 10.1073/pnas.2019276118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Short interfering RNAs (siRNAs) can inhibit mRNA translation or guide chromatin modifications that inhibit transcription, thus impacting gene regulation. In plants, transcriptional gene silencing involves siRNAs whose double-stranded (ds) precursors are generated by the coupled activities of NUCLEAR RNA POLYMERASE IV and RNA-DEPENDENT RNA POLYMERASE 2. We present evidence that Pol IV-RDR2 association involves contact between RDR2 and NRPD1, Pol IV’s largest catalytic subunit. As the only subunit never shared by Pol II or Pol IV, NRPD1 interaction accounts for RDR2's specific association with Pol IV. The positions of the protein docking sites suggest that Pol IV transcripts are generated in close proximity to RDR2’s catalytic site, enabling RDR2 to efficiently engage Pol IV transcripts and convert them into dsRNAs. In plants, transcription of selfish genetic elements such as transposons and DNA viruses is suppressed by RNA-directed DNA methylation. This process is guided by 24-nt short-interfering RNAs (siRNAs) whose double-stranded precursors are synthesized by DNA-dependent NUCLEAR RNA POLYMERASE IV (Pol IV) and RNA-DEPENDENT RNA POLYMERASE 2 (RDR2). Pol IV and RDR2 coimmunoprecipitate, and their activities are tightly coupled, yet the basis for their association is unknown. Here, we show that an interval near the RDR2 active site contacts the Pol IV catalytic subunit, NRPD1, the largest of Pol IV’s 12 subunits. Contacts between the catalytic regions of the two enzymes suggests that RDR2 is positioned to rapidly engage the free 3′ ends of Pol IV transcripts and convert these single-stranded transcripts into double-stranded RNAs (dsRNAs).
Collapse
|
40
|
Salava H, Thula S, Mohan V, Kumar R, Maghuly F. Application of Genome Editing in Tomato Breeding: Mechanisms, Advances, and Prospects. Int J Mol Sci 2021; 22:E682. [PMID: 33445555 PMCID: PMC7827871 DOI: 10.3390/ijms22020682] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 12/31/2020] [Accepted: 01/05/2021] [Indexed: 12/19/2022] Open
Abstract
Plants regularly face the changing climatic conditions that cause biotic and abiotic stress responses. The abiotic stresses are the primary constraints affecting crop yield and nutritional quality in many crop plants. The advances in genome sequencing and high-throughput approaches have enabled the researchers to use genome editing tools for the functional characterization of many genes useful for crop improvement. The present review focuses on the genome editing tools for improving many traits such as disease resistance, abiotic stress tolerance, yield, quality, and nutritional aspects of tomato. Many candidate genes conferring tolerance to abiotic stresses such as heat, cold, drought, and salinity stress have been successfully manipulated by gene modification and editing techniques such as RNA interference, insertional mutagenesis, and clustered regularly interspaced short palindromic repeat (CRISPR/Cas9). In this regard, the genome editing tools such as CRISPR/Cas9, which is a fast and efficient technology that can be exploited to explore the genetic resources for the improvement of tomato and other crop plants in terms of stress tolerance and nutritional quality. The review presents examples of gene editing responsible for conferring both biotic and abiotic stresses in tomato simultaneously. The literature on using this powerful technology to improve fruit quality, yield, and nutritional aspects in tomato is highlighted. Finally, the prospects and challenges of genome editing, public and political acceptance in tomato are discussed.
Collapse
Affiliation(s)
- Hymavathi Salava
- Department of Plant Sciences, University of Hyderabad, Hyderabad 500064, India;
| | - Sravankumar Thula
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic;
| | - Vijee Mohan
- Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA;
| | - Rahul Kumar
- Plant Translational Research Laboratory, Department of Plant Sciences, University of Hyderabad, Hyderabad 500064, India;
| | - Fatemeh Maghuly
- Plant Functional Genomics, Institute of Molecular Biotechnology, Department of Biotechnology, BOKU-VIBT, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| |
Collapse
|
41
|
Markulin L, Škiljaica A, Tokić M, Jagić M, Vuk T, Bauer N, Leljak Levanić D. Taking the Wheel - de novo DNA Methylation as a Driving Force of Plant Embryonic Development. Front Plant Sci 2021; 12:764999. [PMID: 34777448 PMCID: PMC8585777 DOI: 10.3389/fpls.2021.764999] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 10/13/2021] [Indexed: 05/16/2023]
Abstract
During plant embryogenesis, regardless of whether it begins with a fertilized egg cell (zygotic embryogenesis) or an induced somatic cell (somatic embryogenesis), significant epigenetic reprogramming occurs with the purpose of parental or vegetative transcript silencing and establishment of a next-generation epigenetic patterning. To ensure genome stability of a developing embryo, large-scale transposon silencing occurs by an RNA-directed DNA methylation (RdDM) pathway, which introduces methylation patterns de novo and as such potentially serves as a global mechanism of transcription control during developmental transitions. RdDM is controlled by a two-armed mechanism based around the activity of two RNA polymerases. While PolIV produces siRNAs accompanied by protein complexes comprising the methylation machinery, PolV produces lncRNA which guides the methylation machinery toward specific genomic locations. Recently, RdDM has been proposed as a dominant methylation mechanism during gamete formation and early embryo development in Arabidopsis thaliana, overshadowing all other methylation mechanisms. Here, we bring an overview of current knowledge about different roles of DNA methylation with emphasis on RdDM during plant zygotic and somatic embryogenesis. Based on published chromatin immunoprecipitation data on PolV binding sites within the A. thaliana genome, we uncover groups of auxin metabolism, reproductive development and embryogenesis-related genes, and discuss possible roles of RdDM at the onset of early embryonic development via targeted methylation at sites involved in different embryogenesis-related developmental mechanisms.
Collapse
|
42
|
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.
Collapse
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
| |
Collapse
|
43
|
Leone M, Zavallo D, Venturuzzi A, Asurmendi S. RdDM pathway components differentially modulate Tobamovirus symptom development. Plant Mol Biol 2020; 104:467-481. [PMID: 32813230 DOI: 10.1007/s11103-020-01051-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 08/11/2020] [Indexed: 06/11/2023]
Abstract
The crop yield losses induced by phytoviruses are mainly associated with the symptoms of the disease. DNA modifications as methylation can modulate the information coded by the sequence, process named epigenetics. Viral infection can change the expression patterns of different genes linked to defenses and symptoms. This work represents the initial step to expose the role of epigenetic process, in the production of symptoms associated with plants-virus interactions. Small RNAs (sRNAs) are important molecules for gene regulation in plants and play an essential role in plant-pathogen interactions. Researchers have evaluated the relationship between viral infections as well as the endogenous accumulation of sRNAs and the transcriptional changes associated with the production of symptoms, but little is known about a possible direct role of epigenetics, mediated by 24-nt sRNAs, in the induction of these symptoms. Using different RNA directed DNA methylation (RdDM) pathway mutants and a triple demethylase mutant; here we demonstrate that the disruption of RdDM pathway during viral infection produce alterations in the plant transcriptome and in consequence changes in plant symptoms. This study represents the initial step in exposing that DNA methylation directed by endogenous sRNAs has an important role, uncoupled to defense, in the production of symptoms associated with plant-virus interactions.
Collapse
Affiliation(s)
- Melisa Leone
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), De Los Reseros y N. Repetto S/N, Hurlingham, B1686IGC, Buenos Aires, Argentina
- Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT), Buenos Aires, Argentina
| | - Diego Zavallo
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), De Los Reseros y N. Repetto S/N, Hurlingham, B1686IGC, Buenos Aires, Argentina
| | - Andrea Venturuzzi
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), De Los Reseros y N. Repetto S/N, Hurlingham, B1686IGC, Buenos Aires, Argentina
| | - Sebastián Asurmendi
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), De Los Reseros y N. Repetto S/N, Hurlingham, B1686IGC, Buenos Aires, Argentina.
| |
Collapse
|
44
|
Wang L, Ding Y, He L, Zhang G, Zhu JK, Lozano-Duran R. A virus-encoded protein suppresses methylation of the viral genome through its interaction with AGO4 in the Cajal body. eLife 2020; 9:e55542. [PMID: 33064077 PMCID: PMC7567605 DOI: 10.7554/elife.55542] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 09/23/2020] [Indexed: 12/11/2022] Open
Abstract
In plants, establishment of de novo DNA methylation is regulated by the RNA-directed DNA methylation (RdDM) pathway. RdDM machinery is known to concentrate in the Cajal body, but the biological significance of this localization has remained elusive. Here, we show that the antiviral methylation of the Tomato yellow leaf curl virus (TYLCV) genome requires the Cajal body in Nicotiana benthamiana cells. Methylation of the viral genome is countered by a virus-encoded protein, V2, which interacts with the central RdDM component AGO4, interfering with its binding to the viral DNA; Cajal body localization of the V2-AGO4 interaction is necessary for the viral protein to exert this function. Taken together, our results draw a long sought-after functional connection between RdDM, the Cajal body, and antiviral DNA methylation, paving the way for a deeper understanding of DNA methylation and antiviral defences in plants.
Collapse
Affiliation(s)
- Liping Wang
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of SciencesBeijingChina
- University of the Chinese Academy of SciencesBeijingChina
| | - Yi Ding
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of SciencesBeijingChina
- University of the Chinese Academy of SciencesBeijingChina
| | - Li He
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of SciencesBeijingChina
| | - Guiping Zhang
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of SciencesBeijingChina
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of SciencesBeijingChina
| | - Rosa Lozano-Duran
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of SciencesBeijingChina
| |
Collapse
|
45
|
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.
Collapse
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
| |
Collapse
|
46
|
Zhou HR, Lin RN, Huang HW, Li L, Cai T, Zhu JK, Chen S, He XJ. The CCR4-NOT complex component NOT1 regulates RNA-directed DNA methylation and transcriptional silencing by facilitating Pol IV-dependent siRNA production. Plant J 2020; 103:1503-1515. [PMID: 32412137 DOI: 10.1111/tpj.14818] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/29/2020] [Accepted: 05/07/2020] [Indexed: 05/20/2023]
Abstract
Small interfering RNAs (siRNAs) are responsible for establishing and maintaining DNA methylation through the RNA-directed DNA methylation (RdDM) pathway in plants. Although siRNA biogenesis is well known, it is relatively unclear about how the process is regulated. By a forward genetic screen in Arabidopsis thaliana, we identified a mutant defective in NOT1 and demonstrated that NOT1 is required for transcriptional silencing at RdDM target genomic loci. We demonstrated that NOT1 is required for Pol IV-dependent siRNA accumulation and DNA methylation at a subset of RdDM target genomic loci. Furthermore, we revealed that NOT1 is a constituent of a multi-subunit CCR4-NOT deadenylase complex by immunoprecipitation combined with mass spectrometry and demonstrated that the CCR4-NOT components can function as a whole to mediate chromatin silencing. Therefore, our work establishes that the CCR4-NOT complex regulates the biogenesis of Pol IV-dependent siRNAs, and hence facilitates DNA methylation and transcriptional silencing in Arabidopsis.
Collapse
Affiliation(s)
- Hao-Ran Zhou
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Rong-Nan Lin
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Huan-Wei Huang
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Lin Li
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Tao Cai
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology and Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - She Chen
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing, 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| |
Collapse
|
47
|
Wambui Mbichi R, Wang QF, Wan T. RNA directed DNA methylation and seed plant genome evolution. Plant Cell Rep 2020; 39:983-996. [PMID: 32594202 DOI: 10.1007/s00299-] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/08/2020] [Indexed: 05/28/2023]
Abstract
RNA Directed DNA Methylation (RdDM) is a pathway that mediates de novo DNA methylation, an evolutionary conserved chemical modification of cytosine bases, which exists in living organisms and utilizes small interfering RNA. Plants utilize DNA methylation for transposable element (TE) repression, regulation of gene expression and developmental regulation. TE activity strongly influences genome size and evolution, therefore making DNA methylation a key component in understanding divergence in genome evolution among seed plants. Multiple proteins that have extensively been studied in model plant Arabidopsis thaliana catalyze RNA dependent DNA Methylation pathway along with small interfering RNA. Several developmental functions have also been attributed to DNA methylation. This review will highlight aspects of RdDM pathway dynamics, evolution and functions in seed plants with focus on recent findings on conserved and non-conserved attributes between angiosperms and gymnosperms to potentially explain how methylation has impacted variations in evolutionary and developmental complexity among them and advance current understanding of this crucial epigenetic pathway.
Collapse
Affiliation(s)
- R Wambui Mbichi
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan, Hubei, 430074, China
- Key laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qing-Feng Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan, Hubei, 430074, China.
- Sino-Africa Joint Research Center, Chinese Academy of Science, Wuhan, 430074, China.
- Center of Conservation Biology, Core Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
| | - Tao Wan
- Key laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China.
- Sino-Africa Joint Research Center, Chinese Academy of Science, Wuhan, 430074, China.
| |
Collapse
|
48
|
Abstract
RNA Directed DNA Methylation (RdDM) is a pathway that mediates de novo DNA methylation, an evolutionary conserved chemical modification of cytosine bases, which exists in living organisms and utilizes small interfering RNA. Plants utilize DNA methylation for transposable element (TE) repression, regulation of gene expression and developmental regulation. TE activity strongly influences genome size and evolution, therefore making DNA methylation a key component in understanding divergence in genome evolution among seed plants. Multiple proteins that have extensively been studied in model plant Arabidopsis thaliana catalyze RNA dependent DNA Methylation pathway along with small interfering RNA. Several developmental functions have also been attributed to DNA methylation. This review will highlight aspects of RdDM pathway dynamics, evolution and functions in seed plants with focus on recent findings on conserved and non-conserved attributes between angiosperms and gymnosperms to potentially explain how methylation has impacted variations in evolutionary and developmental complexity among them and advance current understanding of this crucial epigenetic pathway.
Collapse
Affiliation(s)
- R Wambui Mbichi
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan, Hubei, 430074, China
- Key laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qing-Feng Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan, Hubei, 430074, China.
- Sino-Africa Joint Research Center, Chinese Academy of Science, Wuhan, 430074, China.
- Center of Conservation Biology, Core Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
| | - Tao Wan
- Key laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China.
- Sino-Africa Joint Research Center, Chinese Academy of Science, Wuhan, 430074, China.
| |
Collapse
|
49
|
Xu L, Yuan K, Yuan M, Meng X, Chen M, Wu J, Li J, Qi Y. Regulation of Rice Tillering by RNA-Directed DNA Methylation at Miniature Inverted-Repeat Transposable Elements. Mol Plant 2020; 13:851-863. [PMID: 32087371 DOI: 10.1016/j.molp.2020.02.009] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 11/15/2019] [Accepted: 12/20/2019] [Indexed: 05/24/2023]
Abstract
Tillering is a major determinant of rice plant architecture and grain yield. Here, we report that depletion of rice OsNRPD1a and OsNRPD1b, two orthologs of the largest subunit of RNA polymerase IV, leads to a high-tillering phenotype, in addition to dwarfism and smaller panicles. OsNRPD1a and OsNRPD1b are required for the production of 24-nt small interfering RNAs that direct DNA methylation at transposable elements (TEs) including miniature inverted-repeat TEs (MITEs). Interestingly, many genes are regulated either positively or negatively by TE methylation. Among them, OsMIR156d and OsMIR156j, which promote rice tillering, are repressed by CHH methylation at two MITEs in the promoters. By contrast, D14, which suppresses rice tillering, is activated by CHH methylation at an MITE in its downstream. Our findings reveal regulation of rice tillering by RNA-directed DNA methylation at MITEs and provide potential targets for agronomic trait enhancement through epigenome editing.
Collapse
Affiliation(s)
- Le Xu
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Kun Yuan
- Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Meng Yuan
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Xiangbing Meng
- Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Min Chen
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Jianguo 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, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiayang Li
- Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Yijun Qi
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.
| |
Collapse
|
50
|
Li J, Yang DL, Huang H, Zhang G, He L, Pang J, Lozano-Durán R, Lang Z, Zhu JK. Epigenetic memory marks determine epiallele stability at loci targeted by de novo DNA methylation. Nat Plants 2020; 6:661-674. [PMID: 32514141 DOI: 10.1038/s41477-020-0671-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 04/22/2020] [Indexed: 05/26/2023]
Abstract
It is generally assumed that DNA methylation changes at genomic regions targeted by the de novo RNA-directed DNA methylation (RdDM) pathway are unstable. Here, we show that RdDM targets in Arabidopsis can be classified into two groups on the basis of whether there is remethylation following the restoration of NRPD1 function in nrpd1 mutant plants-remethylable loci and non-remethylable loci. In contrast to the remethylable loci, the non-remethylable loci contain higher levels of the euchromatic marks of trimethylation at Lys 4 of histone H3 (H3K4me3), which interferes with the recruitment of the RdDM molecular machinery, and acetylation at Lys 18 of histone H3 (H3K18ac), which helps to recruit the DNA demethylase ROS1 to antagonize RdDM. Here, using targeted methylation erasure by CRISPR-dCas9-TET1, we demonstrate that methylated CG (mCG) and mCHG (where H represents A, C or T) are memory marks that are required for targeting the RdDM machinery to remethylable loci. Our results show that histone and DNA methylation marks are critical in determining the ability of RdDM target loci to form stable epialleles, and contribute to understanding the formation and transmission of epialleles.
Collapse
Affiliation(s)
- Jingwen Li
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dong-Lei Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Huan Huang
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Guiping Zhang
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Li He
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jia Pang
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Rosa Lozano-Durán
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zhaobo Lang
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China.
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, USA.
| |
Collapse
|