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Kerckhofs E, Schubert D. Conserved functions of chromatin regulators in basal Archaeplastida. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1301-1311. [PMID: 37680033 DOI: 10.1111/tpj.16446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 08/15/2023] [Accepted: 08/18/2023] [Indexed: 09/09/2023]
Abstract
Chromatin is a dynamic network that regulates genome organization and gene expression. Different types of chromatin regulators are highly conserved among Archaeplastida, including unicellular algae, while some chromatin genes are only present in land plant genomes. Here, we review recent advances in understanding the function of conserved chromatin factors in basal land plants and algae. We focus on the role of Polycomb-group genes which mediate H3K27me3-based silencing and play a role in balancing gene dosage and regulating haploid-to-diploid transitions by tissue-specific repression of the transcription factors KNOX and BELL in many representatives of the green lineage. Moreover, H3K27me3 predominantly occupies repetitive elements which can lead to their silencing in a unicellular alga and basal land plants, while it covers mostly protein-coding genes in higher land plants. In addition, we discuss the role of nuclear matrix constituent proteins as putative functional lamin analogs that are highly conserved among land plants and might have an ancestral function in stress response regulation. In summary, our review highlights the importance of studying chromatin regulation in a wide range of organisms in the Archaeplastida.
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Affiliation(s)
- Elise Kerckhofs
- Epigenetics of Plants, Institute for Biology, Freie Universität Berlin, Berlin, Germany
| | - Daniel Schubert
- Epigenetics of Plants, Institute for Biology, Freie Universität Berlin, Berlin, Germany
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2
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Shao Z, Chen J, Wang S, Wang W, Zhu L. Sulfonamide-induced DNA hypomethylation disturbed sugar metabolism in rice (Oryza sativa L.). ENVIRONMENT INTERNATIONAL 2024; 187:108737. [PMID: 38735075 DOI: 10.1016/j.envint.2024.108737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/15/2024] [Accepted: 05/08/2024] [Indexed: 05/14/2024]
Abstract
DNA methylation is well-accepted as a bridge to unravel the complex interplay between genome and environmental exposures, and its alteration regulated the cellular metabolic responses towards pollutants. However, the mechanism underlying site-specific aberrant DNA methylation and metabolic disorders under pollutant stresses remained elusive. Herein, the multilevel omics interferences of sulfonamides (i.e., sulfadiazine and sulfamerazine), a group of antibiotics pervasive in farmland soils, towards rice in 14 days of 1 mg/L hydroponic exposure were systematically evaluated. Metabolome and transcriptome analyses showed that 57.1-71.4 % of mono- and disaccharides were accumulated, and the differentially expressed genes were involved in the promotion of sugar hydrolysis, as well as the detoxification of sulfonamides. Most differentially methylated regions (DMRs) were hypomethylated ones (accounting for 87-95 %), and 92 % of which were located in the CHH context (H = A, C, or T base). KEGG enrichment analysis revealed that CHH-DMRs in the promoter regions were enriched in sugar metabolism. To reveal the significant hypomethylation of CHH, multi-spectroscopic and thermodynamic approaches, combined with molecular simulation were conducted to investigate the molecular interaction between sulfonamides and DNA in different sequence contexts, and the result demonstrated that sulfonamides would insert into the minor grooves of DNA, and exhibited a stronger affinity with the CHH contexts of DNA compared to CG or CHG contexts. Computational modeling of DNA 3D structures further confirmed that the binding led to a pitch increase of 0.1 Å and a 3.8° decrease in the twist angle of DNA in the CHH context. This specific interaction and the downregulation of methyltransferase CMT2 (log2FC = -4.04) inhibited the DNA methylation. These results indicated that DNA methylation-based assessment was useful for metabolic toxicity prediction and health risk assessment.
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Affiliation(s)
- Zexi Shao
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China
| | - Jie Chen
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China
| | - Shuyuan Wang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China
| | - Wei Wang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China
| | - Lizhong Zhu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China.
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3
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Xie H, Yin W, Zheng Y, Zhang Y, Qin H, Huang Z, Zhao M, Li J. Increased DNA methylation of the splicing regulator SR45 suppresses seed abortion in litchi. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:868-882. [PMID: 37891009 DOI: 10.1093/jxb/erad427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/27/2023] [Indexed: 10/29/2023]
Abstract
The gene regulatory networks that govern seed development are complex, yet very little is known about the genes and processes that are controlled by DNA methylation. Here, we performed single-base resolution DNA methylome analysis and found that CHH methylation increased significantly throughout seed development in litchi. Based on the association analysis of differentially methylated regions and weighted gene co-expression network analysis (WGCNA), 46 genes were identified as essential DNA methylation-regulated candidate genes involved in litchi seed development, including LcSR45, a homolog of the serine/arginine-rich (SR) splicing regulator SR45. LcSR45 is predominately expressed in the funicle, embryo, and seed integument, and displayed increased CHH methylation in the promoter during seed development. Notably, silencing of LcSR45 in a seed-aborted litchi cultivar significantly improved normal seed development, whereas the ectopic expression of LcSR45 in Arabidopsis caused seed abortion. Furthermore, LcSR45-dependent alternative splicing events were found to regulate genes involved in seed development. Together, our findings demonstrate that LcSR45 is hypermethylated, and plays a detrimental role in litchi seed development, indicating a global increase in DNA methylation at this stage.
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Affiliation(s)
- Hanhan Xie
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Wenya Yin
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Yedan Zheng
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Yanshan Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Hongming Qin
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Zhiqiang Huang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Minglei Zhao
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Jianguo Li
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
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Chakraborty T, Payne H, Mosher RA. Expansion and contraction of small RNA and methylation machinery throughout plant evolution. CURRENT OPINION IN PLANT BIOLOGY 2022; 69:102260. [PMID: 35849937 DOI: 10.1016/j.pbi.2022.102260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/09/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
The revolution in sequencing has created a wealth of plant genomes that can be mined to understand the evolution of biological complexity. Complexity is often driven by gene duplication, which allows paralogs to specialize in an activity of the ancestral gene or acquire novel functions. Angiosperms encode a variety of gene silencing pathways that share related machinery for small RNA biosynthesis and function. Recent phylogenetic analysis of these gene families plots the expansion, specialization, and occasional contraction of this core machinery. This analysis reveals the ancient origin of RNA-directed DNA Methylation in early land plants, or possibly their algal ancestors, as well as ongoing duplications that evolve novel small RNA pathways.
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Affiliation(s)
- Tania Chakraborty
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721-0036, USA
| | - Hayden Payne
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721-0036, USA
| | - Rebecca A Mosher
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721-0036, USA.
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5
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Bowman JL, Arteaga-Vazquez M, Berger F, Briginshaw LN, Carella P, Aguilar-Cruz A, Davies KM, Dierschke T, Dolan L, Dorantes-Acosta AE, Fisher TJ, Flores-Sandoval E, Futagami K, Ishizaki K, Jibran R, Kanazawa T, Kato H, Kohchi T, Levins J, Lin SS, Nakagami H, Nishihama R, Romani F, Schornack S, Tanizawa Y, Tsuzuki M, Ueda T, Watanabe Y, Yamato KT, Zachgo S. The renaissance and enlightenment of Marchantia as a model system. THE PLANT CELL 2022; 34:3512-3542. [PMID: 35976122 PMCID: PMC9516144 DOI: 10.1093/plcell/koac219] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 06/21/2022] [Indexed: 05/07/2023]
Abstract
The liverwort Marchantia polymorpha has been utilized as a model for biological studies since the 18th century. In the past few decades, there has been a Renaissance in its utilization in genomic and genetic approaches to investigating physiological, developmental, and evolutionary aspects of land plant biology. The reasons for its adoption are similar to those of other genetic models, e.g. simple cultivation, ready access via its worldwide distribution, ease of crossing, facile genetics, and more recently, efficient transformation, genome editing, and genomic resources. The haploid gametophyte dominant life cycle of M. polymorpha is conducive to forward genetic approaches. The lack of ancient whole-genome duplications within liverworts facilitates reverse genetic approaches, and possibly related to this genomic stability, liverworts possess sex chromosomes that evolved in the ancestral liverwort. As a representative of one of the three bryophyte lineages, its phylogenetic position allows comparative approaches to provide insights into ancestral land plants. Given the karyotype and genome stability within liverworts, the resources developed for M. polymorpha have facilitated the development of related species as models for biological processes lacking in M. polymorpha.
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Affiliation(s)
| | - Mario Arteaga-Vazquez
- Instituto de Biotecnología y Ecología Aplicada, Universidad Veracruzana, Xalapa VER 91090, México
| | - Frederic Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna 1030, Austria
| | - Liam N Briginshaw
- School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, Monash University, Melbourne VIC 3800, Australia
| | - Philip Carella
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Adolfo Aguilar-Cruz
- Instituto de Biotecnología y Ecología Aplicada, Universidad Veracruzana, Xalapa VER 91090, México
| | - Kevin M Davies
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North 4442, New Zealand
| | - Tom Dierschke
- School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia
| | - Liam Dolan
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna 1030, Austria
| | - Ana E Dorantes-Acosta
- Instituto de Biotecnología y Ecología Aplicada, Universidad Veracruzana, Xalapa VER 91090, México
| | - Tom J Fisher
- School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, Monash University, Melbourne VIC 3800, Australia
| | - Eduardo Flores-Sandoval
- School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, Monash University, Melbourne VIC 3800, Australia
| | - Kazutaka Futagami
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | | | - Rubina Jibran
- The New Zealand Institute for Plant & Food Research Limited, Auckland 1142, New Zealand
| | - Takehiko Kanazawa
- Division of Cellular Dynamics, National Institute for Basic Biology, Myodaiji, Okazaki, Aichi 444-8585, Japan
- The Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Hirotaka Kato
- Graduate School of Science, Kobe University, Kobe 657-8501, Japan
- Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Jonathan Levins
- School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia
| | - Shih-Shun Lin
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan
| | - Hirofumi Nakagami
- Basic Immune System of Plants, Max-Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Ryuichi Nishihama
- Department of Applied Biological Science, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Facundo Romani
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | | | - Yasuhiro Tanizawa
- Department of Informatics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Masayuki Tsuzuki
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | - Takashi Ueda
- Division of Cellular Dynamics, National Institute for Basic Biology, Myodaiji, Okazaki, Aichi 444-8585, Japan
- The Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Yuichiro Watanabe
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | - Katsuyuki T Yamato
- Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa, Wakayama 649-6493, Japan
| | - Sabine Zachgo
- Division of Botany, School of Biology and Chemistry, Osnabrück University, Osnabrück 49076, Germany
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6
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Rymen B, Ferrafiat L, Blevins T. Non-coding RNA polymerases that silence transposable elements and reprogram gene expression in plants. Transcription 2020; 11:172-191. [PMID: 33180661 PMCID: PMC7714444 DOI: 10.1080/21541264.2020.1825906] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Multisubunit RNA polymerase (Pol) complexes are the core machinery for gene expression in eukaryotes. The enzymes Pol I, Pol II and Pol III transcribe distinct subsets of nuclear genes. This family of nuclear RNA polymerases expanded in terrestrial plants by the duplication of Pol II subunit genes. Two Pol II-related enzymes, Pol IV and Pol V, are highly specialized in the production of regulatory, non-coding RNAs. Pol IV and Pol V are the central players of RNA-directed DNA methylation (RdDM), an RNA interference pathway that represses transposable elements (TEs) and selected genes. Genetic and biochemical analyses of Pol IV/V subunits are now revealing how these enzymes evolved from ancestral Pol II to sustain non-coding RNA biogenesis in silent chromatin. Intriguingly, Pol IV-RdDM regulates genes that influence flowering time, reproductive development, stress responses and plant–pathogen interactions. Pol IV target genes vary among closely related taxa, indicating that these regulatory circuits are often species-specific. Data from crops like maize, rice, tomato and Brassicarapa suggest that dynamic repositioning of TEs, accompanied by Pol IV targeting to TE-proximal genes, leads to the reprogramming of plant gene expression over short evolutionary timescales.
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Affiliation(s)
- Bart Rymen
- Institut de biologie moléculaire des plantes, Université de Strasbourg , Strasbourg, France
| | - Laura Ferrafiat
- Institut de biologie moléculaire des plantes, Université de Strasbourg , Strasbourg, France
| | - Todd Blevins
- Institut de biologie moléculaire des plantes, Université de Strasbourg , Strasbourg, France
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7
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Diop SI, Subotic O, Giraldo-Fonseca A, Waller M, Kirbis A, Neubauer A, Potente G, Murray-Watson R, Boskovic F, Bont Z, Hock Z, Payton AC, Duijsings D, Pirovano W, Conti E, Grossniklaus U, McDaniel SF, Szövényi P. A pseudomolecule-scale genome assembly of the liverwort Marchantia polymorpha. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:1378-1396. [PMID: 31692190 DOI: 10.1111/tpj.14602] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 10/28/2019] [Indexed: 05/07/2023]
Abstract
Marchantia polymorpha has recently become a prime model for cellular, evo-devo, synthetic biological, and evolutionary investigations. We present a pseudomolecule-scale assembly of the M. polymorpha genome, making comparative genome structure analysis and classical genetic mapping approaches feasible. We anchored 88% of the M. polymorpha draft genome to a high-density linkage map resulting in eight pseudomolecules. We found that the overall genome structure of M. polymorpha is in some respects different from that of the model moss Physcomitrella patens. Specifically, genome collinearity between the two bryophyte genomes and vascular plants is limited, suggesting extensive rearrangements since divergence. Furthermore, recombination rates are greatest in the middle of the chromosome arms in M. polymorpha like in most vascular plant genomes, which is in contrast with P. patens where recombination rates are evenly distributed along the chromosomes. Nevertheless, some other properties of the genome are shared with P. patens. As in P. patens, DNA methylation in M. polymorpha is spread evenly along the chromosomes, which is in stark contrast with the angiosperm model Arabidopsis thaliana, where DNA methylation is strongly enriched at the centromeres. Nevertheless, DNA methylation and recombination rate are anticorrelated in all three species. Finally, M. polymorpha and P. patens centromeres are of similar structure and marked by high abundance of retroelements unlike in vascular plants. Taken together, the highly contiguous genome assembly we present opens unexplored avenues for M. polymorpha research by linking the physical and genetic maps, making novel genomic and genetic analyses, including map-based cloning, feasible.
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Affiliation(s)
- Seydina I Diop
- Department of Systematic and Evolutionary Botany & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
- BaseClear B.V., Sylviusweg 74, 2333 BE, Leiden, the Netherlands
| | - Oliver Subotic
- Department of Systematic and Evolutionary Botany & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
- BaseClear B.V., Sylviusweg 74, 2333 BE, Leiden, the Netherlands
| | - Alejandro Giraldo-Fonseca
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Manuel Waller
- Department of Systematic and Evolutionary Botany & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Alexander Kirbis
- Department of Systematic and Evolutionary Botany & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Anna Neubauer
- Department of Systematic and Evolutionary Botany & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Giacomo Potente
- Department of Systematic and Evolutionary Botany & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
- BaseClear B.V., Sylviusweg 74, 2333 BE, Leiden, the Netherlands
| | - Rachel Murray-Watson
- Department of Systematic and Evolutionary Botany & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Filip Boskovic
- Department of Systematic and Evolutionary Botany & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
- Cavendish Laboratory, University of Cambridge, JJ Thompson Avenue, CB3 0HE, Cambridge, UK
| | - Zoe Bont
- Department of Systematic and Evolutionary Botany & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013, Bern, Switzerland
| | - Zsofia Hock
- Department of Systematic and Evolutionary Botany & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Adam C Payton
- Department of Biology, University of Florida, 876 Newell Drive, Gainesville, FL, 32611, USA
| | | | - Walter Pirovano
- BaseClear B.V., Sylviusweg 74, 2333 BE, Leiden, the Netherlands
| | - Elena Conti
- Department of Systematic and Evolutionary Botany & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Stuart F McDaniel
- Department of Biology, University of Florida, 876 Newell Drive, Gainesville, FL, 32611, USA
| | - Péter Szövényi
- Department of Systematic and Evolutionary Botany & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
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8
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Grimanelli D, Ingouff M. DNA Methylation Readers in Plants. J Mol Biol 2020:S0022-2836(20)30027-9. [PMID: 31931004 DOI: 10.1016/j.jmb.2019.12.043] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 12/13/2019] [Accepted: 12/17/2019] [Indexed: 01/09/2023]
Abstract
In plants, DNA methylation occurs in distinct sequence contexts, including CG, CHG, and CHH. Thus, plants have developed a surprisingly diverse set of DNA methylation readers to cope with an extended repertoire of methylated sites. The Arabidopsis genome contains twelve Methyl-Binding Domain proteins (MBD), and nine SET and RING finger-associated (SRA) domain containing proteins belonging to the SUVH clade, in addition to three homologs of UHRF1, namely VIM1-3, all containing SRA domains. In this review, we will highlight several research questions that remain unresolved with respect to the function of plant DNA methylation readers, which can have both de novo demethylase and maintenance activity. We argue that maintenance of CG methylation in plants likely involved actors not found in their mammalian counterparts, and that new evidence suggests significant reprogramming of DNA methylation during plant reproduction as an important new development in the field.
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Affiliation(s)
- Daniel Grimanelli
- Institut de Recherche pour le Développement (IRD), Université de Montpellier, 911 Avenue Agropolis, 34394, Montpellier, France.
| | - Mathieu Ingouff
- Institut de Recherche pour le Développement (IRD), Université de Montpellier, 911 Avenue Agropolis, 34394, Montpellier, France.
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