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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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Montgomery SA, Berger F. Paternal imprinting in Marchantia polymorpha. THE NEW PHYTOLOGIST 2024; 241:1000-1006. [PMID: 37936346 DOI: 10.1111/nph.19377] [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: 06/22/2023] [Accepted: 10/09/2023] [Indexed: 11/09/2023]
Abstract
We are becoming aware of a growing number of organisms that do not express genetic information equally from both parents as a result of an epigenetic phenomenon called genomic imprinting. Recently, it was shown that the entire paternal genome is repressed during the diploid phase of the life cycle of the liverwort Marchantia polymorpha. The deposition of the repressive epigenetic mark H3K27me3 on the male pronucleus is responsible for the imprinted state, which is reset by the end of meiosis. Here, we put these recent reports in perspective of other forms of imprinting and discuss the potential mechanisms of imprinting in bryophytes and the causes of its evolution.
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Affiliation(s)
- Sean A Montgomery
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), C/ del Dr Aiguader, 88, 08003, Barcelona, Spain
| | - Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr Bohr-Gasse 3, 1030, Vienna, Austria
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3
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Chow HT, Mosher RA. Small RNA-mediated DNA methylation during plant reproduction. THE PLANT CELL 2023; 35:1787-1800. [PMID: 36651080 DOI: 10.1093/plcell/koad010] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 01/11/2023] [Accepted: 01/11/2023] [Indexed: 05/30/2023]
Abstract
Reproductive tissues are a rich source of small RNAs, including several classes of short interfering (si)RNAs that are restricted to this stage of development. In addition to RNA polymerase IV-dependent 24-nt siRNAs that trigger canonical RNA-directed DNA methylation, abundant reproductive-specific siRNAs are produced from companion cells adjacent to the developing germ line or zygote and may move intercellularly before inducing methylation. In some cases, these siRNAs are produced via non-canonical biosynthesis mechanisms or from sequences with little similarity to transposons. While the precise role of these siRNAs and the methylation they trigger is unclear, they have been implicated in specifying a single megaspore mother cell, silencing transposons in the male germ line, mediating parental dosage conflict to ensure proper endosperm development, hypermethylation of mature embryos, and trans-chromosomal methylation in hybrids. In this review, we summarize the current knowledge of reproductive siRNAs, including their biosynthesis, transport, and function.
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Affiliation(s)
- Hiu Tung Chow
- The School of Plant Sciences, The University of Arizona, Tucson, Arizona 85721-0036, USA
| | - Rebecca A Mosher
- The School of Plant Sciences, The University of Arizona, Tucson, Arizona 85721-0036, USA
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4
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Zhang JZ, Wang C, Zhu TT, Fu J, Tan H, Zhang CM, Cheng AX, Lou HX. Spatial Distribution, Antioxidant Capacity, and Spore Germination-Promoting Effect of Bibenzyls from Marchantia polymorpha. Antioxidants (Basel) 2022; 11:2157. [PMID: 36358536 PMCID: PMC9686712 DOI: 10.3390/antiox11112157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/28/2022] [Accepted: 10/28/2022] [Indexed: 08/26/2023] Open
Abstract
Liverworts, considered to be the first plant type to successfully make the transition from water to land, can resist different oxidative stress. As characteristic constituents of liverworts, the bibenzyls are efficient antioxidants. In this study, spatial distributions of the bibenzyls within Marchantia polymorpha L., the model species of liverworts, were mapped using airflow-assisted desorption electrospray ionization imaging mass spectrometry. Bibenzyls were found to largely exist in the female receptacle of M. polymorpha, where lunularic acid was found to focus in the central region and bisbibenzyls were enriched in the periphery. The region-specific gene expression and antioxidant activities were characterized. In line with the spatial feature of bibenzyls, higher MpSTCS1A and Mp4CL expression levels and antioxidant ability were exhibited in the archegoniophore. The expression level of MpSTCS1A, and the content of total phenolic acid was increased after UV-B irradiation, suggesting bibenzyls play an important role in UV-B tolerance. Moreover, lunularic acid and extract of archegoniophore at a certain concentration can stimulate the spore germination under normal conditions and UV-B stress. These works broaden our understanding of the significance of bibenzyls in spore propagation and environmental adaptation.
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Affiliation(s)
| | | | | | | | | | | | - Ai-Xia Cheng
- Key Laboratory of Chemical Biology of Natural Products (Ministry of Education), School of Pharmaceutical Sciences, College of Medicine, Shandong University, Jinan 250012, China
| | - Hong-Xiang Lou
- Key Laboratory of Chemical Biology of Natural Products (Ministry of Education), School of Pharmaceutical Sciences, College of Medicine, Shandong University, Jinan 250012, China
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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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Mounger JM, van Riemsdijk I, Boquete MT, Wagemaker CAM, Fatma S, Robertson MH, Voors SA, Oberstaller J, Gawehns F, Hanley TC, Grosse I, Verhoeven KJF, Sotka EE, Gehring CA, Hughes AR, Lewis DB, Schmid MW, Richards CL. Genetic and Epigenetic Differentiation Across Intertidal Gradients in the Foundation Plant Spartina alterniflora. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.868826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Ecological genomics approaches have informed us about the structure of genetic diversity in natural populations that might underlie patterns in trait variation. However, we still know surprisingly little about the mechanisms that permit organisms to adapt to variable environmental conditions. The salt marsh foundation plant Spartina alterniflora exhibits a dramatic range in phenotype that is associated with a pronounced intertidal environmental gradient across a narrow spatial scale. Both genetic and non-genetic molecular mechanisms might underlie this phenotypic variation. To investigate both, we used epigenotyping-by-sequencing (epiGBS) to evaluate the make-up of natural populations across the intertidal environmental gradient. Based on recent findings, we expected that both DNA sequence and DNA methylation diversity would be explained by source population and habitat within populations. However, we predicted that epigenetic variation might be more strongly associated with habitat since similar epigenetic modifications could be rapidly elicited across different genetic backgrounds by similar environmental conditions. Overall, with PERMANOVA we found that population of origin explained a significant amount of the genetic (8.6%) and epigenetic (3.2%) variance. In addition, we found that a small but significant amount of genetic and epigenetic variance (<1%) was explained by habitat within populations. The interaction of population and habitat explained an additional 2.9% of the genetic variance and 1.4% of the epigenetic variance. By examining genetic and epigenetic variation within the same fragments (variation in close-cis), we found that population explained epigenetic variation in 9.2% of 8,960 tested loci, even after accounting for differences in the DNA sequence of the fragment. Habitat alone explained very little (<0.1%) of the variation in these close-cis comparisons, but the interaction of population and habitat explained 2.1% of the epigenetic variation in these loci. Using multiple matrix regression with randomization (MMRR) we found that phenotypic differences in natural populations were correlated with epigenetic and environmental differences even when accounting for genetic differences. Our results support the contention that sequence variation explains most of the variation in DNA methylation, but we have provided evidence that DNA methylation distinctly contributes to plant responses in natural populations.
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7
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Gueno J, Borg M, Bourdareau S, Cossard G, Godfroy O, Lipinska A, Tirichine L, Cock J, Coelho S. Chromatin landscape associated with sexual differentiation in a UV sex determination system. Nucleic Acids Res 2022; 50:3307-3322. [PMID: 35253891 PMCID: PMC8989524 DOI: 10.1093/nar/gkac145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 02/15/2022] [Accepted: 03/04/2022] [Indexed: 12/12/2022] Open
Abstract
In many eukaryotes, such as dioicous mosses and many algae, sex is determined by UV sex chromosomes and is expressed during the haploid phase of the life cycle. In these species, the male and female developmental programs are initiated by the presence of the U- or V-specific regions of the sex chromosomes but, as in XY and ZW systems, sexual differentiation is largely driven by autosomal sex-biased gene expression. The mechanisms underlying the regulation of sex-biased expression of genes during sexual differentiation remain elusive. Here, we investigated the extent and nature of epigenomic changes associated with UV sexual differentiation in the brown alga Ectocarpus, a model UV system. Six histone modifications were quantified in near-isogenic lines, leading to the identification of 16 chromatin signatures across the genome. Chromatin signatures correlated with levels of gene expression and histone PTMs changes in males versus females occurred preferentially at genes involved in sex-specific pathways. Despite the absence of chromosome scale dosage compensation and the fact that UV sex chromosomes recombine across most of their length, the chromatin landscape of these chromosomes was remarkably different to that of autosomes. Hotspots of evolutionary young genes in the pseudoautosomal regions appear to drive the exceptional chromatin features of UV sex chromosomes.
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Affiliation(s)
- Josselin Gueno
- Sorbonne Université, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
| | - Michael Borg
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen72076, Tübingen, Germany
| | - Simon Bourdareau
- Sorbonne Université, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
| | - Guillaume Cossard
- Sorbonne Université, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
| | - Olivier Godfroy
- Sorbonne Université, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
| | - Agnieszka Lipinska
- Sorbonne Université, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen72076, Tübingen, Germany
| | - Leila Tirichine
- Nantes Universite, CNRS, US2B, UMR 6286, F-44000, Nantes, France
| | - J Mark Cock
- Sorbonne Université, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
| | - Susana M Coelho
- Sorbonne Université, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen72076, Tübingen, Germany
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8
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Sanchez-Vera V, Landberg K, Lopez-Obando M, Thelander M, Lagercrantz U, Muñoz-Viana R, Schmidt A, Grossniklaus U, Sundberg E. The Physcomitrium patens egg cell expresses several distinct epigenetic components and utilizes homologues of BONOBO genes for cell specification. THE NEW PHYTOLOGIST 2022; 233:2614-2628. [PMID: 34942024 DOI: 10.1111/nph.17938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
Although land plant germ cells have received much attention, knowledge about their specification is still limited. We thus identified transcripts enriched in egg cells of the bryophyte model species Physcomitrium patens, compared the results with angiosperm egg cells, and selected important candidate genes for functional analysis. We used laser-assisted microdissection to perform a cell-type-specific transcriptome analysis on egg cells for comparison with available expression profiles of vegetative tissues and male reproductive organs. We made reporter lines and knockout mutants of the two BONOBO (PbBNB) genes and studied their role in reproduction. We observed an overlap in gene activity between bryophyte and angiosperm egg cells, but also clear differences. Strikingly, several processes that are male-germline specific in Arabidopsis are active in the P. patens egg cell. Among those were the moss PbBNB genes, which control proliferation and identity of both female and male germlines. Pathways shared between male and female germlines were most likely present in the common ancestors of land plants, besides sex-specifying factors. A set of genes may also be involved in the switches between the diploid and haploid moss generations. Nonangiosperm gene networks also contribute to the specification of the P. patens egg cell.
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Affiliation(s)
- Victoria Sanchez-Vera
- Department of Plant Biology, The Linnean Centre of Plant Biology in Uppsala, Swedish University of Agricultural Sciences, PO Box 7080, Uppsala, SE-75007, Sweden
| | - Katarina Landberg
- Department of Plant Biology, The Linnean Centre of Plant Biology in Uppsala, Swedish University of Agricultural Sciences, PO Box 7080, Uppsala, SE-75007, Sweden
| | - Mauricio Lopez-Obando
- Department of Plant Biology, The Linnean Centre of Plant Biology in Uppsala, Swedish University of Agricultural Sciences, PO Box 7080, Uppsala, SE-75007, Sweden
| | - Mattias Thelander
- Department of Plant Biology, The Linnean Centre of Plant Biology in Uppsala, Swedish University of Agricultural Sciences, PO Box 7080, Uppsala, SE-75007, Sweden
| | - Ulf Lagercrantz
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18 D, Uppsala, SE-752 36, Sweden
| | - Rafael Muñoz-Viana
- Department of Plant Biology, The Linnean Centre of Plant Biology in Uppsala, Swedish University of Agricultural Sciences, PO Box 7080, Uppsala, SE-75007, Sweden
| | - Anja Schmidt
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, Zurich, CH-8008, Switzerland
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, Zurich, CH-8008, Switzerland
| | - Eva Sundberg
- Department of Plant Biology, The Linnean Centre of Plant Biology in Uppsala, Swedish University of Agricultural Sciences, PO Box 7080, Uppsala, SE-75007, Sweden
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9
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Montgomery SA, Berger F. The evolution of imprinting in plants: beyond the seed. PLANT REPRODUCTION 2021; 34:373-383. [PMID: 33914165 PMCID: PMC8566399 DOI: 10.1007/s00497-021-00410-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/12/2021] [Indexed: 05/14/2023]
Abstract
Genomic imprinting results in the biased expression of alleles depending on if the allele was inherited from the mother or the father. Despite the prevalence of sexual reproduction across eukaryotes, imprinting is only found in placental mammals, flowering plants, and some insects, suggesting independent evolutionary origins. Numerous hypotheses have been proposed to explain the selective pressures that favour the innovation of imprinted gene expression and each differs in their experimental support and predictions. Due to the lack of investigation of imprinting in land plants, other than angiosperms with triploid endosperm, we do not know whether imprinting occurs in species lacking endosperm and with embryos developing on maternal plants. Here, we discuss the potential for uncovering additional examples of imprinting in land plants and how these observations may provide additional support for one or more existing imprinting hypotheses.
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Affiliation(s)
- Sean A Montgomery
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr Gasse 3, 1030, Vienna, Austria
| | - Frédéric Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr Gasse 3, 1030, Vienna, Austria.
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10
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Vigneau J, Borg M. The epigenetic origin of life history transitions in plants and algae. PLANT REPRODUCTION 2021; 34:267-285. [PMID: 34236522 PMCID: PMC8566409 DOI: 10.1007/s00497-021-00422-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/14/2021] [Indexed: 05/17/2023]
Abstract
Plants and algae have a complex life history that transitions between distinct life forms called the sporophyte and the gametophyte. This phenomenon-called the alternation of generations-has fascinated botanists and phycologists for over 170 years. Despite the mesmerizing array of life histories described in plants and algae, we are only now beginning to learn about the molecular mechanisms controlling them and how they evolved. Epigenetic silencing plays an essential role in regulating gene expression during multicellular development in eukaryotes, raising questions about its impact on the life history strategy of plants and algae. Here, we trace the origin and function of epigenetic mechanisms across the plant kingdom, from unicellular green algae through to angiosperms, and attempt to reconstruct the evolutionary steps that influenced life history transitions during plant evolution. Central to this evolutionary scenario is the adaption of epigenetic silencing from a mechanism of genome defense to the repression and control of alternating generations. We extend our discussion beyond the green lineage and highlight the peculiar case of the brown algae. Unlike their unicellular diatom relatives, brown algae lack epigenetic silencing pathways common to animals and plants yet display complex life histories, hinting at the emergence of novel life history controls during stramenopile evolution.
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Affiliation(s)
- Jérômine Vigneau
- Department of Algal Development and Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Michael Borg
- Department of Algal Development and Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany.
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11
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Sow MD, Le Gac AL, Fichot R, Lanciano S, Delaunay A, Le Jan I, Lesage-Descauses MC, Citerne S, Caius J, Brunaud V, Soubigou-Taconnat L, Cochard H, Segura V, Chaparro C, Grunau C, Daviaud C, Tost J, Brignolas F, Strauss SH, Mirouze M, Maury S. RNAi suppression of DNA methylation affects the drought stress response and genome integrity in transgenic poplar. THE NEW PHYTOLOGIST 2021; 232:80-97. [PMID: 34128549 DOI: 10.1111/nph.17555] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 06/08/2021] [Indexed: 05/27/2023]
Abstract
Trees are long-lived organisms that continuously adapt to their environments, a process in which epigenetic mechanisms are likely to play a key role. Via downregulation of the chromatin remodeler DECREASED IN DNA METHYLATION 1 (DDM1) in poplar (Populus tremula × Populus alba) RNAi lines, we examined how DNA methylation coordinates genomic and physiological responses to moderate water deficit. We compared the growth and drought response of two RNAi-ddm1 lines to wild-type (WT) trees under well-watered and water deficit/rewatering conditions, and analyzed their methylomes, transcriptomes, mobilomes and phytohormone contents in the shoot apical meristem. The RNAi-ddm1 lines were more tolerant to drought-induced cavitation but did not differ in height or stem diameter growth. About 5000 differentially methylated regions were consistently detected in both RNAi-ddm1 lines, colocalizing with 910 genes and 89 active transposable elements. Under water deficit conditions, 136 differentially expressed genes were found, including many involved in phytohormone pathways; changes in phytohormone concentrations were also detected. Finally, the combination of hypomethylation and drought led to the mobility of two transposable elements. Our findings suggest major roles for DNA methylation in regulation of genes involved in hormone-related stress responses, and the maintenance of genome integrity through repression of transposable elements.
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Affiliation(s)
- Mamadou D Sow
- LBLGC, INRAE, Université d'Orléans, EA 1207 USC 1328, Orléans, 45067, France
| | - Anne-Laure Le Gac
- LBLGC, INRAE, Université d'Orléans, EA 1207 USC 1328, Orléans, 45067, France
| | - Régis Fichot
- LBLGC, INRAE, Université d'Orléans, EA 1207 USC 1328, Orléans, 45067, France
| | - Sophie Lanciano
- IRD, UMR 232 DIADE, Université de Montpellier, Montpellier, 34090, France
- Laboratory of Plant Genome and Development, Université de Perpignan, Perpignan, 66860, France
| | - Alain Delaunay
- LBLGC, INRAE, Université d'Orléans, EA 1207 USC 1328, Orléans, 45067, France
| | - Isabelle Le Jan
- LBLGC, INRAE, Université d'Orléans, EA 1207 USC 1328, Orléans, 45067, France
| | | | - Sylvie Citerne
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, 78000, France
| | - Jose Caius
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Orsay, 91405, France
| | - Véronique Brunaud
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Orsay, 91405, France
| | - Ludivine Soubigou-Taconnat
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Orsay, 91405, France
| | - Hervé Cochard
- Université Clermont Auvergne, INRAE, PIAF, Clermont-Ferrand, 63000, France
| | - Vincent Segura
- BioForA, INRAE, ONF, UMR 0588, Orléans, 45075, France
- UMR AGAP Institut, Université Montpellier, CIRAD, INRAE, Institut Montpellier SupAgro, UMR 1334, Montpellier, F-34398, France
| | | | - Christoph Grunau
- UMR 5244, IHPE, Université de Perpignan, Perpignan, 66100, France
| | - Christian Daviaud
- Laboratory for Epigenetics and Environment Centre National de Recherche en Génomique Humaine, CEA- Institut de Biologie Francois Jacob, Université Paris-Saclay, Evry, 91057, France
| | - Jörg Tost
- Laboratory for Epigenetics and Environment Centre National de Recherche en Génomique Humaine, CEA- Institut de Biologie Francois Jacob, Université Paris-Saclay, Evry, 91057, France
| | - Franck Brignolas
- LBLGC, INRAE, Université d'Orléans, EA 1207 USC 1328, Orléans, 45067, France
| | - Steven H Strauss
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, 97331-5752, USA
| | - Marie Mirouze
- IRD, UMR 232 DIADE, Université de Montpellier, Montpellier, 34090, France
- Laboratory of Plant Genome and Development, Université de Perpignan, Perpignan, 66860, France
| | - Stéphane Maury
- LBLGC, INRAE, Université d'Orléans, EA 1207 USC 1328, Orléans, 45067, France
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12
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Investigating the Viral Suppressor HC-Pro Inhibiting Small RNA Methylation through Functional Comparison of HEN1 in Angiosperm and Bryophyte. Viruses 2021; 13:v13091837. [PMID: 34578418 PMCID: PMC8473176 DOI: 10.3390/v13091837] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/09/2021] [Accepted: 09/09/2021] [Indexed: 12/27/2022] Open
Abstract
In plants, HEN1-facilitated methylation at 3′ end ribose is a critical step of small-RNA (sRNA) biogenesis. A mutant of well-studied Arabidopsis HEN1 (AtHEN1), hen1-1, showed a defective developmental phenotype, indicating the importance of sRNA methylation. Moreover, Marchantia polymorpha has been identified to have a HEN1 ortholog gene (MpHEN1); however, its function remained unfathomed. Our in vivo and in vitro data have shown MpHEN1 activity being comparable with AtHEN1, and their substrate specificity towards duplex microRNA (miRNA) remained consistent. Furthermore, the phylogenetic tree and multiple alignment highlighted the conserved molecular evolution of the HEN1 family in plants. The P1/HC-Pro of the turnip mosaic virus (TuMV) is a known RNA silencing suppressor and inhibits HEN1 methylation of sRNAs. Here, we report that the HC-Pro physically binds with AtHEN1 through FRNK motif, inhibiting HEN1’s methylation activity. Moreover, the in vitro EMSA data indicates GST-HC-Pro of TuMV lacks sRNA duplex-binding ability. Surprisingly, the HC-Pro also inhibits MpHEN1 activity in a dosage-dependent manner, suggesting the possibility of interaction between HC-Pro and MpHEN1 as well. Further investigations on understanding interaction mechanisms of HEN1 and various HC-Pros can advance the knowledge of viral suppressors.
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13
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Kakoulidou I, Avramidou EV, Baránek M, Brunel-Muguet S, Farrona S, Johannes F, Kaiserli E, Lieberman-Lazarovich M, Martinelli F, Mladenov V, Testillano PS, Vassileva V, Maury S. Epigenetics for Crop Improvement in Times of Global Change. BIOLOGY 2021; 10:766. [PMID: 34439998 PMCID: PMC8389687 DOI: 10.3390/biology10080766] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/04/2021] [Accepted: 08/06/2021] [Indexed: 12/15/2022]
Abstract
Epigenetics has emerged as an important research field for crop improvement under the on-going climatic changes. Heritable epigenetic changes can arise independently of DNA sequence alterations and have been associated with altered gene expression and transmitted phenotypic variation. By modulating plant development and physiological responses to environmental conditions, epigenetic diversity-naturally, genetically, chemically, or environmentally induced-can help optimise crop traits in an era challenged by global climate change. Beyond DNA sequence variation, the epigenetic modifications may contribute to breeding by providing useful markers and allowing the use of epigenome diversity to predict plant performance and increase final crop production. Given the difficulties in transferring the knowledge of the epigenetic mechanisms from model plants to crops, various strategies have emerged. Among those strategies are modelling frameworks dedicated to predicting epigenetically controlled-adaptive traits, the use of epigenetics for in vitro regeneration to accelerate crop breeding, and changes of specific epigenetic marks that modulate gene expression of traits of interest. The key challenge that agriculture faces in the 21st century is to increase crop production by speeding up the breeding of resilient crop species. Therefore, epigenetics provides fundamental molecular information with potential direct applications in crop enhancement, tolerance, and adaptation within the context of climate change.
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Affiliation(s)
- Ioanna Kakoulidou
- Department of Molecular Life Sciences, Technical University of Munich, Liesel-Beckmann-Str. 2, 85354 Freising, Germany; (I.K.); (F.J.)
| | - Evangelia V. Avramidou
- Laboratory of Forest Genetics and Biotechnology, Institute of Mediterranean Forest Ecosystems, Hellenic Agricultural Organization-Dimitra (ELGO-DIMITRA), 11528 Athens, Greece;
| | - Miroslav Baránek
- Faculty of Horticulture, Mendeleum—Institute of Genetics, Mendel University in Brno, Valtická 334, 69144 Lednice, Czech Republic;
| | - Sophie Brunel-Muguet
- UMR 950 Ecophysiologie Végétale, Agronomie et Nutritions N, C, S, UNICAEN, INRAE, Normandie Université, CEDEX, F-14032 Caen, France;
| | - Sara Farrona
- Plant and AgriBiosciences Centre, Ryan Institute, National University of Ireland (NUI) Galway, H91 TK33 Galway, Ireland;
| | - Frank Johannes
- Department of Molecular Life Sciences, Technical University of Munich, Liesel-Beckmann-Str. 2, 85354 Freising, Germany; (I.K.); (F.J.)
- Institute for Advanced Study, Technical University of Munich, Lichtenberg Str. 2a, 85748 Garching, Germany
| | - Eirini Kaiserli
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, Bower Building, University of Glasgow, Glasgow G12 8QQ, UK;
| | - Michal Lieberman-Lazarovich
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion 7505101, Israel;
| | - Federico Martinelli
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy;
| | - Velimir Mladenov
- Faculty of Agriculture, University of Novi Sad, Sq. Dositeja Obradovića 8, 21000 Novi Sad, Serbia;
| | - Pilar S. Testillano
- Pollen Biotechnology of Crop Plants Group, Centro de Investigaciones Biológicas Margarita Salas-(CIB-CSIC), Ramiro Maeztu 9, 28040 Madrid, Spain;
| | - Valya Vassileva
- Department of Molecular Biology and Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. Georgi Bonchev Str., Bldg. 21, 1113 Sofia, Bulgaria;
| | - Stéphane Maury
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRAE, EA1207 USC1328, Université d’Orléans, F-45067 Orléans, France
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14
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Long J, Walker J, She W, Aldridge B, Gao H, Deans S, Vickers M, Feng X. Nurse cell--derived small RNAs define paternal epigenetic inheritance in Arabidopsis. Science 2021; 373:373/6550/eabh0556. [PMID: 34210850 DOI: 10.1126/science.abh0556] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 05/10/2021] [Indexed: 11/02/2022]
Abstract
The plant male germline undergoes DNA methylation reprogramming, which methylates genes de novo and thereby alters gene expression and regulates meiosis. Here, we reveal the molecular mechanism underlying this reprogramming. We demonstrate that genic methylation in the male germline, from meiocytes to sperm, is established by 24-nucleotide small interfering RNAs (siRNAs) transcribed from transposons with imperfect sequence homology. These siRNAs are synthesized by meiocyte nurse cells (tapetum) through activity of CLSY3, a chromatin remodeler absent in other anther cells. Tapetal siRNAs govern germline methylation throughout the genome, including the inherited methylation patterns in sperm. Tapetum-derived siRNAs also silence germline transposons, safeguarding genome integrity. Our results reveal that tapetal siRNAs are sufficient to reconstitute germline methylation patterns and drive functional methylation reprogramming throughout the male germline.
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Affiliation(s)
- Jincheng Long
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - James Walker
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Wenjing She
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Billy Aldridge
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Hongbo Gao
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Samuel Deans
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Martin Vickers
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Xiaoqi Feng
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK.
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15
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Kohchi T, Yamato KT, Ishizaki K, Yamaoka S, Nishihama R. Development and Molecular Genetics of Marchantia polymorpha. ANNUAL REVIEW OF PLANT BIOLOGY 2021; 72:677-702. [PMID: 33684298 DOI: 10.1146/annurev-arplant-082520-094256] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Bryophytes occupy a basal position in the monophyletic evolution of land plants and have a life cycle in which the gametophyte generation dominates over the sporophyte generation, offering a significant advantage in conducting genetics. Owing to its low genetic redundancy and the availability of an array of versatile molecular tools, including efficient genome editing, the liverwort Marchantia polymorpha has become a model organism of choice that provides clues to the mechanisms underlying eco-evo-devo biology in plants. Recent analyses of developmental mutants have revealed that key genes in developmental processes are functionally well conserved in plants, despite their morphological differences, and that lineage-specific evolution occurred by neo/subfunctionalization of common ancestral genes. We suggest that M. polymorpha is an excellent platform to uncover the conserved and diversified mechanisms underlying land plant development.
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Affiliation(s)
- Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; , ,
| | - Katsuyuki T Yamato
- Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa 649-6493, Japan;
| | | | - Shohei Yamaoka
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; , ,
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; , ,
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16
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Ritter EJ, Niederhuth CE. Intertwined evolution of plant epigenomes and genomes. CURRENT OPINION IN PLANT BIOLOGY 2021; 61:101990. [PMID: 33445143 DOI: 10.1016/j.pbi.2020.101990] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/08/2020] [Accepted: 12/17/2020] [Indexed: 06/12/2023]
Abstract
DNA methylation is found across eukaryotes; however, plants have evolved patterns and pathways of DNA methylation that are distinct from animals and fungi. DNA methylation shapes the evolution of genomes through its direct roles in transposon silencing, gene expression, genome stability, and its impact on mutation rates. In return the diversity of DNA methylation across species is shaped by genome sequence evolution. Extensive diversification of key DNA methylation pathways has continued in plants through gene duplication and loss. Meanwhile, frequent movement of transposons has altered local DNA methylation patterns and the genes affected. Only recently has the diversity and evolutionary history of plant DNA methylation become evident with the availability of increasing genomic and epigenomic data. However, much remains unresolved regarding the evolutionary forces that have shaped the dynamics of the complex and intertwined history of plant genome and epigenome evolution.
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Affiliation(s)
- Eleanore J Ritter
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Chad E Niederhuth
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA; AgBioResearch, Michigan State University, East Lansing, MI 48824, USA.
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17
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Szövényi P, Gunadi A, Li FW. Charting the genomic landscape of seed-free plants. NATURE PLANTS 2021; 7:554-565. [PMID: 33820965 DOI: 10.1038/s41477-021-00888-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 02/25/2021] [Indexed: 05/02/2023]
Abstract
During the past few years several high-quality genomes has been published from Charophyte algae, bryophytes, lycophytes and ferns. These genomes have not only elucidated the origin and evolution of early land plants, but have also provided important insights into the biology of the seed-free lineages. However, critical gaps across the phylogeny remain and many new questions have been raised through comparing seed-free and seed plant genomes. Here, we review the reference genomes available and identify those that are missing in the seed-free lineages. We compare patterns of various levels of genome and epigenomic organization found in seed-free plants to those of seed plants. Some genomic features appear to be fundamentally different. For instance, hornworts, Selaginella and most liverworts are devoid of whole-genome duplication, in stark contrast to other land plants. In addition, the distribution of genes and repeats appear to be less structured in seed-free genomes than in other plants, and the levels of gene body methylation appear to be much lower. Finally, we highlight the currently available (or needed) model systems, which are crucial to further our understanding about how changes in genes translate into evolutionary novelties.
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Affiliation(s)
- Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich and Zurich-Basel Plant Science Center, Zurich, Switzerland.
| | | | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, USA
- Plant Biology Section, Cornell University, Ithaca, NY, USA
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18
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Goffová I, Fajkus J. The rDNA Loci-Intersections of Replication, Transcription, and Repair Pathways. Int J Mol Sci 2021; 22:1302. [PMID: 33525595 PMCID: PMC7865372 DOI: 10.3390/ijms22031302] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 01/25/2021] [Accepted: 01/25/2021] [Indexed: 12/28/2022] Open
Abstract
Genes encoding ribosomal RNA (rDNA) are essential for cell survival and are particularly sensitive to factors leading to genomic instability. Their repetitive character makes them prone to inappropriate recombinational events arising from collision of transcriptional and replication machineries, resulting in unstable rDNA copy numbers. In this review, we summarize current knowledge on the structure and organization of rDNA, its role in sensing changes in the genome, and its linkage to aging. We also review recent findings on the main factors involved in chromatin assembly and DNA repair in the maintenance of rDNA stability in the model plants Arabidopsis thaliana and the moss Physcomitrella patens, providing a view across the plant evolutionary tree.
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Affiliation(s)
- Ivana Goffová
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, CZ-61137 Brno, Czech Republic;
- Chromatin Molecular Complexes, Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, CZ-62500 Brno, Czech Republic
| | - Jiří Fajkus
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, CZ-61137 Brno, Czech Republic;
- Chromatin Molecular Complexes, Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, CZ-62500 Brno, Czech Republic
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, CZ-61265 Brno, Czech Republic
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19
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Borg M, Papareddy RK, Dombey R, Axelsson E, Nodine MD, Twell D, Berger F. Epigenetic reprogramming rewires transcription during the alternation of generations in Arabidopsis. eLife 2021; 10:e61894. [PMID: 33491647 PMCID: PMC7920552 DOI: 10.7554/elife.61894] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 01/25/2021] [Indexed: 12/18/2022] Open
Abstract
Alternation between morphologically distinct haploid and diploid life forms is a defining feature of most plant and algal life cycles, yet the underlying molecular mechanisms that govern these transitions remain unclear. Here, we explore the dynamic relationship between chromatin accessibility and epigenetic modifications during life form transitions in Arabidopsis. The diploid-to-haploid life form transition is governed by the loss of H3K9me2 and DNA demethylation of transposon-associated cis-regulatory elements. This event is associated with dramatic changes in chromatin accessibility and transcriptional reprogramming. In contrast, the global loss of H3K27me3 in the haploid form shapes a chromatin accessibility landscape that is poised to re-initiate the transition back to diploid life after fertilisation. Hence, distinct epigenetic reprogramming events rewire transcription through major reorganisation of the regulatory epigenome to guide the alternation of generations in flowering plants.
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Affiliation(s)
- Michael Borg
- Gregor Mendel Institute (GMI), Austrian Academy of SciencesViennaAustria
| | | | - Rodolphe Dombey
- Gregor Mendel Institute (GMI), Austrian Academy of SciencesViennaAustria
| | - Elin Axelsson
- Gregor Mendel Institute (GMI), Austrian Academy of SciencesViennaAustria
| | - Michael D Nodine
- Gregor Mendel Institute (GMI), Austrian Academy of SciencesViennaAustria
| | - David Twell
- Gregor Mendel Institute (GMI), Austrian Academy of SciencesViennaAustria
- Department of Genetics, University of LeicesterLeicesterUnited Kingdom
| | - Frédéric Berger
- Gregor Mendel Institute (GMI), Austrian Academy of SciencesViennaAustria
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20
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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. FRONTIERS IN PLANT SCIENCE 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] [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.
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21
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Karaaslan ES, Wang N, Faiß N, Liang Y, Montgomery SA, Laubinger S, Berendzen KW, Berger F, Breuninger H, Liu C. Marchantia TCP transcription factor activity correlates with three-dimensional chromatin structure. NATURE PLANTS 2020; 6:1250-1261. [PMID: 32895530 DOI: 10.1038/s41477-020-00766-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 08/07/2020] [Indexed: 05/04/2023]
Abstract
Information in the genome is not only encoded within sequence or epigenetic modifications, but is also found in how it folds in three-dimensional space. The formation of self-interacting genomic regions, named topologically associated domains (TADs), is known as a key feature of genome organization beyond the nucleosomal level. However, our understanding of the formation and function of TADs in plants is extremely limited. Here we show that the genome of Marchantia polymorpha, a member of a basal land plant lineage, exhibits TADs with epigenetic features similar to those of higher plants. By analysing various epigenetic marks across Marchantia TADs, we find that these regions generally represent interstitial heterochromatin and their borders are enriched with Marchantia transcription factor TCP1. We also identify a type of TAD that we name 'TCP1-rich TAD', in which genomic regions are highly accessible and are densely bound by TCP1 proteins. Transcription of TCP1 target genes differs on the basis gene location, and those in TCP1-rich TADs clearly show a lower expression level. In tcp1 mutant lines, neither TCP1-bound TAD borders nor TCP1-rich TADs display drastically altered chromatin organization patterns, suggesting that, in Marchantia, TCP1 is dispensable for TAD formation. However, we find that in tcp1 mutants, genes residing in TCP1-rich TADs have a greater extent of expression fold change as opposed to genes that do not belong to these TADs. Our results suggest that, besides standing as spatial chromatin-packing modules, plant TADs function as nuclear microcompartments associated with transcription factor activities.
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Affiliation(s)
| | - Nan Wang
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Natalie Faiß
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Yuyu Liang
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Sean A Montgomery
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Sascha Laubinger
- Institute for Biology and Environmental Science, University of Oldenburg, Oldenburg, Germany
| | | | - Frédéric Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Holger Breuninger
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Chang Liu
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany.
- Institute of Biology, University of Hohenheim, Stuttgart, Germany.
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22
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Harris KD, Zemach A. Contiguous and stochastic CHH methylation patterns of plant DRM2 and CMT2 revealed by single-read methylome analysis. Genome Biol 2020; 21:194. [PMID: 32762764 PMCID: PMC7412668 DOI: 10.1186/s13059-020-02099-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 07/08/2020] [Indexed: 12/12/2022] Open
Abstract
Cytosine methylome data is commonly generated through next-generation sequencing, with analyses averaging methylation states of individual reads. We propose an alternative method of analysing single-read methylome data. Using this method, we identify patterns relating to the mechanism of two plant non-CG-methylating enzymes, CMT2 and DRM2. CMT2-methylated regions show higher stochasticity, while DRM2-methylated regions have higher variation among cells. Based on these patterns, we develop a classifier that predicts enzyme activity in different species and tissues. To facilitate further single-read analyses, we develop a genome browser, SRBrowse, optimised for visualising and analysing sequencing data at single-read resolution.
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Affiliation(s)
- Keith D Harris
- School of Plant Sciences and Food Security, Tel Aviv University, Haim Levanon, Tel Aviv, Israel
| | - Assaf Zemach
- School of Plant Sciences and Food Security, Tel Aviv University, Haim Levanon, Tel Aviv, Israel.
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23
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Henikoff S, Ahmad K. Evolution: Heterochromatin Diversity in Early-Branching Land Plants. Curr Biol 2020; 30:R161-R163. [PMID: 32097641 DOI: 10.1016/j.cub.2019.12.044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Chromatin profiling of a liverwort genome reveals an epigenomic landscape where the major mark of developmental silencing in later-branching land plants and in animals also targets subsets of transposons in this early-branching land plant lineage.
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Affiliation(s)
- Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue, North Seattle, WA 98109, USA; Howard Hughes Medical Institute.
| | - Kami Ahmad
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue, North Seattle, WA 98109, USA
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24
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Meyberg R, Perroud PF, Haas FB, Schneider L, Heimerl T, Renzaglia KS, Rensing SA. Characterisation of evolutionarily conserved key players affecting eukaryotic flagellar motility and fertility using a moss model. THE NEW PHYTOLOGIST 2020; 227:440-454. [PMID: 32064607 PMCID: PMC8224819 DOI: 10.1111/nph.16486] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 02/07/2020] [Indexed: 05/18/2023]
Abstract
Defects in flagella/cilia are often associated with infertility and disease. Motile male gametes (sperm cells) are an ancestral eukaryotic trait that has been lost in several lineages like flowering plants. Here, we made use of a phenotypic male fertility difference between two moss (Physcomitrella patens) ecotypes to explore spermatozoid function. We compare genetic and epigenetic variation as well as expression profiles between the Gransden and Reute ecotype to identify a set of candidate genes associated with moss male infertility. We generated a loss-of-function mutant of a coiled-coil domain containing 39 (ccdc39) gene that is part of the flagellar hydin network. Defects in mammal and algal homologues of this gene coincide with a loss of fertility, demonstrating the evolutionary conservation of flagellar function related to male fertility across kingdoms. The Ppccdc39 mutant resembles the Gransden phenotype in terms of male fertility. Potentially, several somatic (epi-)mutations occurred during prolonged vegetative propagation of Gransden, causing regulatory differences of for example the homeodomain transcription factor BELL1. Probably these somatic changes are causative for the observed male fertility defect. We propose that moss spermatozoids might be employed as an easily accessible system to study male infertility of humans and animals in terms of flagellar structure and movement.
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Affiliation(s)
- Rabea Meyberg
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch Str. 8, 35043 Marburg, Germany
| | - Pierre-François Perroud
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch Str. 8, 35043 Marburg, Germany
| | - Fabian B. Haas
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch Str. 8, 35043 Marburg, Germany
| | - Lucas Schneider
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch Str. 8, 35043 Marburg, Germany
| | - Thomas Heimerl
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), University of Marburg, Karl-von-Frisch Str. 8, 35043 Marburg, Germany
| | - Karen S. Renzaglia
- Department of Plant Biology, Southern Illinois University, Mail Code 6509, 1125 Lincoln Drive, Carbondale, IL 62901, USA
| | - Stefan A. Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch Str. 8, 35043 Marburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestraße 18, 79104 Freiburg, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), University of Marburg, Karl-von-Frisch Str. 8, 35043 Marburg, Germany
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Cesarino I, Dello Ioio R, Kirschner GK, Ogden MS, Picard KL, Rast-Somssich MI, Somssich M. Plant science's next top models. ANNALS OF BOTANY 2020; 126:1-23. [PMID: 32271862 PMCID: PMC7304477 DOI: 10.1093/aob/mcaa063] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 04/08/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Model organisms are at the core of life science research. Notable examples include the mouse as a model for humans, baker's yeast for eukaryotic unicellular life and simple genetics, or the enterobacteria phage λ in virology. Plant research was an exception to this rule, with researchers relying on a variety of non-model plants until the eventual adoption of Arabidopsis thaliana as primary plant model in the 1980s. This proved to be an unprecedented success, and several secondary plant models have since been established. Currently, we are experiencing another wave of expansion in the set of plant models. SCOPE Since the 2000s, new model plants have been established to study numerous aspects of plant biology, such as the evolution of land plants, grasses, invasive and parasitic plant life, adaptation to environmental challenges, and the development of morphological diversity. Concurrent with the establishment of new plant models, the advent of the 'omics' era in biology has led to a resurgence of the more complex non-model plants. With this review, we introduce some of the new and fascinating plant models, outline why they are interesting subjects to study, the questions they will help to answer, and the molecular tools that have been established and are available to researchers. CONCLUSIONS Understanding the molecular mechanisms underlying all aspects of plant biology can only be achieved with the adoption of a comprehensive set of models, each of which allows the assessment of at least one aspect of plant life. The model plants described here represent a step forward towards our goal to explore and comprehend the diversity of plant form and function. Still, several questions remain unanswered, but the constant development of novel technologies in molecular biology and bioinformatics is already paving the way for the next generation of plant models.
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Affiliation(s)
- Igor Cesarino
- Department of Botany, Institute of Biosciences, University of São Paulo, Rua do Matão 277, Butantã, São Paulo, Brazil
| | - Raffaele Dello Ioio
- Dipartimento di Biologia e Biotecnologie, Università di Roma La Sapienza, Rome, Italy
| | - Gwendolyn K Kirschner
- University of Bonn, Institute of Crop Science and Resource Conservation (INRES), Division of Crop Functional Genomics, Bonn, Germany
| | - Michael S Ogden
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Kelsey L Picard
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
| | - Madlen I Rast-Somssich
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, VIC, Australia
| | - Marc Somssich
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
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Chow HT, Chakraborty T, Mosher RA. RNA-directed DNA Methylation and sexual reproduction: expanding beyond the seed. CURRENT OPINION IN PLANT BIOLOGY 2020; 54:11-17. [PMID: 31881293 DOI: 10.1016/j.pbi.2019.11.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 11/20/2019] [Accepted: 11/22/2019] [Indexed: 05/12/2023]
Abstract
Two trends are changing our understanding of RNA-directed DNA methylation. In model systems like Arabidopsis, tissue-specific analysis of DNA methylation is uncovering dynamic changes in methylation during sexual reproduction and unraveling the contribution of maternal and paternal epigenomes to the developing embryo. These studies indicate that RNA-directed DNA Methylation might be important for mediating balance between maternal and paternal contributions to the endosperm. At the same time, researchers are moving beyond Arabidopsis to illuminate the ancestral role of RdDM in non-flowering plants that lack an endosperm, suggesting that RdDM might play a broader role in sexual reproduction.
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Affiliation(s)
- Hiu Tung Chow
- The School of Plant Sciences, The University of Arizona, Tucson, AZ 85721, United States
| | - Tania Chakraborty
- The School of Plant Sciences, The University of Arizona, Tucson, AZ 85721, United States
| | - Rebecca A Mosher
- The School of Plant Sciences, The University of Arizona, Tucson, AZ 85721, United States.
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27
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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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28
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Montgomery SA, Tanizawa Y, Galik B, Wang N, Ito T, Mochizuki T, Akimcheva S, Bowman JL, Cognat V, Maréchal-Drouard L, Ekker H, Hong SF, Kohchi T, Lin SS, Liu LYD, Nakamura Y, Valeeva LR, Shakirov EV, Shippen DE, Wei WL, Yagura M, Yamaoka S, Yamato KT, Liu C, Berger F. Chromatin Organization in Early Land Plants Reveals an Ancestral Association between H3K27me3, Transposons, and Constitutive Heterochromatin. Curr Biol 2020; 30:573-588.e7. [PMID: 32004456 PMCID: PMC7209395 DOI: 10.1016/j.cub.2019.12.015] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/03/2019] [Accepted: 12/05/2019] [Indexed: 12/16/2022]
Abstract
Genome packaging by nucleosomes is a hallmark of eukaryotes. Histones and the pathways that deposit, remove, and read histone modifications are deeply conserved. Yet, we lack information regarding chromatin landscapes in extant representatives of ancestors of the main groups of eukaryotes, and our knowledge of the evolution of chromatin-related processes is limited. We used the bryophyte Marchantia polymorpha, which diverged from vascular plants circa 400 mya, to obtain a whole chromosome genome assembly and explore the chromatin landscape and three-dimensional genome organization in an early diverging land plant lineage. Based on genomic profiles of ten chromatin marks, we conclude that the relationship between active marks and gene expression is conserved across land plants. In contrast, we observed distinctive features of transposons and other repetitive sequences in Marchantia compared with flowering plants. Silenced transposons and repeats did not accumulate around centromeres. Although a large fraction of constitutive heterochromatin was marked by H3K9 methylation as in flowering plants, a significant proportion of transposons were marked by H3K27me3, which is otherwise dedicated to the transcriptional repression of protein-coding genes in flowering plants. Chromatin compartmentalization analyses of Hi-C data revealed that repressed B compartments were densely decorated with H3K27me3 but not H3K9 or DNA methylation as reported in flowering plants. We conclude that, in early plants, H3K27me3 played an essential role in heterochromatin function, suggesting an ancestral role of this mark in transposon silencing.
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Affiliation(s)
- Sean A Montgomery
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - Yasuhiro Tanizawa
- Department of Informatics, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Japan
| | - Bence Galik
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - Nan Wang
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany
| | - Tasuku Ito
- John Innes Centre, Colney lane, Norwich NR4 7UH, UK
| | - Takako Mochizuki
- Department of Informatics, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Japan
| | - Svetlana Akimcheva
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - John L Bowman
- School of Biological Sciences, Monash University, Melbourne, 3800 VIC, Australia
| | - Valérie Cognat
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
| | - Laurence Maréchal-Drouard
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
| | - Heinz Ekker
- Vienna BioCenter Core Facilities (VBCF), Next Generation Sequencing facility, Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - Syuan-Fei Hong
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Shih-Shun Lin
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan
| | - Li-Yu Daisy Liu
- Department of Agronomy, National Taiwan University, Taipei 106, Taiwan
| | - Yasukazu Nakamura
- Department of Informatics, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Japan
| | - Lia R Valeeva
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Republic of Tatarstan 420008, Russia
| | - Eugene V Shakirov
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Republic of Tatarstan 420008, Russia; Department of Biological Sciences, Marshall University, Huntington, WV 25701, USA
| | - Dorothy E Shippen
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843-2128, USA
| | - Wei-Lun Wei
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan
| | - Masaru Yagura
- Department of Informatics, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Japan
| | - Shohei Yamaoka
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Katsuyuki T Yamato
- Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa, Wakayama 649-6493, Japan
| | - Chang Liu
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany.
| | - Frédéric Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr Gasse 3, 1030 Vienna, Austria.
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Pu X, Yang L, Liu L, Dong X, Chen S, Chen Z, Liu G, Jia Y, Yuan W, Liu L. Genome-Wide Analysis of the MYB Transcription Factor Superfamily in Physcomitrella patens. Int J Mol Sci 2020; 21:ijms21030975. [PMID: 32024128 PMCID: PMC7037163 DOI: 10.3390/ijms21030975] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/25/2020] [Accepted: 01/28/2020] [Indexed: 01/19/2023] Open
Abstract
MYB transcription factors (TFs) are one of the largest TF families in plants to regulate numerous biological processes. However, our knowledge of the MYB family in Physcomitrella patens is limited. We identified 116 MYB genes in the P. patens genome, which were classified into the R2R3-MYB, R1R2R3-MYB, 4R-MYB, and MYB-related subfamilies. Most R2R3 genes contain 3 exons and 2 introns, whereas R1R2R3 MYB genes contain 10 exons and 9 introns. N3R-MYB (novel 3RMYB) and NR-MYBs (novel RMYBs) with complicated gene structures appear to be novel MYB proteins. In addition, we found that the diversity of the MYB domain was mainly contributed by domain shuffling and gene duplication. RNA-seq analysis suggested that MYBs exhibited differential expression to heat and might play important roles in heat stress responses, whereas CCA1-like MYB genes might confer greater flexibility to the circadian clock. Some R2R3-MYB and CCA1-like MYB genes are preferentially expressed in the archegonium and during the transition from the chloronema to caulonema stage, suggesting their roles in development. Compared with that of algae, the numbers of MYBs have significantly increased, thus our study lays the foundation for further exploring the potential roles of MYBs in the transition from aquatic to terrestrial environments.
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Affiliation(s)
- Xiaojun Pu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430000, China; (X.P.); (W.Y.)
- Key Laboratory for Economic Plants and Biotechnology, Germplasm Bank of Wild Species, National Wild Seed Resource Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (L.Y.); (L.L.); (X.D.); (S.C.); (Z.C.); (G.L.); (Y.J.)
| | - Lixin Yang
- Key Laboratory for Economic Plants and Biotechnology, Germplasm Bank of Wild Species, National Wild Seed Resource Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (L.Y.); (L.L.); (X.D.); (S.C.); (Z.C.); (G.L.); (Y.J.)
| | - Lina Liu
- Key Laboratory for Economic Plants and Biotechnology, Germplasm Bank of Wild Species, National Wild Seed Resource Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (L.Y.); (L.L.); (X.D.); (S.C.); (Z.C.); (G.L.); (Y.J.)
| | - Xiumei Dong
- Key Laboratory for Economic Plants and Biotechnology, Germplasm Bank of Wild Species, National Wild Seed Resource Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (L.Y.); (L.L.); (X.D.); (S.C.); (Z.C.); (G.L.); (Y.J.)
| | - Silin Chen
- Key Laboratory for Economic Plants and Biotechnology, Germplasm Bank of Wild Species, National Wild Seed Resource Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (L.Y.); (L.L.); (X.D.); (S.C.); (Z.C.); (G.L.); (Y.J.)
| | - Zexi Chen
- Key Laboratory for Economic Plants and Biotechnology, Germplasm Bank of Wild Species, National Wild Seed Resource Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (L.Y.); (L.L.); (X.D.); (S.C.); (Z.C.); (G.L.); (Y.J.)
| | - Gaojing Liu
- Key Laboratory for Economic Plants and Biotechnology, Germplasm Bank of Wild Species, National Wild Seed Resource Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (L.Y.); (L.L.); (X.D.); (S.C.); (Z.C.); (G.L.); (Y.J.)
| | - Yanxia Jia
- Key Laboratory for Economic Plants and Biotechnology, Germplasm Bank of Wild Species, National Wild Seed Resource Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (L.Y.); (L.L.); (X.D.); (S.C.); (Z.C.); (G.L.); (Y.J.)
| | - Wenya Yuan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430000, China; (X.P.); (W.Y.)
| | - Li Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430000, China; (X.P.); (W.Y.)
- Key Laboratory for Economic Plants and Biotechnology, Germplasm Bank of Wild Species, National Wild Seed Resource Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (L.Y.); (L.L.); (X.D.); (S.C.); (Z.C.); (G.L.); (Y.J.)
- Correspondence:
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30
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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: 15] [Impact Index Per Article: 3.8] [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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31
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Nakamura M, Köhler C, Hennig L. Tissue-specific transposon-associated small RNAs in the gymnosperm tree, Norway spruce. BMC Genomics 2019; 20:997. [PMID: 31856707 PMCID: PMC6923980 DOI: 10.1186/s12864-019-6385-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 12/11/2019] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Small RNAs (sRNAs) are regulatory molecules impacting on gene expression and transposon activity. MicroRNAs (miRNAs) are responsible for tissue-specific and environmentally-induced gene repression. Short interfering RNAs (siRNA) are constitutively involved in transposon silencing across different type of tissues. The male gametophyte in angiosperms has a unique set of sRNAs compared to vegetative tissues, including phased siRNAs from intergenic or genic regions, or epigenetically activated siRNAs. This is contrasted by a lack of knowledge about the sRNA profile of the male gametophyte of gymnosperms. RESULTS Here, we isolated mature pollen from male cones of Norway spruce and investigated its sRNA profiles. While 21-nt sRNAs is the major size class of sRNAs in needles, in pollen 21-nt and 24-nt sRNAs are the most abundant size classes. Although the 24-nt sRNAs were exclusively derived from TEs in pollen, both 21-nt and 24-nt sRNAs were associated with TEs. We also investigated sRNAs from somatic embryonic callus, which has been reported to contain 24-nt sRNAs. Our data show that the 24-nt sRNA profiles are tissue-specific and differ between pollen and cell culture. CONCLUSION Our data reveal that gymnosperm pollen, like angiosperm pollen, has a unique sRNA profile, differing from vegetative leaf tissue. Thus, our results reveal that angiosperm and gymnosperm pollen produce new size classes not present in vegetative tissues; while in angiosperm pollen 21-nt sRNAs are generated, in the gymnosperm Norway spruce 24-nt sRNAs are generated. The tissue-specific production of distinct TE-derived sRNAs in angiosperms and gymnosperms provides insights into the diversification process of sRNAs in TE silencing pathways between the two groups of seed plants.
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Affiliation(s)
- Miyuki Nakamura
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden.
| | - Claudia Köhler
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Lars Hennig
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
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Matyášek R, Krumpolcová A, Lunerová J, Mikulášková E, Rosselló JA, Kovařík A. Unique Epigenetic Features of Ribosomal RNA Genes (rDNA) in Early Diverging Plants (Bryophytes). FRONTIERS IN PLANT SCIENCE 2019; 10:1066. [PMID: 31543890 PMCID: PMC6739443 DOI: 10.3389/fpls.2019.01066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 08/06/2019] [Indexed: 05/03/2023]
Abstract
Introduction: In plants, the multicopy genes encoding ribosomal RNA (rDNA) typically exhibit heterochromatic features and high level of DNA methylation. Here, we explored rDNA methylation in early diverging land plants from Bryophyta (15 species, 14 families) and Marchantiophyta (4 species, 4 families). DNA methylation was investigated by methylation-sensitive Southern blot hybridization in all species. We also carried out whole genomic bisulfite sequencing in Polytrichum formosum (Polytrichaceae) and Dicranum scoparium (Dicranaceae) and used available model plant methyloms (Physcomitrella patents and Marchantia polymorpha) to determine rDNA unit-wide methylation patterns. Chromatin structure was analyzed using fluorescence in situ hybridization (FISH) and immunoprecipitation (CHIP) assays. Results: In contrast to seed plants, bryophyte rDNAs were efficiently digested with methylation-sensitive enzymes indicating no or low levels of CG and CHG methylation in these loci. The rDNA methylom analyses revealed variation between species ranging from negligible (<3%, P. formosum, P. patens) to moderate (7 and 17% in M. polymorpha and D. scoparium, respectively) methylation levels. There were no differences between coding and noncoding parts of rDNA units and between gametophyte and sporophyte tissues. However, major satellite repeat and transposable elements were heavily methylated in P. formosum and D. scoparium. In P. formosum rDNA, the euchromatic H3K4m3 and heterochromatic H3K9m2 histone marks were nearly balanced contrasting the angiosperms data where H3K9m2 typically dominates rDNA chromatin. In moss interphase nuclei, rDNA was localized at the nucleolar periphery and its condensation level was high. Conclusions: Unlike seed plants, the rRNA genes seem to escape global methylation machinery in bryophytes. Distinct epigenetic features may be related to rDNA expression and the physiology of these early diverging plants that exist in haploid state for most of their life cycles.
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Affiliation(s)
- Roman Matyášek
- Department of Molecular Epigenetics, Institute of Biophysics of the Czech Academy of Sciences, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czechia
| | - Alice Krumpolcová
- Department of Molecular Epigenetics, Institute of Biophysics of the Czech Academy of Sciences, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czechia
| | - Jana Lunerová
- Department of Molecular Epigenetics, Institute of Biophysics of the Czech Academy of Sciences, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czechia
| | - Eva Mikulášková
- Department of Botany and Zoology, Masaryk University, Brno, Czechia
| | - Josep A. Rosselló
- Jardín Botánico, ICBiBE-Unidad Asociada CSIC, Universidad de Valencia, Valencia, Spain
| | - Aleš Kovařík
- Department of Molecular Epigenetics, Institute of Biophysics of the Czech Academy of Sciences, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czechia
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33
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van Moorsel SJ, Schmid MW, Wagemaker NCAM, van Gurp T, Schmid B, Vergeer P. Evidence for rapid evolution in a grassland biodiversity experiment. Mol Ecol 2019; 28:4097-4117. [PMID: 31336411 DOI: 10.1111/mec.15191] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 07/18/2019] [Accepted: 07/18/2019] [Indexed: 12/14/2022]
Abstract
In long-term grassland experiments, positive biodiversity effects on plant productivity commonly increase with time. Subsequent glasshouse experiments showed that these strengthened positive biodiversity effects persist not only in the local environment but also when plants are transferred into a common environment. Thus, we hypothesized that community diversity had acted as a selective agent, resulting in the emergence of plant monoculture and mixture types with differing genetic composition. To test our hypothesis, we grew offspring from plants that were grown for eleven years in monoculture or mixture environments in a biodiversity experiment (Jena Experiment) under controlled glasshouse conditions in monocultures or two-species mixtures. We used epiGBS, a genotyping-by-sequencing approach combined with bisulphite conversion, to provide integrative genetic and epigenetic (i.e., DNA methylation) data. We observed significant divergence in genetic and DNA methylation data according to selection history in three out of five perennial grassland species, namely Galium mollugo, Prunella vulgaris and Veronica chamaedrys, with DNA methylation differences mostly reflecting the genetic differences. In addition, current diversity levels in the glasshouse had weak effects on epigenetic variation. However, given the limited genome coverage of the reference-free bisulphite method epiGBS, it remains unclear how much of the differences in DNA methylation was independent of underlying genetic differences. Our results thus suggest that selection of genetic variants, and possibly epigenetic variants, caused the rapid emergence of monoculture and mixture types within plant species in the Jena Experiment.
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Affiliation(s)
- Sofia J van Moorsel
- Department of Evolutionary Biology and Environmental Sciences, University of Zürich, Zürich, Switzerland
| | - Marc W Schmid
- Department of Evolutionary Biology and Environmental Sciences, University of Zürich, Zürich, Switzerland.,MWSchmid GmbH, Zürich, Switzerland
| | - Niels C A M Wagemaker
- Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands
| | | | - Bernhard Schmid
- Department of Evolutionary Biology and Environmental Sciences, University of Zürich, Zürich, Switzerland.,Department of Geography, University of Zürich, Zürich, Switzerland
| | - Philippine Vergeer
- Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands.,Department of Environmental Sciences, Plant Ecology and Nature Conservation Group, Wageningen University, Wageningen, The Netherlands
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34
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Sun RZ, Zuo EH, Qi JF, Liu Y, Lin CT, Deng X. A role of age-dependent DNA methylation reprogramming in regulating the regeneration capacity of Boea hygrometrica leaves. Funct Integr Genomics 2019; 20:133-149. [PMID: 31414312 DOI: 10.1007/s10142-019-00701-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 06/09/2019] [Accepted: 07/15/2019] [Indexed: 11/30/2022]
Abstract
Plants can regenerate new individuals under appropriate culture conditions. Although the molecular basis of shoot regeneration has steadily been unraveled, the role of age-dependent DNA methylation status in the regulation of explant regeneration remains practically unknown. Here, we established an effective auxin/cytokinin-induced shoot regeneration system for the resurrection plant Boea hygrometrica via direct organogenesis and observed that regeneration was postponed with increasing age of donor plants. Global transcriptome analysis revealed significant upregulation of genes required for hormone signaling and phenylpropanoid biosynthesis and downregulation of photosynthetic genes during regeneration. Transcriptional changes in the positive/negative regulators and cell wall-related proteins involved in plant regeneration, such as ELONGATED HYPOCOTYL5 (HY5), LATERAL ORGAN BOUNDARIES DOMAIN, SHOOT-MERISTEMLESS, and WUSCHEL, were associated with the regeneration process. Comparison of DNA methylation profiling between leaves from young seedlings (YL) and mature plants (ML) revealed increased asymmetrical methylation in ML, which was predominantly distributed in promoter regions of genes, such as HY5 and a member of ABA-responsive element (ABRE) binding protein/ABRE binding factor, as well as genes encoding glycine-rich cell wall structural protein, CENTRORADIALIS-like protein, and beta-glucosidase 40-like essential for shoot meristem and cell wall architecture. Their opposite transcription response in ML explants during regeneration compared with those from YL demonstrated the putative involvement of DNA methylation in regeneration. Moreover, a significant lower expression of DNA glycosylase-lyase required for DNA demethylation in ML was coincident with its postponed regeneration compared with those in YL. Taken together, our results suggest a role of promoter demethylation in B. hygrometrica regeneration.
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Affiliation(s)
- Run-Ze Sun
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - En-Hui Zuo
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jin-Feng Qi
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yang Liu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Chih-Ta Lin
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xin Deng
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
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35
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Hisanaga T, Yamaoka S, Kawashima T, Higo A, Nakajima K, Araki T, Kohchi T, Berger F. Building new insights in plant gametogenesis from an evolutionary perspective. NATURE PLANTS 2019; 5:663-669. [PMID: 31285561 DOI: 10.1038/s41477-019-0466-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 05/29/2019] [Indexed: 05/18/2023]
Abstract
Extant bryophytes are thought to preserve characteristics of ancestral land plants, with a life cycle dominated by the haploid gametophyte. The gametophyte produces gametes in specialized organs that differentiate after an extensive phase of vegetative development. During land plant evolution, these organs became extremely reduced. As a result, in flowers of angiosperms the haploid phase of the life cycle is reduced to few-celled gametophytes, namely the embryo sac (female) and pollen (male). Although many factors contributing to gametogenesis have been identified in flowering plants, the extreme reduction of the gametophytes has prevented a clear molecular dissection of key processes of gametogenesis. Recent studies in the model bryophyte Marchantia polymorpha have identified conserved transcription factors regulating the equivalent steps in the sexual reproduction of land plants. These include FEMALE GAMETOPHYTE MYB for female gametophyte development, BONOBO for gamete progenitor cell specification, DUO POLLEN1 for sperm differentiation and members of the RWP-RK domain family for female gamete formation. These studies demonstrate that M. polymorpha is a powerful model to untangle the core processes of gametogenesis in land plants. We anticipate that a deeper understanding of gametogenesis in bryophytes will circumscribe the origin of plant germ cells and define the differentiation programmes of sperm and eggs.
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Affiliation(s)
- Tetsuya Hisanaga
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Shohei Yamaoka
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Tomokazu Kawashima
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, USA
| | - Asuka Higo
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Keiji Nakajima
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Takashi Araki
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria.
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36
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Aguilar-Cruz A, Grimanelli D, Haseloff J, Arteaga-Vázquez MA. DNA methylation in Marchantia polymorpha. THE NEW PHYTOLOGIST 2019; 223:575-581. [PMID: 30920664 DOI: 10.1111/nph.15818] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 03/13/2019] [Indexed: 06/09/2023]
Abstract
Methylation of DNA is an epigenetic mechanism for the control of gene expression. Alterations in the regulatory pathways involved in the establishment, perpetuation and removal of DNA methylation can lead to severe developmental alterations. Our understanding of the mechanistic aspects and relevance of DNA methylation comes from remarkable studies in well-established angiosperm plant models including maize and Arabidopsis. The study of plant models positioned at basal lineages opens exciting opportunities to expand our knowledge on the function and evolution of the components of DNA methylation. In this Tansley Insight, we summarize current progress in our understanding of the molecular basis and relevance of DNA methylation in the liverwort Marchantia polymorpha.
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Affiliation(s)
- Adolfo Aguilar-Cruz
- Instituto de Biotecnología y Ecología Aplicada, Universidad Veracruzana, Avenida de las Culturas Veracruzanas 101, Col. Emiliano Zapata, C.P. 91090, Xalapa, Veracruz, México
| | - Daniel Grimanelli
- Institut de Recherche pour le Développement (IRD), UMR232, Université de Montpellier, Montpellier, 34394, France
| | - Jim Haseloff
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Mario Alberto Arteaga-Vázquez
- Instituto de Biotecnología y Ecología Aplicada, Universidad Veracruzana, Avenida de las Culturas Veracruzanas 101, Col. Emiliano Zapata, C.P. 91090, Xalapa, Veracruz, México
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37
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RdDM-independent de novo and heterochromatin DNA methylation by plant CMT and DNMT3 orthologs. Nat Commun 2019; 10:1613. [PMID: 30962443 PMCID: PMC6453930 DOI: 10.1038/s41467-019-09496-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Accepted: 03/13/2019] [Indexed: 12/31/2022] Open
Abstract
To properly regulate the genome, cytosine methylation is established by animal DNA methyltransferase 3 s (DNMT3s). While altered DNMT3 homologs, Domains rearranged methyltransferases (DRMs), have been shown to establish methylation via the RNA directed DNA methylation (RdDM) pathway, the role of true-plant DNMT3 orthologs remains elusive. Here, we profile de novo (RPS transgene) and genomic methylation in the basal plant, Physcomitrella patens, mutated in each of its PpDNMTs. We show that PpDNMT3b mediates CG and CHH de novo methylation, independently of PpDRMs. Complementary de novo CHG methylation is specifically mediated by the CHROMOMETHYLASE, PpCMT. Intragenomically, PpDNMT3b functions preferentially within heterochromatin and is affected by PpCMT. In comparison, PpDRMs target active-euchromatic transposons. Overall, our data resolve how DNA methylation in plants can be established in heterochromatin independently of RdDM; suggest that DRMs have emerged to target euchromatin; and link DNMT3 loss in angiosperms to the initiation of heterochromatic CHH methylation by CMT2. Whether plants have true DNMT3 orthologs and their role in establishing DNA methylation are still unclear. Here, the authors show that DNMT3s are persistent through plant evolution and mediates both de novo and heterochromatin DNA methylation in the early divergent land plant Physcomitrella patens.
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38
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Schmid MW, Heichinger C, Coman Schmid D, Guthörl D, Gagliardini V, Bruggmann R, Aluri S, Aquino C, Schmid B, Turnbull LA, Grossniklaus U. Contribution of epigenetic variation to adaptation in Arabidopsis. Nat Commun 2018; 9:4446. [PMID: 30361538 PMCID: PMC6202389 DOI: 10.1038/s41467-018-06932-5] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 10/05/2018] [Indexed: 12/20/2022] Open
Abstract
In plants, transgenerational inheritance of some epialleles has been demonstrated but it remains controversial whether epigenetic variation is subject to selection and contributes to adaptation. Simulating selection in a rapidly changing environment, we compare phenotypic traits and epigenetic variation between Arabidopsis thaliana populations grown for five generations under selection and their genetically nearly identical ancestors. Selected populations of two distinct genotypes show significant differences in flowering time and plant architecture, which are maintained for at least 2–3 generations in the absence of selection. While we cannot detect consistent genetic changes, we observe a reduction of epigenetic diversity and changes in the methylation state of about 50,000 cytosines, some of which are associated with phenotypic changes. Thus, we propose that epigenetic variation is subject to selection and can contribute to rapid adaptive responses, although the extent to which epigenetics plays a role in adaptation is still unclear. Whether plant epigenetic variation is subject to selection and contributes to adaptation is under debate. Here, the authors compare DNA methylation and phenotypes of Arabidopsis lines subject to simulated selection and their nearly isogenic ancestors and provide evidence that epigenetic variation contributes to adaptive responses.
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Affiliation(s)
- Marc W Schmid
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland.,Zurich-Basel Plant Science Center, University of Zurich, ETH Zurich and University of Basel, Tannenstrasse 1, 8092, Zurich, Switzerland.,Service and Support for Science IT, University of Zurich, Stampfenbachstrasse 73, 8006, Zurich, Switzerland.,MWSchmid GmbH, Möhrlistrasse 25, 8006, Zurich, Switzerland
| | - Christian Heichinger
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland.,Zurich-Basel Plant Science Center, University of Zurich, ETH Zurich and University of Basel, Tannenstrasse 1, 8092, Zurich, Switzerland.,L. Hoffmann-La Roche AG, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Diana Coman Schmid
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland.,Zurich-Basel Plant Science Center, University of Zurich, ETH Zurich and University of Basel, Tannenstrasse 1, 8092, Zurich, Switzerland.,Scientific IT Services, ETH Zurich, Weinbergstrasse 11, 8092, Zurich, Switzerland
| | - Daniela Guthörl
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland.,Zurich-Basel Plant Science Center, University of Zurich, ETH Zurich and University of Basel, Tannenstrasse 1, 8092, Zurich, Switzerland
| | - Valeria Gagliardini
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland.,Zurich-Basel Plant Science Center, University of Zurich, ETH Zurich and University of Basel, Tannenstrasse 1, 8092, Zurich, Switzerland
| | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Hochschulstrasse 6, 3012, Bern, Switzerland
| | - Sirisha Aluri
- Functional Genomics Center Zurich, ETH and University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Catharine Aquino
- Functional Genomics Center Zurich, ETH and University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Bernhard Schmid
- Zurich-Basel Plant Science Center, University of Zurich, ETH Zurich and University of Basel, Tannenstrasse 1, 8092, Zurich, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Lindsay A Turnbull
- Zurich-Basel Plant Science Center, University of Zurich, ETH Zurich and University of Basel, Tannenstrasse 1, 8092, Zurich, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.,Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland. .,Zurich-Basel Plant Science Center, University of Zurich, ETH Zurich and University of Basel, Tannenstrasse 1, 8092, Zurich, Switzerland.
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39
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Schmid MW, Giraldo-Fonseca A, Rövekamp M, Smetanin D, Bowman JL, Grossniklaus U. Extensive epigenetic reprogramming during the life cycle of Marchantia polymorpha. Genome Biol 2018; 19:9. [PMID: 29368664 PMCID: PMC5784723 DOI: 10.1186/s13059-017-1383-z] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 12/21/2017] [Indexed: 12/19/2022] Open
Abstract
Background In plants, the existence and possible role of epigenetic reprogramming has been questioned because of the occurrence of stably inherited epialleles. Evidence suggests that epigenetic reprogramming does occur during land plant reproduction, but there is little consensus on the generality and extent of epigenetic reprogramming in plants. We studied DNA methylation dynamics during the life cycle of the liverwort Marchantia polymorpha. We isolated thalli and meristems from male and female gametophytes, archegonia, antherozoids, as well as sporophytes at early and late developmental stages, and compared their DNA methylation profiles. Results Of all cytosines tested for differential DNA methylation, 42% vary significantly in their methylation pattern throughout the life cycle. However, the differences are limited to few comparisons between specific stages of the life cycle and suggest four major epigenetic states specific to sporophytes, vegetative gametophytes, antherozoids, and archegonia. Further analyses indicated clear differences in the mechanisms underlying reprogramming in the gametophytic and sporophytic generations, which are paralleled by differences in the expression of genes involved in DNA methylation. Differentially methylated cytosines with a gain in methylation in antherozoids and archegonia are enriched in the CG and CHG contexts, as well as in gene bodies and gene flanking regions. In contrast, gain of DNA methylation during sporophyte development is mostly limited to the CHH context, LTR retrotransposons, DNA transposons, and repeats. Conclusion We conclude that epigenetic reprogramming occurs at least twice during the life cycle of M. polymorpha and that the underlying mechanisms are likely different between the two events. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1383-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marc W Schmid
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Alejandro Giraldo-Fonseca
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Moritz Rövekamp
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Dmitry Smetanin
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - John L Bowman
- Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland.
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40
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Bräutigam K, Cronk Q. DNA Methylation and the Evolution of Developmental Complexity in Plants. FRONTIERS IN PLANT SCIENCE 2018; 9:1447. [PMID: 30349550 PMCID: PMC6186995 DOI: 10.3389/fpls.2018.01447] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 09/12/2018] [Indexed: 05/20/2023]
Abstract
All land plants so far examined use DNA methylation to silence transposons (TEs). DNA methylation therefore appears to have been co-opted in evolution from an original function in TE management to a developmental function (gene regulation) in both phenotypic plasticity and in normal development. The significance of DNA methylation to the evolution of developmental complexity in plants lies in its role in the management of developmental pathways. As such it is more important in fine tuning the presence, absence, and placement of organs rather than having a central role in the evolution of new organs. Nevertheless, its importance should not be underestimated as it contributes considerably to the range of phenotypic expression and complexity available to plants: the subject of the emerging field of epi-evodevo. Furthermore, changes in DNA methylation can function as a "soft" mutation that may be important in the early stages of major evolutionary novelty.
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Affiliation(s)
- Katharina Bräutigam
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Quentin Cronk
- Department of Botany, The University of British Columbia, Vancouver, BC, Canada
- *Correspondence: Quentin Cronk,
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