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Wambui Mbichi R, Wang QF, Wan T. RNA directed DNA methylation and seed plant genome evolution. PLANT CELL REPORTS 2020; 39:983-996. [PMID: 32594202 DOI: 10.1007/s00299-] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/08/2020] [Indexed: 05/28/2023]
Abstract
RNA Directed DNA Methylation (RdDM) is a pathway that mediates de novo DNA methylation, an evolutionary conserved chemical modification of cytosine bases, which exists in living organisms and utilizes small interfering RNA. Plants utilize DNA methylation for transposable element (TE) repression, regulation of gene expression and developmental regulation. TE activity strongly influences genome size and evolution, therefore making DNA methylation a key component in understanding divergence in genome evolution among seed plants. Multiple proteins that have extensively been studied in model plant Arabidopsis thaliana catalyze RNA dependent DNA Methylation pathway along with small interfering RNA. Several developmental functions have also been attributed to DNA methylation. This review will highlight aspects of RdDM pathway dynamics, evolution and functions in seed plants with focus on recent findings on conserved and non-conserved attributes between angiosperms and gymnosperms to potentially explain how methylation has impacted variations in evolutionary and developmental complexity among them and advance current understanding of this crucial epigenetic pathway.
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Affiliation(s)
- R Wambui Mbichi
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan, Hubei, 430074, China
- Key laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qing-Feng Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan, Hubei, 430074, China.
- Sino-Africa Joint Research Center, Chinese Academy of Science, Wuhan, 430074, China.
- Center of Conservation Biology, Core Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
| | - Tao Wan
- Key laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China.
- Sino-Africa Joint Research Center, Chinese Academy of Science, Wuhan, 430074, China.
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52
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Wambui Mbichi R, Wang QF, Wan T. RNA directed DNA methylation and seed plant genome evolution. PLANT CELL REPORTS 2020; 39:983-996. [PMID: 32594202 PMCID: PMC7359171 DOI: 10.1007/s00299-020-02558-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/08/2020] [Indexed: 05/11/2023]
Abstract
RNA Directed DNA Methylation (RdDM) is a pathway that mediates de novo DNA methylation, an evolutionary conserved chemical modification of cytosine bases, which exists in living organisms and utilizes small interfering RNA. Plants utilize DNA methylation for transposable element (TE) repression, regulation of gene expression and developmental regulation. TE activity strongly influences genome size and evolution, therefore making DNA methylation a key component in understanding divergence in genome evolution among seed plants. Multiple proteins that have extensively been studied in model plant Arabidopsis thaliana catalyze RNA dependent DNA Methylation pathway along with small interfering RNA. Several developmental functions have also been attributed to DNA methylation. This review will highlight aspects of RdDM pathway dynamics, evolution and functions in seed plants with focus on recent findings on conserved and non-conserved attributes between angiosperms and gymnosperms to potentially explain how methylation has impacted variations in evolutionary and developmental complexity among them and advance current understanding of this crucial epigenetic pathway.
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Affiliation(s)
- R Wambui Mbichi
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan, Hubei, 430074, China
- Key laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qing-Feng Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan, Hubei, 430074, China.
- Sino-Africa Joint Research Center, Chinese Academy of Science, Wuhan, 430074, China.
- Center of Conservation Biology, Core Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
| | - Tao Wan
- Key laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China.
- Sino-Africa Joint Research Center, Chinese Academy of Science, Wuhan, 430074, China.
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53
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Williams BP, Gehring M. Principles of Epigenetic Homeostasis Shared Between Flowering Plants and Mammals. Trends Genet 2020; 36:751-763. [PMID: 32711945 DOI: 10.1016/j.tig.2020.06.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/30/2020] [Accepted: 06/30/2020] [Indexed: 12/18/2022]
Abstract
In diverse eukaryotes, epigenetic information such as DNA methylation is stably propagated over many cell divisions and generations, and can remain the same over thousands or millions of years. However, this stability is the product of dynamic processes that add and remove DNA methylation by specialized enzymatic pathways. The activities of these dynamic pathways must therefore be finely orchestrated in order to ensure that the DNA methylation landscape is maintained with high fidelity - a concept we term epigenetic homeostasis. In this review, we summarize recent insights into epigenetic homeostasis mechanisms in flowering plants and mammals, highlighting analogous mechanisms that have independently evolved to achieve the same goal of stabilizing the epigenetic landscape.
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Affiliation(s)
- Ben P Williams
- Whitehead Institute for Biomedical Research, 455 Main St, Cambridge, MA 02142, USA.
| | - Mary Gehring
- Whitehead Institute for Biomedical Research, 455 Main St, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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54
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Kreutz C, Can NS, Bruening RS, Meyberg R, Mérai Z, Fernandez-Pozo N, Rensing SA. A blind and independent benchmark study for detecting differeally methylated regions in plants. Bioinformatics 2020; 36:3314-3321. [PMID: 32181821 DOI: 10.1093/bioinformatics/btaa191] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 01/31/2020] [Accepted: 03/13/2020] [Indexed: 01/03/2023] Open
Abstract
MOTIVATION Bisulfite sequencing (BS-seq) is a state-of-the-art technique for investigating methylation of the DNA to gain insights into the epigenetic regulation. Several algorithms have been published for identification of differentially methylated regions (DMRs). However, the performances of the individual methods remain unclear and it is difficult to optimally select an algorithm in application settings. RESULTS We analyzed BS-seq data from four plants covering three taxonomic groups. We first characterized the data using multiple summary statistics describing methylation levels, coverage, noise, as well as frequencies, magnitudes and lengths of methylated regions. Then, simulated datasets with most similar characteristics to real experimental data were created. Seven different algorithms (metilene, methylKit, MOABS, DMRcate, Defiant, BSmooth, MethylSig) for DMR identification were applied and their performances were assessed. A blind and independent study design was chosen to reduce bias and to derive practical method selection guidelines. Overall, metilene had superior performance in most settings. Data attributes, such as coverage and spread of the DMR lengths, were found to be useful for selecting the best method for DMR detection. A decision tree to select the optimal approach based on these data attributes is provided. The presented procedure might serve as a general strategy for deriving algorithm selection rules tailored to demands in specific application settings. AVAILABILITY AND IMPLEMENTATION Scripts that were used for the analyses and that can be used for prediction of the optimal algorithm are provided at https://github.com/kreutz-lab/DMR-DecisionTree. Simulated and experimental data are available at https://doi.org/10.6084/m9.figshare.11619045. CONTACT ckreutz@imbi.uni-freiburg.de. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Clemens Kreutz
- Faculty of Medicine and Medical Center, Institute of Medical Biometry and Statistics, University of Freiburg, 79104 Freiburg, Germany
- Centre for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, 79104 Freiburg, Germany
| | - Nilay S Can
- Plant Cell Biology, Faculty of Biology, University of Marburg, 35043 Marburg, Germany
| | - Ralf Schulze Bruening
- Plant Cell Biology, Faculty of Biology, University of Marburg, 35043 Marburg, Germany
| | - Rabea Meyberg
- Plant Cell Biology, Faculty of Biology, University of Marburg, 35043 Marburg, Germany
| | - Zsuzsanna Mérai
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Noe Fernandez-Pozo
- Plant Cell Biology, Faculty of Biology, University of Marburg, 35043 Marburg, Germany
| | - Stefan A Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, 35043 Marburg, Germany
- Centre for Biological Signaling Studies (BIOSS), University of Freiburg, 79104 Freiburg, Germany
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55
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Zhang M, Li W, Feng J, Gong Z, Yao Y, Zheng C. Integrative transcriptomics and proteomics analysis constructs a new molecular model for ovule abortion in the female-sterile line of Pinus tabuliformis Carr. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 294:110462. [PMID: 32234230 DOI: 10.1016/j.plantsci.2020.110462] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 02/26/2020] [Accepted: 02/28/2020] [Indexed: 06/11/2023]
Abstract
Ovule development is critical to plant reproduction and free nuclear mitosis of megagametophyte (FNMM) is vital for ovule development. However, most results of ovule development were based on the studies in angiosperms, and its molecular regulation remained largely unknown in gymnosperms, particularly, during FNMM. In this context, we studied the genome-wide difference between sterile line (SL) and fertile line (FL) ovules using transcriptomics and proteomics approaches in Pinus tabuliformis Carr. Comparative analyses revealed that genes involved in DNA replication, DNA damage repair, Cell cycle, Apoptosis and Energy metabolism were highlighted. Further results showed the low expressions of MCM 2-7, RRM1, etc. perhaps led to abnormal DNA replication and damage repair, and the significantly different expressions of PARP2, CCs1, CCs3, etc. implied that the accumulated DNA double-stranded breaks were failed to be repaired and the cell cycle was arrested at G2/M in SL ovules, potentially resulting in the occurrence of apoptosis. Moreover, the deficiency of ETF-QO might hinder FNMM. Consequently, FNMM stopped and ovule aborted in SL ovules. Our results suggested a selective regulatory mechanism led to FNMM half-stop and ovule abortion in P. tabuliformis and these insights could be exploited to investigate the molecular regulations of ovule development in woody gymnosperms.
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Affiliation(s)
- Min Zhang
- College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Tsinghua East Road, Beijing, 100083, China
| | - Wenhai Li
- College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Tsinghua East Road, Beijing, 100083, China
| | - Jun Feng
- College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Tsinghua East Road, Beijing, 100083, China
| | - Zaixin Gong
- College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Tsinghua East Road, Beijing, 100083, China
| | - Yang Yao
- College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Tsinghua East Road, Beijing, 100083, China
| | - Caixia Zheng
- College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Tsinghua East Road, Beijing, 100083, China.
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56
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Wang Z, Baulcombe DC. Transposon age and non-CG methylation. Nat Commun 2020; 11:1221. [PMID: 32144266 PMCID: PMC7060349 DOI: 10.1038/s41467-020-14995-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 02/11/2020] [Indexed: 11/09/2022] Open
Abstract
Silencing of transposable elements (TEs) is established by small RNA-directed DNA methylation (RdDM). Maintenance of silencing is then based on a combination of RdDM and RNA-independent mechanisms involving DNA methyltransferase MET1 and chromodomain DNA methyltransferases (CMTs). Involvement of RdDM, according to this model should decrease with TE age but here we show a different pattern in tomato and Arabidopsis. In these species the CMTs silence long terminal repeat (LTR) transposons in the distal chromatin that are younger than those affected by RdDM. To account for these findings we propose that, after establishment of primary RdDM as in the original model, there is an RNA-independent maintenance phase involving CMTs followed by secondary RdDM. This progression of epigenetic silencing in the gene-rich distal chromatin is likely to influence the transcriptome either in cis or in trans depending on whether the mechanisms are RNA-dependent or -independent. RNA-directed DNA methylation (RdDM) is thought to silence newly inserted transposable elements (TEs) with RNA-independent mechanisms becoming more prominent as TEs age. Here, the authors show that RdDM continues to silence the oldest intact distal TEs in tomato and Arabidopsis suggesting a second, later phase of RdDM.
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Affiliation(s)
- Zhengming Wang
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - David C Baulcombe
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK.
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57
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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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58
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Natural variation in DNA methylation homeostasis and the emergence of epialleles. Proc Natl Acad Sci U S A 2020; 117:4874-4884. [PMID: 32071208 DOI: 10.1073/pnas.1918172117] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In plants and mammals, DNA methylation plays a critical role in transcriptional silencing by delineating heterochromatin from transcriptionally active euchromatin. A homeostatic balance between heterochromatin and euchromatin is essential to genomic stability. This is evident in many diseases and mutants for heterochromatin maintenance, which are characterized by global losses of DNA methylation coupled with localized ectopic gains of DNA methylation that alter transcription. Furthermore, we have shown that genome-wide methylation patterns in Arabidopsis thaliana are highly stable over generations, with the exception of rare epialleles. However, the extent to which natural variation in the robustness of targeting DNA methylation to heterochromatin exists, and the phenotypic consequences of such variation, remain to be fully explored. Here we describe the finding that heterochromatin and genic DNA methylation are highly variable among 725 A. thaliana accessions. We found that genic DNA methylation is inversely correlated with that in heterochromatin, suggesting that certain methylation pathway(s) may be redirected to genes upon the loss of heterochromatin. This redistribution likely involves a feedback loop involving the DNA methyltransferase, CHROMOMETHYLASE 3 (CMT3), H3K9me2, and histone turnover, as highly expressed, long genes with a high density of CMT3-preferred CWG sites are more likely to be methylated. Importantly, although the presence of CG methylation in genes alone may not affect transcription, genes containing CG methylation are more likely to become methylated at non-CG sites and silenced. These findings are consistent with the hypothesis that natural variation in DNA methylation homeostasis may underlie the evolution of epialleles that alter phenotypes.
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59
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Zhu C, Zhang S, Zhou C, Chen L, Fu H, Li X, Lin Y, Lai Z, Guo Y. Genome-wide investigation and transcriptional analysis of cytosine-5 DNA methyltransferase and DNA demethylase gene families in tea plant ( Camellia sinensis) under abiotic stress and withering processing. PeerJ 2020; 8:e8432. [PMID: 31976183 PMCID: PMC6968495 DOI: 10.7717/peerj.8432] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 12/19/2019] [Indexed: 12/11/2022] Open
Abstract
DNA methylation is a highly conserved epigenetic modification involved in many biological processes, including growth and development, stress response, and secondary metabolism. In the plant kingdom, cytosine-5 DNA methyltransferase (C5-MTase) and DNA demethylase (dMTase) genes have been identified in some plant species. However, to the best of our knowledge, no investigator has focused on the identification and analysis of C5-MTase and dMTase genes in tea plants (Camellia sinensis) based on genome-wide levels. In this study, eight CsC5-MTases and four dMTases were identified in tea plants. These CsC5-MTase genes were divided into four subfamilies, including CsMET, CsCMT, CsDRM and CsDNMT2. The CsdMTase genes can be classified into CsROS, CsDME and CsDML. Based on conserved domain analysis of these genes, the gene loss and duplication events occurred during the evolution of CsC5-MTase and CsdMTase. Furthermore, multiple cis-acting elements were observed in the CsC5-MTase and CsdMTase, including light responsiveness, phytohormone responsiveness, stress responsiveness, and plant growth and development-related elements. Then, we investigated the transcript abundance of CsC5-MTase and CsdMTase under abiotic stress (cold and drought) and withering processing (white tea and oolong tea). Notably, most CsC5-MTases, except for CsCMT1 and CsCMT2, were significantly downregulated under abiotic stress, while the transcript abundance of all four CsdMTase genes was significantly induced. Similarly, the same transcript abundance of CsC5-MTase and CsdMTase was found during withering processing of white tea and oolong tea, respectively. In total, our findings will provide a basis for the roles of CsC5-MTase and CsdMTase in response to abiotic stress and the potential functions of these two gene families in affecting tea flavor during tea withering processing.
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Affiliation(s)
- Chen Zhu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.,Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Shuting Zhang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.,Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Chengzhe Zhou
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Lan Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Haifeng Fu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Xiaozhen Li
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yuling Lin
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.,Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Zhongxiong Lai
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.,Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yuqiong Guo
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
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60
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Grimanelli D, Ingouff M. DNA Methylation Readers in Plants. J Mol Biol 2020:S0022-2836(20)30027-9. [PMID: 31931004 DOI: 10.1016/j.jmb.2019.12.043] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 12/13/2019] [Accepted: 12/17/2019] [Indexed: 01/09/2023]
Abstract
In plants, DNA methylation occurs in distinct sequence contexts, including CG, CHG, and CHH. Thus, plants have developed a surprisingly diverse set of DNA methylation readers to cope with an extended repertoire of methylated sites. The Arabidopsis genome contains twelve Methyl-Binding Domain proteins (MBD), and nine SET and RING finger-associated (SRA) domain containing proteins belonging to the SUVH clade, in addition to three homologs of UHRF1, namely VIM1-3, all containing SRA domains. In this review, we will highlight several research questions that remain unresolved with respect to the function of plant DNA methylation readers, which can have both de novo demethylase and maintenance activity. We argue that maintenance of CG methylation in plants likely involved actors not found in their mammalian counterparts, and that new evidence suggests significant reprogramming of DNA methylation during plant reproduction as an important new development in the field.
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Affiliation(s)
- Daniel Grimanelli
- Institut de Recherche pour le Développement (IRD), Université de Montpellier, 911 Avenue Agropolis, 34394, Montpellier, France.
| | - Mathieu Ingouff
- Institut de Recherche pour le Développement (IRD), Université de Montpellier, 911 Avenue Agropolis, 34394, Montpellier, France.
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61
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Liang Z, Geng Y, Ji C, Du H, Wong CE, Zhang Q, Zhang Y, Zhang P, Riaz A, Chachar S, Ding Y, Wen J, Wu Y, Wang M, Zheng H, Wu Y, Demko V, Shen L, Han X, Zhang P, Gu X, Yu H. Mesostigma viride Genome and Transcriptome Provide Insights into the Origin and Evolution of Streptophyta. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:1901850. [PMID: 31921561 PMCID: PMC6947507 DOI: 10.1002/advs.201901850] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 10/10/2019] [Indexed: 05/02/2023]
Abstract
The Streptophyta include unicellular and multicellular charophyte green algae and land plants. Colonization of the terrestrial habitat by land plants is a major evolutionary event that has transformed the planet. So far, lack of genome information on unicellular charophyte algae hinders the understanding of the origin and the evolution from unicellular to multicellular life in Streptophyta. This work reports the high-quality reference genome and transcriptome of Mesostigma viride, a single-celled charophyte alga with a position at the base of Streptophyta. There are abundant segmental duplications and transposable elements in M. viride, which contribute to a relatively large genome with high gene content compared to other algae and early diverging land plants. This work identifies the origin of genetic tools that multicellular Streptophyta have inherited and key genetic innovations required for the evolution of land plants from unicellular aquatic ancestors. The findings shed light on the age-old questions of the evolution of multicellularity and the origin of land plants.
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Affiliation(s)
- Zhe Liang
- Department of Biological SciencesNational University of SingaporeSingapore117543Singapore
| | - Yuke Geng
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
| | - Changmian Ji
- Biomarker TechnologiesBeijing101300China
- Institute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikou571101China
| | - Hai Du
- College of Agronomy and BiotechnologySouthwest UniversityChongqing400715China
| | - Chui Eng Wong
- Department of Biological SciencesNational University of SingaporeSingapore117543Singapore
| | - Qian Zhang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
| | - Ye Zhang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
| | - Pingxian Zhang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
| | - Adeel Riaz
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
| | - Sadaruddin Chachar
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
| | - Yike Ding
- Department of EntomologyUniversity of California RiversideRiversideCA92521USA
| | - Jing Wen
- College of Agronomy and BiotechnologySouthwest UniversityChongqing400715China
| | - Yunwen Wu
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
- College of Agronomy and BiotechnologySouthwest UniversityChongqing400715China
| | | | | | - Yanmin Wu
- College of Agronomy and BiotechnologySouthwest UniversityChongqing400715China
| | - Viktor Demko
- Department of Plant PhysiologyFaculty of Natural SciencesComenius University in BratislavaBratislava84215Slovakia
| | - Lisha Shen
- Temasek Life Sciences LaboratoryNational University of SingaporeSingapore117604Singapore
| | - Xiao Han
- College of Biological Science and EngineeringFuzhou UniversityFuzhou350108China
| | - Pengpeng Zhang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
| | - Xiaofeng Gu
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
| | - Hao Yu
- Department of Biological SciencesNational University of SingaporeSingapore117543Singapore
- Temasek Life Sciences LaboratoryNational University of SingaporeSingapore117604Singapore
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Kenchanmane Raju SK, Ritter EJ, Niederhuth CE. Establishment, maintenance, and biological roles of non-CG methylation in plants. Essays Biochem 2019; 63:743-755. [PMID: 31652316 PMCID: PMC6923318 DOI: 10.1042/ebc20190032] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/18/2019] [Accepted: 09/20/2019] [Indexed: 12/18/2022]
Abstract
Cytosine DNA methylation is prevalent throughout eukaryotes and prokaryotes. While most commonly thought of as being localized to dinucleotide CpG sites, non-CG sites can also be modified. Such non-CG methylation is widespread in plants, occurring at trinucleotide CHG and CHH (H = A, T, or C) sequence contexts. The prevalence of non-CG methylation in plants is due to the plant-specific CHROMOMETHYLASE (CMT) and RNA-directed DNA Methylation (RdDM) pathways. These pathways have evolved through multiple rounds of gene duplication and gene loss, generating epigenomic variation both within and between species. They regulate both transposable elements and genes, ensure genome integrity, and ultimately influence development and environmental responses. In these capacities, non-CG methylation influence and shape plant genomes.
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Affiliation(s)
| | | | - Chad E Niederhuth
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, U.S.A
- AgBioResearch, Michigan State University, East Lansing, MI 48824, U.S.A
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63
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de Mendoza A, Lister R, Bogdanovic O. Evolution of DNA Methylome Diversity in Eukaryotes. J Mol Biol 2019:S0022-2836(19)30659-X. [PMID: 31726061 DOI: 10.1016/j.jmb.2019.11.003] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/03/2019] [Accepted: 11/04/2019] [Indexed: 12/23/2022]
Abstract
Cytosine DNA methylation (5mC) is a widespread base modification in eukaryotic genomes with critical roles in transcriptional regulation. In recent years, our understanding of 5mC has changed because of advances in 5mC detection techniques that allow mapping of this mark on the whole genome scale. Profiling DNA methylomes from organisms across the eukaryotic tree of life has reshaped our views on the evolution of 5mC. In this review, we explore the macroevolution of 5mC in major eukaryotic groups, and then focus on recent advances made in animals. Genomic 5mC patterns as well as the mechanisms of 5mC deposition tend to be evolutionary labile across large phylogenetic distances; however, some common patterns are starting to emerge. Within the animal kingdom, 5mC diversity has proven to be much greater than anticipated. For example, a previously held common view that genome hypermethylation is a trait exclusive to vertebrates has recently been challenged. Also, data from genome-wide studies are starting to yield insights into the potential roles of 5mC in invertebrate cis regulation. Here we provide an evolutionary perspective of both the well-known and enigmatic roles of 5mC across the eukaryotic tree of life.
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Affiliation(s)
- Alex de Mendoza
- ARC CoE Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia; Harry Perkins Institute of Medical Research, Perth, WA 6009, Australia.
| | - Ryan Lister
- ARC CoE Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia; Harry Perkins Institute of Medical Research, Perth, WA 6009, Australia
| | - Ozren Bogdanovic
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
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64
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Alonso C, Medrano M, Pérez R, Canto A, Parra-Tabla V, Herrera CM. Interspecific variation across angiosperms in global DNA methylation: phylogeny, ecology and plant features in tropical and Mediterranean communities. THE NEW PHYTOLOGIST 2019; 224:949-960. [PMID: 31276214 DOI: 10.1111/nph.16046] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 06/28/2019] [Indexed: 06/09/2023]
Abstract
The interspecific range of epigenetic variation and the degree to which differences between angiosperm species are related to geography, evolutionary history, ecological settings or species-specific traits, remain essentially unexplored. Genome-wide global DNA cytosine methylation is a tractable 'epiphenotypic' feature suitable for exploring these relationships. Global cytosine methylation was estimated in 279 species from two distant, ecologically disparate geographical regions: Mediterranean Spain and tropical México. At each region, four distinct plant communities were analyzed. Global methylation spanned a 10-fold range among species (4.8-42.2%). Interspecific differences were related to evolutionary trajectories, as denoted by a strong phylogenetic signal. Genomes of tropical species were on average less methylated than those of Mediterranean ones. Woody plants have genomes with lower methylation than perennial herbs, and genomes of widespread species were less methylated than those of species with restricted geographical distribution. The eight communities studied exhibited broad and overlapping interspecific variances in global cytosine methylation and only two of them differed in average methylation. Altogether, our broad taxonomic survey supported global methylation as a plant 'epiphenotypic' trait largely associated with species evolutionary history, genome size, range size and woodiness. Additional studies are required for better understanding the environmental components underlying local and geographical variation.
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Affiliation(s)
- Conchita Alonso
- Estación Biológica de Doñana, CSIC, Avenida Américo Vespucio 26, 41092, Sevilla, Spain
| | - Mónica Medrano
- Estación Biológica de Doñana, CSIC, Avenida Américo Vespucio 26, 41092, Sevilla, Spain
| | - Ricardo Pérez
- Instituto de Investigaciones Químicas, Centro de Investigaciones Científicas Isla de La Cartuja, CSIC-US, Avenida Américo Vespucio 49, 41092, Sevilla, Spain
| | - Azucena Canto
- Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico
| | - Víctor Parra-Tabla
- Departamento de Ecología Tropical, Universidad Autónoma de Yucatán, Campus de Ciencias Biológicas y Agropecuarias, Km. 15.5 Carretera Mérida-Xtmakui, 97000, Mérida, Yucatán, Mexico
| | - Carlos M Herrera
- Estación Biológica de Doñana, CSIC, Avenida Américo Vespucio 26, 41092, Sevilla, Spain
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65
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Ji L, Mathioni SM, Johnson S, Tucker D, Bewick AJ, Do Kim K, Daron J, Slotkin RK, Jackson SA, Parrott WA, Meyers BC, Schmitz RJ. Genome-Wide Reinforcement of DNA Methylation Occurs during Somatic Embryogenesis in Soybean. THE PLANT CELL 2019; 31:2315-2331. [PMID: 31439802 PMCID: PMC6790092 DOI: 10.1105/tpc.19.00255] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/29/2019] [Accepted: 08/19/2019] [Indexed: 05/06/2023]
Abstract
Somatic embryogenesis is an important tissue culture technique that sometimes leads to phenotypic variation via genetic and/or epigenetic changes. To understand the genomic and epigenomic impacts of somatic embryogenesis, we characterized soybean (Glycine max) epigenomes sampled from embryos at 10 different stages ranging from 6 weeks to 13 years of continuous culture. We identified genome-wide increases in DNA methylation from cultured samples, especially at CHH sites. The hypermethylation almost exclusively occurred in regions previously possessing non-CG methylation and was accompanied by increases in the expression of genes encoding the RNA-directed DNA methylation (RdDM) machinery. The epigenomic changes were similar between somatic and zygotic embryogenesis. Following the initial global wave of hypermethylation, rare decay events of maintenance methylation were observed, and the extent of the decay increased with time in culture. These losses in DNA methylation were accompanied by downregulation of genes encoding the RdDM machinery and transcriptome reprogramming reminiscent of transcriptomes during late-stage seed development. These results reveal a process for reinforcing already silenced regions to maintain genome integrity during somatic embryogenesis over the short term, which eventually decays at certain loci over longer time scales.
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Affiliation(s)
- Lexiang Ji
- Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602
| | | | - Sarah Johnson
- Institute for Plant Breeding Genetics and Genomics, University of Georgia, Athens, Georgia 30602
| | - Donna Tucker
- Institute for Plant Breeding Genetics and Genomics, University of Georgia, Athens, Georgia 30602
| | - Adam J Bewick
- Department of Genetics, University of Georgia, Athens, Georgia 30602
| | - Kyung Do Kim
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602
| | - Josquin Daron
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210
| | - R Keith Slotkin
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602
| | - Wayne A Parrott
- Institute for Plant Breeding Genetics and Genomics, University of Georgia, Athens, Georgia 30602
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
- Division of Plant Sciences, University of Missouri, Columbia, Missouri 63132
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, Georgia 30602
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66
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Mathers TC, Mugford ST, Percival-Alwyn L, Chen Y, Kaithakottil G, Swarbreck D, Hogenhout SA, van Oosterhout C. Sex-specific changes in the aphid DNA methylation landscape. Mol Ecol 2019; 28:4228-4241. [PMID: 31472081 PMCID: PMC6857007 DOI: 10.1111/mec.15216] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 07/22/2019] [Indexed: 12/15/2022]
Abstract
Aphids present an ideal system to study epigenetics as they can produce diverse, but genetically identical, morphs in response to environmental stimuli. Here, using whole genome bisulphite sequencing and transcriptome sequencing of the green peach aphid (Myzus persicae), we present the first detailed analysis of cytosine methylation in an aphid and investigate differences in the methylation and transcriptional landscapes of male and asexual female morphs. We found that methylation primarily occurs in a CG dinucleotide (CpG) context and that exons are highly enriched for methylated CpGs, particularly at the 3' end of genes. Methylation is positively associated with gene expression, and methylated genes are more stably expressed than unmethylated genes. Male and asexual female morphs have distinct methylation profiles. Strikingly, these profiles are divergent between the sex chromosome and the autosomes; autosomal genes are hypomethylated in males compared to asexual females, whereas genes belonging to the sex chromosome, which is haploid in males, are hypermethylated. Overall, we found correlated changes in methylation and gene expression between males and asexual females, and this correlation was particularly strong for genes located on the sex chromosome. Our results suggest that differential methylation of sex-biased genes plays a role in aphid sexual differentiation.
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Affiliation(s)
- Thomas C Mathers
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Sam T Mugford
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
| | | | - Yazhou Chen
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
| | | | | | - Saskia A Hogenhout
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
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67
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Abstract
DNA methylation is a conserved epigenetic modification that is important for gene regulation and genome stability. Aberrant patterns of DNA methylation can lead to plant developmental abnormalities. A specific DNA methylation state is an outcome of dynamic regulation by de novo methylation, maintenance of methylation and active demethylation, which are catalysed by various enzymes that are targeted by distinct regulatory pathways. In this Review, we discuss DNA methylation in plants, including methylating and demethylating enzymes and regulatory factors, and the coordination of methylation and demethylation activities by a so-called methylstat mechanism; the functions of DNA methylation in regulating transposon silencing, gene expression and chromosome interactions; the roles of DNA methylation in plant development; and the involvement of DNA methylation in plant responses to biotic and abiotic stress conditions.
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68
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Evolutionary and Experimental Loss of Gene Body Methylation and Its Consequence to Gene Expression. G3-GENES GENOMES GENETICS 2019; 9:2441-2445. [PMID: 31147389 PMCID: PMC6686912 DOI: 10.1534/g3.119.400365] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
In flowering plants, gene body methylation (gbM) is associated with a subset of constitutively expressed genes. It has been proposed that gbM modulates gene expression. Here, we show that there are no consistent and direct differences to expression following the loss of gbM. By comparing expression of gbM genes in Arabidopsis thaliana accessions to orthologous genes in two Eutrema salsugineum genotypes, we identified both positive and negative expression differences associated with gbM loss. However, expression is largely unaffected by gbM loss in E. salsugineum Expression differences between species were within the variation of expression observed within A. thaliana accessions that displayed variation in gbM. Furthermore, experimentally induced loss of gbM did not consistently lead to differences in expression compared to wild type. To date, there is no convincing data to support a direct causal link between the presence/absence of gbM and the modulation of expression in flowering plants.
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69
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Schmitz RJ, Lewis ZA, Goll MG. DNA Methylation: Shared and Divergent Features across Eukaryotes. Trends Genet 2019; 35:818-827. [PMID: 31399242 DOI: 10.1016/j.tig.2019.07.007] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 07/01/2019] [Accepted: 07/15/2019] [Indexed: 02/02/2023]
Abstract
Chemical modification of nucleotide bases in DNA provides one mechanism for conveying information in addition to the genetic code. 5-methylcytosine (5mC) represents the most common chemically modified base in eukaryotic genomes. Sometimes referred to simply as DNA methylation, in eukaryotes 5mC is most prevalent at CpG dinucleotides and is frequently associated with transcriptional repression of transposable elements. However, 5mC levels and distributions are variable across phylogenies, and emerging evidence suggests that the functions of DNA methylation may be more diverse and complex than was previously appreciated. We summarize the current understanding of DNA methylation profiles and functions in different eukaryotic lineages.
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Affiliation(s)
- Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Zachary A Lewis
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Mary G Goll
- Department of Genetics, University of Georgia, Athens, GA 30602, USA.
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70
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Kiefer C, Willing EM, Jiao WB, Sun H, Piednoël M, Hümann U, Hartwig B, Koch MA, Schneeberger K. Interspecies association mapping links reduced CG to TG substitution rates to the loss of gene-body methylation. NATURE PLANTS 2019; 5:846-855. [PMID: 31358959 DOI: 10.1038/s41477-019-0486-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 06/25/2019] [Indexed: 05/18/2023]
Abstract
Comparative genomics can unravel the genetic basis of species differences; however, successful reports on quantitative traits are still scarce. Here we present genome assemblies of 31 so-far unassembled Brassicaceae plant species and combine them with 16 previously published assemblies to establish the Brassicaceae Diversity Panel. Using a new interspecies association strategy for quantitative traits, we found a so-far unknown association between the unexpectedly high variation in CG to TG substitution rates in genes and the absence of CHROMOMETHYLASE3 (CMT3) orthologues. Low substitution rates were associated with the loss of CMT3, while species with conserved CMT3 orthologues showed high substitution rates. Species without CMT3 also lacked gene-body methylation (gbM), suggesting an evolutionary trade-off between the unknown function of gbM and low substitution rates in Brassicaceae, possibly due to low mutability of non-methylated cytosines.
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Affiliation(s)
- Christiane Kiefer
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Eva-Maria Willing
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- NEO New Oncology, Cologne, Germany
| | - Wen-Biao Jiao
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Hequan Sun
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Mathieu Piednoël
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Ulrike Hümann
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Benjamin Hartwig
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- NEO New Oncology, Cologne, Germany
| | - Marcus A Koch
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Korbinian Schneeberger
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
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71
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Johannes F. DNA methylation makes mutational history. NATURE PLANTS 2019; 5:772-773. [PMID: 31358963 DOI: 10.1038/s41477-019-0491-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Affiliation(s)
- Frank Johannes
- Department of Plant Sciences, Technical University of Munich, Freising, Germany.
- Institute for Advanced Study, Technical University of Munich, Garching, Germany.
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72
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Wendte JM, Zhang Y, Ji L, Shi X, Hazarika RR, Shahryary Y, Johannes F, Schmitz RJ. Epimutations are associated with CHROMOMETHYLASE 3-induced de novo DNA methylation. eLife 2019; 8:e47891. [PMID: 31356150 PMCID: PMC6663294 DOI: 10.7554/elife.47891] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 07/19/2019] [Indexed: 12/20/2022] Open
Abstract
In many plant species, a subset of transcribed genes are characterized by strictly CG-context DNA methylation, referred to as gene body methylation (gbM). The mechanisms that establish gbM are unclear, yet flowering plant species naturally without gbM lack the DNA methyltransferase, CMT3, which maintains CHG (H = A, C, or T) and not CG methylation at constitutive heterochromatin. Here, we identify the mechanistic basis for gbM establishment by expressing CMT3 in a species naturally lacking CMT3. CMT3 expression reconstituted gbM through a progression of de novo CHG methylation on expressed genes, followed by the accumulation of CG methylation that could be inherited even following loss of the CMT3 transgene. Thus, gbM likely originates from the simultaneous targeting of loci by pathways that promote euchromatin and heterochromatin, which primes genes for the formation of stably inherited epimutations in the form of CG DNA methylation.
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Affiliation(s)
- Jered M Wendte
- Department of GeneticsUniversity of GeorgiaAthensUnited States
| | - Yinwen Zhang
- Institute of BioinformaticsUniversity of GeorgiaAthensUnited States
| | - Lexiang Ji
- Institute of BioinformaticsUniversity of GeorgiaAthensUnited States
| | - Xiuling Shi
- Department of GeneticsUniversity of GeorgiaAthensUnited States
| | - Rashmi R Hazarika
- Department of Plant ScienceTechnical University of MunichFreisingGermany
| | - Yadollah Shahryary
- Department of Plant ScienceTechnical University of MunichFreisingGermany
| | - Frank Johannes
- Department of Plant ScienceTechnical University of MunichFreisingGermany
- Institute for Advanced StudyTechnical University of MunichGarchingGermany
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73
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Wendte JM, Zhang Y, Ji L, Shi X, Hazarika RR, Shahryary Y, Johannes F, Schmitz RJ. Epimutations are associated with CHROMOMETHYLASE 3-induced de novo DNA methylation. eLife 2019. [PMID: 31356150 DOI: 10.7554/elife.47891.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
In many plant species, a subset of transcribed genes are characterized by strictly CG-context DNA methylation, referred to as gene body methylation (gbM). The mechanisms that establish gbM are unclear, yet flowering plant species naturally without gbM lack the DNA methyltransferase, CMT3, which maintains CHG (H = A, C, or T) and not CG methylation at constitutive heterochromatin. Here, we identify the mechanistic basis for gbM establishment by expressing CMT3 in a species naturally lacking CMT3. CMT3 expression reconstituted gbM through a progression of de novo CHG methylation on expressed genes, followed by the accumulation of CG methylation that could be inherited even following loss of the CMT3 transgene. Thus, gbM likely originates from the simultaneous targeting of loci by pathways that promote euchromatin and heterochromatin, which primes genes for the formation of stably inherited epimutations in the form of CG DNA methylation.
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Affiliation(s)
- Jered M Wendte
- Department of Genetics, University of Georgia, Athens, United States
| | - Yinwen Zhang
- Institute of Bioinformatics, University of Georgia, Athens, United States
| | - Lexiang Ji
- Institute of Bioinformatics, University of Georgia, Athens, United States
| | - Xiuling Shi
- Department of Genetics, University of Georgia, Athens, United States
| | - Rashmi R Hazarika
- Department of Plant Science, Technical University of Munich, Freising, Germany
| | - Yadollah Shahryary
- Department of Plant Science, Technical University of Munich, Freising, Germany
| | - Frank Johannes
- Department of Plant Science, Technical University of Munich, Freising, Germany
- Institute for Advanced Study, Technical University of Munich, Garching, Germany
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, United States
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74
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Pei L, Zhang L, Li J, Shen C, Qiu P, Tu L, Zhang X, Wang M. Tracing the origin and evolution history of methylation-related genes in plants. BMC PLANT BIOLOGY 2019; 19:307. [PMID: 31299897 PMCID: PMC6624907 DOI: 10.1186/s12870-019-1923-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 07/03/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND DNA methylation is a crucial epigenetic modification, which is involved in many biological processes, including gene expression regulation, embryonic development, cell differentiation and genomic imprinting etc. And it also involves many key regulatory genes in eukaryotes. By tracing the evolutionary history of methylation-related genes, we can understand the origin and expansion time of these genes, which helps to understand the evolutionary history of plants, and we can also understand the changes of DNA methylation patterns in different species. However, most studies on the evolution of methylation-related genes failed to be carried out for the whole DNA methylation pathway. RESULTS In this study, we conducted a comprehensive identification of 33 methylation-related genes in 77 species, and investigated gene origin and evolution throughout the plant kingdom. We found that the origin of genes responsible for methylation maintenance and demethylation evolved early, while most de novo methylation-related genes appeared late. The methylation-related genes were expanded by whole genome duplication and tandem replication, but were also accompanied by a large number of gene absence events in different species. The gene length and intron length varied a lot in different species, but exon structure and functional domains were relatively conserved. The phylogenetic relationships of methylation-related genes were traced to reveal the evolution history of DNA methylation in different species. The expression patterns of methylation-related genes have changed during the evolution of species, and the expression patterns of these genes in different species can be clustered into four categories. CONCLUSIONS The study describes a global characterization of DNA methylation-related genes in the plant kingdom. The similarities and differences in origin time, gene structure and phylogenetic relationship of these genes lead us to understand the evolutionary conservation and dynamics of DNA methylation in plants.
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Affiliation(s)
- Liuling Pei
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Lin Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Jianying Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Chao Shen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Ping Qiu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Lili Tu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 Hubei China
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75
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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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76
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Muyle A, Gaut BS. Loss of Gene Body Methylation in Eutrema salsugineum Is Associated with Reduced Gene Expression. Mol Biol Evol 2019; 36:155-158. [PMID: 30398664 PMCID: PMC6340462 DOI: 10.1093/molbev/msy204] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Gene body methylation (gbM) is typically characterized by DNA methylation in the CG context within coding regions and is associated with constitutive genes that have moderate to high expression levels. A recent study discovered the loss of gbM in two plant species (Eutrema salsugineum and Conringia planisiliqua), illustrating that gbM is not necessary for survival and reproduction. The same paper stated there was no detectable effect of gbM loss on gene expression (GE). Here, we reanalyzed the GE data and accounted for experimental variability in expression level estimates. We show that the loss of gbM in E. salsugineum is associated with a small but highly significant decrease in GE relative to the closely related species Arabidospis thaliana. Our results are consistent with various evolutionary analyses that suggest gbM has a function, perhaps as a homeostatic effect on GE.
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Affiliation(s)
- Aline Muyle
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA
| | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA
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77
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Long JC, Xia AA, Liu JH, Jing JL, Wang YZ, Qi CY, He Y. Decrease in DNA methylation 1 (DDM1) is required for the formation of m CHH islands in maize. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:749-764. [PMID: 30387549 DOI: 10.1111/jipb.12733] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 10/23/2018] [Indexed: 05/26/2023]
Abstract
DNA methylation plays a crucial role in suppressing mobilization of transposable elements and regulation of gene expression. A number of studies have indicated that DNA methylation pathways and patterns exhibit distinct properties in different species, including Arabidopsis, rice, and maize. Here, we characterized the function of DDM1 in regulating genome-wide DNA methylation in maize. Two homologs of ZmDDM1 are abundantly expressed in the embryo and their simultaneous disruption caused embryo lethality with abnormalities in cell proliferation from the early stage of kernel development. We establish that ZmDDM1 is critical for DNA methylation, at CHG sites, and to a lesser extent at CG sites, in heterochromatic regions, and unexpectedly, it is required for the formation of m CHH islands. In addition, ZmDDM1 is indispensable for the presence of 24-nt siRNA, suggesting its involvement in the RdDM pathway. Our results provide novel insight into the role of ZmDDM1 in regulating the formation of m CHH islands, via the RdDM pathway maize, suggesting that, in comparison to Arabidopsis, maize may have adopted distinct mechanisms for regulating m CHH.
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Affiliation(s)
- Jin Cheng Long
- National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China
| | - Ai Ai Xia
- National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China
| | - Jing Han Liu
- National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China
| | - Ju Li Jing
- National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China
| | - Ya Zhong Wang
- National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China
| | - Chuang Ye Qi
- National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China
| | - Yan He
- National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China
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78
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You WJ, Feng YR, Shen YH, Chen YR, Chen TY, Fu SF. Silencing of NbCMT3s has Pleiotropic Effects on Development by Interfering with Autophagy-Related Genes in Nicotiana benthamiana. PLANT & CELL PHYSIOLOGY 2019; 60:1120-1135. [PMID: 30785195 DOI: 10.1093/pcp/pcz034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 02/14/2019] [Indexed: 05/25/2023]
Abstract
DNA methylation is a chromatin mark that has a crucial role in regulating gene expression. The chromomethylase (CMT) protein family is a plant-specific DNA methyltransferase that mediates growth and development. However, the roles of CMT3 in autophagy remain to be elucidated. Here, we identified the potential targets of CMT3 in Nicotiana benthamiana (NbCMT3) during developmental programs. Virus-induced gene silencing of NbCMT3/3-2 in N. benthamiana had pleiotropic effects on plant morphology, which indicates its indispensible role in development. Genome-wide transcriptome analysis of NbCMT3/3-2-silenced plants revealed interference with genes related to autophagy and ubiquitination. The expression of NbBeclin 1 and NbHRD1B was higher in NbCMT3/3-2-silenced than control plants. The formation of autophagosomes and starch degradation was disrupted in NbCMT3/3-2-silenced plants, which implies a perturbed autophagic processes. We further generated transgenic N. benthamiana plants carrying a chimeric promoter-reporter construct linking the NbBeclin 1 promoter region and β-glucuronidase (GUS) reporter (pNbBeclin::GUS). NbBeclin 1 promoter activity was significantly enhanced in NbCMT3/3-2-silenced plants. Thus, NbCMT3/3-2 silencing had pleiotropic effects on development by interfering with NbBeclin 1 expression and autophagy-related processes.
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Affiliation(s)
- Wen-Jing You
- Department of Biology, National Changhua University of Education, No.1, Jin-De Road, Changhua, Taiwan
| | - Yun-Ru Feng
- Department of Biology, National Changhua University of Education, No.1, Jin-De Road, Changhua, Taiwan
| | - Ya-Han Shen
- Department of Biology, National Changhua University of Education, No.1, Jin-De Road, Changhua, Taiwan
| | - Yi-Ru Chen
- Department of Biology, National Changhua University of Education, No.1, Jin-De Road, Changhua, Taiwan
| | - Tzy-Yi Chen
- Department of Biology, National Changhua University of Education, No.1, Jin-De Road, Changhua, Taiwan
| | - Shih-Feng Fu
- Department of Biology, National Changhua University of Education, No.1, Jin-De Road, Changhua, Taiwan
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79
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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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80
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Forgione I, Wołoszyńska M, Pacenza M, Chiappetta A, Greco M, Araniti F, Abenavoli MR, Van Lijsebettens M, Bitonti MB, Bruno L. Hypomethylated drm1 drm2 cmt3 mutant phenotype of Arabidopsis thaliana is related to auxin pathway impairment. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 280:383-396. [PMID: 30824017 DOI: 10.1016/j.plantsci.2018.12.029] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/27/2018] [Accepted: 12/29/2018] [Indexed: 05/28/2023]
Abstract
DNA methylation carried out by different methyltransferase classes is a relevant epigenetic modification of DNA which plays a relevant role in the development of eukaryotic organisms. Accordingly, in Arabidopsis thaliana loss of DNA methylation due to combined mutations in genes encoding for DNA methyltransferases causes several developmental abnormalities. The present study describes novel growth disorders in the drm1 drm2 cmt3 triple mutant of Arabidopsis thaliana, defective both in maintenance and de novo DNA methylation, and highlights the correlation between DNA methylation and the auxin hormone pathway. By using an auxin responsive reporter gene, we discovered that auxin accumulation and distribution were affected in the mutant compared to the wild type, from embryo to adult plant stage. In addition, we demonstrated that the defective methylation status also affected the expression of genes that regulate auxin hormone pathways from synthesis to transport and signalling and a direct relationship between differentially expressed auxin-related genes and altered auxin accumulation and distribution in embryo, leaf and root was observed. Finally, we provided evidence of the direct and organ-specific modulation of auxin-related genes through the DNA methylation process.
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Affiliation(s)
- Ivano Forgione
- Dipartimento di Biologia, Ecologia e Scienze della Terra, Università della Calabria, Arcavacata di Rende (CS), 87036 Arcavacata di Rende, CS, Italy; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Magdalena Wołoszyńska
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Marianna Pacenza
- Dipartimento di Biologia, Ecologia e Scienze della Terra, Università della Calabria, Arcavacata di Rende (CS), 87036 Arcavacata di Rende, CS, Italy
| | - Adriana Chiappetta
- Dipartimento di Biologia, Ecologia e Scienze della Terra, Università della Calabria, Arcavacata di Rende (CS), 87036 Arcavacata di Rende, CS, Italy
| | - Maria Greco
- Dipartimento di Biologia, Ecologia e Scienze della Terra, Università della Calabria, Arcavacata di Rende (CS), 87036 Arcavacata di Rende, CS, Italy; The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Fabrizio Araniti
- Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, 89124 Reggio Calabria, Italy
| | - Maria Rosa Abenavoli
- Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, 89124 Reggio Calabria, Italy
| | - Mieke Van Lijsebettens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Maria Beatrice Bitonti
- Dipartimento di Biologia, Ecologia e Scienze della Terra, Università della Calabria, Arcavacata di Rende (CS), 87036 Arcavacata di Rende, CS, Italy
| | - Leonardo Bruno
- Dipartimento di Biologia, Ecologia e Scienze della Terra, Università della Calabria, Arcavacata di Rende (CS), 87036 Arcavacata di Rende, CS, Italy.
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81
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Bewick AJ, Hofmeister BT, Powers RA, Mondo SJ, Grigoriev IV, James TY, Stajich JE, Schmitz RJ. Diversity of cytosine methylation across the fungal tree of life. Nat Ecol Evol 2019; 3:479-490. [PMID: 30778188 PMCID: PMC6533610 DOI: 10.1038/s41559-019-0810-9] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 01/13/2019] [Indexed: 12/22/2022]
Abstract
The generation of thousands of fungal genomes is leading to a better understanding of genes and genomic organization within the kingdom. However, the epigenome, which includes DNA and chromatin modifications, remains poorly investigated in fungi. Large comparative studies in animals and plants have deepened our understanding of epigenomic variation, particularly of the modified base 5-methylcytosine (5mC), but taxonomic sampling of disparate groups is needed to develop unifying explanations for 5mC variation. Here we utilize the largest phylogenetic resolution of 5mC methyltransferases (5mC MTases) and genome evolution to better understand levels and patterns of 5mC across fungi. We show that extant 5mC MTase genotypes are descendent from ancestral maintenance and de novo genotypes, whereas the 5mC MTases DIM-2 and RID are more recently derived, and that 5mC levels are correlated with 5mC MTase genotype and transposon content. Our survey also revealed that fungi lack canonical gene body methylation, which distinguishes fungal epigenomes from certain insect and plant species. However, some fungal species possess independently derived clusters of contiguous 5mC encompassing many genes. In some cases, DNA repair pathways and the N6-methyladenine (6mA) DNA modification negatively coevolved with 5mC pathways, which additionally contributed to interspecific epigenomic variation across fungi.
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Affiliation(s)
- Adam J Bewick
- Department of Genetics, University of Georgia, Athens, GA, USA.
| | | | - Rob A Powers
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Stephen J Mondo
- US Department of Energy Joint Genome Institute, Walnut Creek, Berkeley, CA, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, Berkeley, CA, USA.,Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, USA
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82
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Furci L, Jain R, Stassen J, Berkowitz O, Whelan J, Roquis D, Baillet V, Colot V, Johannes F, Ton J. Identification and characterisation of hypomethylated DNA loci controlling quantitative resistance in Arabidopsis. eLife 2019; 8:40655. [PMID: 30608232 PMCID: PMC6342528 DOI: 10.7554/elife.40655] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 01/03/2019] [Indexed: 12/12/2022] Open
Abstract
Variation in DNA methylation enables plants to inherit traits independently of changes to DNA sequence. Here, we have screened an Arabidopsis population of epigenetic recombinant inbred lines (epiRILs) for resistance against Hyaloperonospora arabidopsidis (Hpa). These lines share the same genetic background, but show variation in heritable patterns of DNA methylation. We identified four epigenetic quantitative trait loci (epiQTLs) that provide quantitative resistance without reducing plant growth or resistance to other (a)biotic stresses. Phenotypic characterisation and RNA-sequencing analysis revealed that Hpa-resistant epiRILs are primed to activate defence responses at the relatively early stages of infection. Collectively, our results show that hypomethylation at selected pericentromeric regions is sufficient to provide quantitative disease resistance, which is associated with genome-wide priming of defence-related genes. Based on comparisons of global gene expression and DNA methylation between the wild-type and resistant epiRILs, we discuss mechanisms by which the pericentromeric epiQTLs could regulate the defence-related transcriptome. In plants, animals and microbes genetic information is encoded by DNA, which are made up of sequences of building blocks, called nucleotide bases. These sequences can be separated into sections known as genes that each encode specific traits. It was previously thought that only changes to the sequence of bases in a DNA molecule could alter the traits passed on to future generations. However, it has recently become clear that some traits can also be inherited through modifications to the DNA that do not alter its sequence. One such modification is to attach a tag, known as a methyl group, to a nucleotide base known as cytosine. These methyl tags can be added to, or removed from, DNA to create different patterns of methylation. Previous studies have shown that plants whose DNA is less methylated than normal (‘hypo-methylated’) are more resistant to plant diseases. However, the location and identity of the hypo-methylated DNA regions controlling this resistance remained unknown. To address this problem, Furci, Jain et al. studied how DNA methylation in a small weed known as Arabidopsis thaliana affects how well the plants can resist a disease known as downy mildew. Furci, Jain et al. studied a population of over 100 A. thaliana lines that have the same DNA sequences but different patterns of DNA methylation. The experiments identified four DNA locations that were less methylated in lines with enhanced resistance to downy mildew. Importantly, this form of resistance did not appear to reduce how well the plants grew, or make them less able to resist other diseases or environmental stresses. The results of further experiments suggested that reduced methylation at the four DNA regions prime the plant’s immune system, enabling a faster and stronger activation of a multitude of defence genes across the genome after attack by downy mildew. The next steps following on from this work are to investigate exactly how the four DNA regions with reduced methylation can prime so many different defence genes in the plant. Further research is also needed to determine whether it is possible to breed crop plants with lower levels of methylation at specific DNA locations to improve disease resistance, but without decreasing the amount and quality of food produced.
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Affiliation(s)
- Leonardo Furci
- P3 Centre for Plant and Soil Biology, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Ritushree Jain
- P3 Centre for Plant and Soil Biology, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Joost Stassen
- P3 Centre for Plant and Soil Biology, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Oliver Berkowitz
- Department of Animal, Plant and Soil Science, ARC Centre of Excellence in Plant Energy Biology, La Trobe University, Melbourne, Australia
| | - James Whelan
- Department of Animal, Plant and Soil Science, ARC Centre of Excellence in Plant Energy Biology, La Trobe University, Melbourne, Australia
| | - David Roquis
- Department of Plant Sciences, Technical University of Munich, Freising, Germany.,Institute for Advanced Study, Technical University of Munich, Garching, Germany
| | - Victoire Baillet
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), PSL Université Paris, Paris, France
| | - Vincent Colot
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), PSL Université Paris, Paris, France
| | - Frank Johannes
- Department of Plant Sciences, Technical University of Munich, Freising, Germany.,Institute for Advanced Study, Technical University of Munich, Garching, Germany
| | - Jurriaan Ton
- P3 Centre for Plant and Soil Biology, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
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83
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Alakärppä E, Salo HM, Valledor L, Cañal MJ, Häggman H, Vuosku J. Natural variation of DNA methylation and gene expression may determine local adaptations of Scots pine populations. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:5293-5305. [PMID: 30113688 DOI: 10.1093/jxb/ery292] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 08/01/2018] [Indexed: 05/27/2023]
Abstract
Long-lived conifers are vulnerable to climate change because classical evolutionary processes are slow in developing adaptive responses. Therefore, the capacity of a genotype to adopt different phenotypes is important. Gene expression is the primary mechanism that converts genome-encoded information into phenotypes, and DNA methylation is employed in the epigenetic regulation of gene expression. We investigated variations in global DNA methylation and gene expression between three Scots pine (Pinus sylvestris L.) populations located in northern and southern Finland using mature seeds. Gene expression levels were studied in six DNA methyltransferase (DNMT) genes, which were characterized in this study, and in 19 circadian clock genes regulating adaptive traits. In embryos, expression diversity was found for three DNMT genes, which maintain DNA methylation. The expression of two DNMT genes was strongly correlated with climate variables, which suggests a role for DNA methylation in local adaptation. For adaptation-related genes, expression levels showed between-population variation in 11 genes in megagametophytes and in eight genes in embryos, and many of these genes were linked to climate factors. Altogether, our results suggest that differential DNA methylation and gene expression contribute to local adaptation in Scots pine populations and may enhance the fitness of trees under rapidly changing climatic conditions.
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Affiliation(s)
- Emmi Alakärppä
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Heikki M Salo
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Luis Valledor
- Plant Physiology, Faculty of Biology, University of Oviedo, Oviedo, Spain
| | - Maria Jesús Cañal
- Plant Physiology, Faculty of Biology, University of Oviedo, Oviedo, Spain
| | - Hely Häggman
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Jaana Vuosku
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
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84
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Heer K, Ullrich KK, Hiss M, Liepelt S, Schulze Brüning R, Zhou J, Opgenoorth L, Rensing SA. Detection of somatic epigenetic variation in Norway spruce via targeted bisulfite sequencing. Ecol Evol 2018; 8:9672-9682. [PMID: 30386566 PMCID: PMC6202725 DOI: 10.1002/ece3.4374] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 06/18/2018] [Accepted: 06/22/2018] [Indexed: 12/24/2022] Open
Abstract
Epigenetic mechanisms represent a possible mechanism for achieving a rapid response of long-lived trees to changing environmental conditions. However, our knowledge on plant epigenetics is largely limited to a few model species. With increasing availability of genomic resources for many tree species, it is now possible to adopt approaches from model species that permit to obtain single-base pair resolution data on methylation at a reasonable cost. Here, we used targeted bisulfite sequencing (TBS) to study methylation patterns in the conifer species Norway spruce (Picea abies). To circumvent the challenge of disentangling epigenetic and genetic differences, we focused on four clone pairs, where clone members were growing in different climatic conditions for 24 years. We targeted >26.000 genes using TBS and determined the performance and reproducibility of this approach. We characterized gene body methylation and compared methylation patterns between environments. We found highly comparable capture efficiency and coverage across libraries. Methylation levels were relatively constant across gene bodies, with 21.3 ± 0.3%, 11.0 ± 0.4% and 1.3 ± 0.2% in the CG, CHG, and CHH context, respectively. The variance in methylation profiles did not reveal consistent changes between environments, yet we could identify 334 differentially methylated positions (DMPs) between environments. This supports that changes in methylation patterns are a possible pathway for a plant to respond to environmental change. After this successful application of TBS in Norway spruce, we are confident that this approach can contribute to broaden our knowledge of methylation patterns in natural tree populations.
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Affiliation(s)
- Katrin Heer
- Conservation BiologyFaculty of BiologyPhilipps University MarburgMarburgGermany
- Department of EcologyFaculty of BiologyPhilipps University MarburgMarburgGermany
| | - Kristian K. Ullrich
- Plant Cell BiologyFaculty of BiologyPhilipps University MarburgMarburgGermany
- Department of Evolutionary GeneticsMax Planck Institute for Evolutionary BiologyPloenGermany
| | - Manuel Hiss
- Plant Cell BiologyFaculty of BiologyPhilipps University MarburgMarburgGermany
| | - Sascha Liepelt
- Conservation BiologyFaculty of BiologyPhilipps University MarburgMarburgGermany
| | | | - Jiabin Zhou
- College of Life SciencesShaanxi Normal UniversityXi'anChina
- State Key Laboratory of Grassland Agro‐EcosystemsSchool of Life SciencesLanzhou UniversityLanzhouChina
| | - Lars Opgenoorth
- Department of EcologyFaculty of BiologyPhilipps University MarburgMarburgGermany
| | - Stefan A. Rensing
- Plant Cell BiologyFaculty of BiologyPhilipps University MarburgMarburgGermany
- BIOSS Biological Signaling StudiesUniversity of FreiburgFreiburgGermany
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85
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Li Z, Wan X. Long-term evolutionary DNA methylation dynamic of protein-coding genes and its underlying mechanism. Gene 2018; 677:96-104. [PMID: 30031907 DOI: 10.1016/j.gene.2018.07.051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 07/05/2018] [Accepted: 07/18/2018] [Indexed: 10/28/2022]
Abstract
DNA methylation is an important type of epigenetic modifications for the maintenance of genome functionality and stability. Although there are many studies on DNA methylation patterns, mechanisms, and functions, no study has focused on the evolutionary dynamic of DNA methylation. Here, we present the first genome-wide pattern of evolutionary DNA methylation dynamic in protein-coding genes, by grouping the Arabidopsis thaliana protein-coding genes into several conservation levels representing different evolutionary ages, and by investigating their DNA methylation features for three methylation contexts in both genic and flanking regions. The main results include: in a long-term evolutionary period, (1) genic CHG and CHH methylation levels tend to be decreased over time, which is mainly due to the reductions in the number of siRNA target sites in genes; (2) genic CG methylation levels are firstly reduced and then increased on average over evolutionary time, which is the interactional result of increased proportion and decreased CG methylation level of CG methylated genes; and (3) increased gene length and the stochastic methylation mechanism in CG context may further account for genic CG methylation trend in evolution. The diverse DNA methylation mechanisms in different contexts, together with altered gene length in evolution, could interpret the methylation dynamic of protein-coding genes over evolutionary time. This evolutionary perspective provides a dynamic understanding of the intrinsic relationship between DNA methylation and its functional and evolutionary effects on the genomes.
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Affiliation(s)
- Ziwen Li
- Biology and Agriculture Research Center, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100024, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Biotechnology Breeding, Beijing Solidwill Sci-Tech Co. Ltd., Beijing 100192, China
| | - Xiangyuan Wan
- Biology and Agriculture Research Center, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100024, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Biotechnology Breeding, Beijing Solidwill Sci-Tech Co. Ltd., Beijing 100192, China.
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86
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Rodríguez Lorenzo JL, Hobza R, Vyskot B. DNA methylation and genetic degeneration of the Y chromosome in the dioecious plant Silene latifolia. BMC Genomics 2018; 19:540. [PMID: 30012097 PMCID: PMC6048894 DOI: 10.1186/s12864-018-4936-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 07/10/2018] [Indexed: 02/01/2023] Open
Abstract
Background S. latifolia is a model organism for the study of sex chromosome evolution in plants. Its sex chromosomes include large regions in which recombination became gradually suppressed. The regions tend to expand over time resulting in the formation of evolutionary strata. Non-recombination and later accumulation of repetitive sequences is a putative cause of the size increase in the Y chromosome. Gene decay and accumulation of repetitive DNA are identified as key evolutionary events. Transposons in the X and Y chromosomes are distributed differently and there is a regulation of transposon insertion by DNA methylation of the target sequences, this points to an important role of DNA methylation during sex chromosome evolution in Silene latifolia. The aim of this study was to elucidate whether the reduced expression of the Y allele in S. latifolia is caused by genetic degeneration or if the cause is methylation triggered by transposons and repetitive sequences. Results Gene expression analysis in S. latifolia males has shown expression bias in both X and Y alleles. To determine whether these differences are caused by genetic degeneration or methylation spread by transposons and repetitive sequences, we selected several sex-linked genes with varying degrees of degeneration and from different evolutionary strata. Immunoprecipitation of methylated DNA (MeDIP) from promoter, exon and intron regions was used and validated through bisulfite sequencing. We found DNA methylation in males, and only in the promoter of genes of stratum I (older). The Y alleles in genes of stratum I were methylation enriched compared to X alleles. There was also abundant and high percentage methylation in the CHH context in most sequences, indicating de novo methylation through the RdDM pathway. Conclusions We speculate that TE accumulation and not gene decay is the cause of DNA methylation in the S. latifolia Y sex chromosome with influence on the process of heterochromatinization. Electronic supplementary material The online version of this article (10.1186/s12864-018-4936-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- José Luis Rodríguez Lorenzo
- Plant Developmental Genetics, Institute of Biophysics v.v.i, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65, Brno, Czech Republic.
| | - Roman Hobza
- Plant Developmental Genetics, Institute of Biophysics v.v.i, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65, Brno, Czech Republic
| | - Boris Vyskot
- Plant Developmental Genetics, Institute of Biophysics v.v.i, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65, Brno, Czech Republic
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87
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Fu FF, Dawe RK, Gent JI. Loss of RNA-Directed DNA Methylation in Maize Chromomethylase and DDM1-Type Nucleosome Remodeler Mutants. THE PLANT CELL 2018; 30:1617-1627. [PMID: 29884624 PMCID: PMC6096594 DOI: 10.1105/tpc.18.00053] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 05/16/2018] [Accepted: 06/07/2018] [Indexed: 05/02/2023]
Abstract
Plants make use of distinct types of DNA methylation characterized by their DNA methyltransferases and modes of regulation. One type, RNA-directed DNA methylation (RdDM), is guided by small interfering RNAs (siRNAs) to the edges of transposons that are close to genes, areas called mCHH islands in maize (Zea mays). Another type, chromomethylation, is guided by histone H3 lysine 9 methylation to heterochromatin across the genome. We examined DNA methylation and small RNA expression in plant tissues that were mutant for both copies of the genes encoding chromomethylases as well as mutants for both copies of the genes encoding DECREASED DNA METHYLATION1 (DDM1)-type nucleosome remodelers, which facilitate chromomethylation. Both sets of double mutants were nonviable but produced embryos and endosperm. RdDM was severely compromised in the double mutant embryos, both in terms of DNA methylation and siRNAs. Loss of 24-nucleotide siRNA from mCHH islands was coupled with a gain of 21-, 22-, and 24-nucleotide siRNAs in heterochromatin. These results reveal a requirement for both chromomethylation and DDM1-type nucleosome remodeling for RdDM in mCHH islands, which we hypothesize is due to dilution of RdDM components across the genome when heterochromatin is compromised.
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Affiliation(s)
- Fang-Fang Fu
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602
| | - R Kelly Dawe
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602
- Department of Genetics, University of Georgia, Athens, Georgia 30602
| | - Jonathan I Gent
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602
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88
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Anderson SN, Zynda GJ, Song J, Han Z, Vaughn MW, Li Q, Springer NM. Subtle Perturbations of the Maize Methylome Reveal Genes and Transposons Silenced by Chromomethylase or RNA-Directed DNA Methylation Pathways. G3 (BETHESDA, MD.) 2018; 8:1921-1932. [PMID: 29618467 PMCID: PMC5982821 DOI: 10.1534/g3.118.200284] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 04/03/2018] [Indexed: 01/17/2023]
Abstract
DNA methylation is a chromatin modification that can provide epigenetic regulation of gene and transposon expression. Plants utilize several pathways to establish and maintain DNA methylation in specific sequence contexts. The chromomethylase (CMT) genes maintain CHG (where H = A, C or T) methylation. The RNA-directed DNA methylation (RdDM) pathway is important for CHH methylation. Transcriptome analysis was performed in a collection of Zea mays lines carrying mutant alleles for CMT or RdDM-associated genes. While the majority of the transcriptome was not affected, we identified sets of genes and transposon families sensitive to context-specific decreases in DNA methylation in mutant lines. Many of the genes that are up-regulated in CMT mutant lines have high levels of CHG methylation, while genes that are differentially expressed in RdDM mutants are enriched for having nearby mCHH islands, implicating context-specific DNA methylation in the regulation of expression for a small number of genes. Many genes regulated by CMTs exhibit natural variation for DNA methylation and transcript abundance in a panel of diverse inbred lines. Transposon families with differential expression in the mutant genotypes show few defining features, though several families up-regulated in RdDM mutants show enriched expression in endosperm tissue, highlighting the potential importance for this pathway during reproduction. Taken together, our findings suggest that while the number of genes and transposon families whose expression is reproducibly affected by mild perturbations in context-specific methylation is small, there are distinct patterns for loci impacted by RdDM and CMT mutants.
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Affiliation(s)
- Sarah N Anderson
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108
| | - Gregory J Zynda
- Texas Advanced Computing Center, University of Texas, Austin, TX 78758
| | - Jawon Song
- Texas Advanced Computing Center, University of Texas, Austin, TX 78758
| | - Zhaoxue Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Matthew W Vaughn
- Texas Advanced Computing Center, University of Texas, Austin, TX 78758
| | - Qing Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108
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89
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Lee J, Yang EC, Graf L, Yang JH, Qiu H, Zelzion U, Chan CX, Stephens TG, Weber APM, Boo GH, Boo SM, Kim KM, Shin Y, Jung M, Lee SJ, Yim HS, Lee JH, Bhattacharya D, Yoon HS. Analysis of the Draft Genome of the Red Seaweed Gracilariopsis chorda Provides Insights into Genome Size Evolution in Rhodophyta. Mol Biol Evol 2018; 35:1869-1886. [DOI: 10.1093/molbev/msy081] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- JunMo Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Eun Chan Yang
- Marine Ecosystem Research Center, Korea Institute of Ocean Science and Technology, Busan, Korea
| | - Louis Graf
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Ji Hyun Yang
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Huan Qiu
- Department of Ecology Evolution and Natural Resources, Rutgers University, New Brunswick, NJ
| | - Udi Zelzion
- Department of Ecology Evolution and Natural Resources, Rutgers University, New Brunswick, NJ
| | - Cheong Xin Chan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Timothy G Stephens
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Andreas P M Weber
- Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine-University, Duesseldorf, Germany
| | - Ga Hun Boo
- Department of Biology, Chungnam National University, Daejeon, Korea
| | - Sung Min Boo
- Department of Biology, Chungnam National University, Daejeon, Korea
| | - Kyeong Mi Kim
- National Marine Biodiversity Institute of Korea, Seocheon, Korea
| | - Younhee Shin
- Bioinformatics Group, R&D Center, Insilicogen, Inc., Suwon, Korea
| | - Myunghee Jung
- Bioinformatics Group, R&D Center, Insilicogen, Inc., Suwon, Korea
| | | | - Hyung-Soon Yim
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Busan, Korea
| | - Jung-Hyun Lee
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Busan, Korea
| | | | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
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90
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Li J, Li C, Lu S. Identification and characterization of the cytosine-5 DNA methyltransferase gene family in Salvia miltiorrhiza. PeerJ 2018. [PMID: 29527415 PMCID: PMC5842782 DOI: 10.7717/peerj.4461] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Cytosine DNA methylation is highly conserved epigenetic modification involved in a wide range of biological processes in eukaryotes. It was established and maintained by cytosine-5 DNA methyltransferases (C5-MTases) in plants. Through genome-wide identification, eight putative SmC5-MTase genes were identified from the genome of Salvia miltiorrhiza, a well-known traditional Chinese medicine material and an emerging model medicinal plant. Based on conserved domains and phylogenetic analysis, eight SmC5-MTase genes were divided into four subfamilies, including MET, CMT, DRM and DNMT2. Genome-wide comparative analysis of the C5-MTase gene family in S. miltiorrhiza and Arabidopsis thaliana, including gene structure, sequence features, sequence alignment and conserved motifs, was carried out. The results showed conservation and divergence of the members of each subfamily in plants. The length of SmC5-MTase open reading frames ranges widely from 1,152 (SmDNMT2) to 5,034 bp (SmMET1). The intron number of SmC5-MTases varies between 7 (SmDRM1) and 20 (SmCMT1 and SmCMT2b). These features were similar to their counterparts from Arabidopsis. Sequence alignment and conserved motif analysis showed the existence of highly conserved and subfamily-specific motifs in the C5-MTases analyzed. Differential transcript abundance was detected for SmC5-MTases, implying genome-wide variance of DNA methylation in different organs and tissues. Transcriptome-wide analysis showed that the transcript levels of all SmC5-MTase genes was slightly changed under yeast extract and methyl jasmonate treatments. Six SmC5-MTases, including SmMET1, SmCMT1, SmCMT2a, SmCMT2b, SmCMT3 and SmDRM1, were salicylic acid-responsive, suggesting the involvement of SmC5-MTases in salicylic acid-dependent immunity. These results provide useful information for demonstrating the role of DNA methylation in bioactive compound biosynthesis and Dao-di herb formation in medicinal plants.
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Affiliation(s)
- Jiang Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Caili Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Shanfa Lu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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91
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Wendte JM, Schmitz RJ. Specifications of Targeting Heterochromatin Modifications in Plants. MOLECULAR PLANT 2018; 11:381-387. [PMID: 29032247 DOI: 10.1016/j.molp.2017.10.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 10/06/2017] [Accepted: 10/08/2017] [Indexed: 05/19/2023]
Abstract
Plants encode a diverse repertoire of DNA methyltransferases that have specialized to target cytosines for methylation in specific sequence contexts. These include the de novo methyltransferase, DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2), which methylates cytosines in all sequence contexts through an RNA-guided process, the CHROMOMETHYLASES (CMTs), which methylate CHH and CHG cytosines (where H is A, T, or C), and METHYLTRANSFERASE 1 (MET1), which maintains methylation of symmetrical CG contexts. In this review, we discuss the sequence specificities and targeting of each of these pathways. In particular, we highlight recent studies that indicate CMTs preferentially target CWG or CWA/CAW motifs (where W is A or T), and discuss how self-reinforcing feedback loops between DNA methyltransferases and histone modifications characteristic of heterochromatin specify targeting. Finally, the initiating events that lead to gene body methylation are discussed as a model illustrating how interdependent targeting of different silencing pathways can potentiate the establishment of off-target epialleles.
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Affiliation(s)
- Jered M Wendte
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA 30602, USA.
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92
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Lang D, Ullrich KK, Murat F, Fuchs J, Jenkins J, Haas FB, Piednoel M, Gundlach H, Van Bel M, Meyberg R, Vives C, Morata J, Symeonidi A, Hiss M, Muchero W, Kamisugi Y, Saleh O, Blanc G, Decker EL, van Gessel N, Grimwood J, Hayes RD, Graham SW, Gunter LE, McDaniel SF, Hoernstein SNW, Larsson A, Li FW, Perroud PF, Phillips J, Ranjan P, Rokshar DS, Rothfels CJ, Schneider L, Shu S, Stevenson DW, Thümmler F, Tillich M, Villarreal Aguilar JC, Widiez T, Wong GKS, Wymore A, Zhang Y, Zimmer AD, Quatrano RS, Mayer KFX, Goodstein D, Casacuberta JM, Vandepoele K, Reski R, Cuming AC, Tuskan GA, Maumus F, Salse J, Schmutz J, Rensing SA. The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:515-533. [PMID: 29237241 DOI: 10.1111/tpj.13801] [Citation(s) in RCA: 253] [Impact Index Per Article: 42.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 11/20/2017] [Accepted: 11/24/2017] [Indexed: 05/18/2023]
Abstract
The draft genome of the moss model, Physcomitrella patens, comprised approximately 2000 unordered scaffolds. In order to enable analyses of genome structure and evolution we generated a chromosome-scale genome assembly using genetic linkage as well as (end) sequencing of long DNA fragments. We find that 57% of the genome comprises transposable elements (TEs), some of which may be actively transposing during the life cycle. Unlike in flowering plant genomes, gene- and TE-rich regions show an overall even distribution along the chromosomes. However, the chromosomes are mono-centric with peaks of a class of Copia elements potentially coinciding with centromeres. Gene body methylation is evident in 5.7% of the protein-coding genes, typically coinciding with low GC and low expression. Some giant virus insertions are transcriptionally active and might protect gametes from viral infection via siRNA mediated silencing. Structure-based detection methods show that the genome evolved via two rounds of whole genome duplications (WGDs), apparently common in mosses but not in liverworts and hornworts. Several hundred genes are present in colinear regions conserved since the last common ancestor of plants. These syntenic regions are enriched for functions related to plant-specific cell growth and tissue organization. The P. patens genome lacks the TE-rich pericentromeric and gene-rich distal regions typical for most flowering plant genomes. More non-seed plant genomes are needed to unravel how plant genomes evolve, and to understand whether the P. patens genome structure is typical for mosses or bryophytes.
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Affiliation(s)
- Daniel Lang
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
- Plant Genome and Systems Biology, Helmholtz Center Munich, 85764, Neuherberg, Germany
| | - Kristian K Ullrich
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Florent Murat
- INRA, UMR 1095 Genetics, Diversity and Ecophysiology of Cereals (GDEC), 5 Chemin de Beaulieu, 63100, Clermont-Ferrand, France
| | - Jörg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, OT Gatersleben, D-06466, Stadt Seeland, Germany
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Fabian B Haas
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Mathieu Piednoel
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829, Cologne, Germany
| | - Heidrun Gundlach
- Plant Genome and Systems Biology, Helmholtz Center Munich, 85764, Neuherberg, Germany
| | - Michiel Van Bel
- VIB Center for Plant Systems Biology, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Rabea Meyberg
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Cristina Vives
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Bellaterra, Cerdanyola del Vallès, 08193, Barcelona, Spain
| | - Jordi Morata
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Bellaterra, Cerdanyola del Vallès, 08193, Barcelona, Spain
| | | | - Manuel Hiss
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Yasuko Kamisugi
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Omar Saleh
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Guillaume Blanc
- Structural and Genomic Information Laboratory (IGS), Aix-Marseille Université, CNRS, UMR 7256 (IMM FR 3479), Marseille, France
| | - Eva L Decker
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Nico van Gessel
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | | | - Sean W Graham
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Lee E Gunter
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Stuart F McDaniel
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Sebastian N W Hoernstein
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Anders Larsson
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | | | | | - Priya Ranjan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Daniel S Rokshar
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
| | - Carl J Rothfels
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, CA, 94720-2465, USA
| | - Lucas Schneider
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Shengqiang Shu
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | | | - Fritz Thümmler
- Vertis Biotechnologie AG, Lise-Meitner-Str. 30, 85354, Freising, Germany
| | - Michael Tillich
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam-Golm, Germany
| | | | - Thomas Widiez
- Department of Plant Biology, University of Geneva, Sciences III, Geneva 4, CH-1211, Switzerland
- Department of Plant Biology & Pathology Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Gane Ka-Shu Wong
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
- Department of Medicine, University of Alberta, Edmonton, AB, T6G 2E1, Canada
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Ann Wymore
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Yong Zhang
- Shenzhen Huahan Gene Life Technology Co. Ltd, Shenzhen, China
| | - Andreas D Zimmer
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Ralph S Quatrano
- Department of Biology, Washington University, St. Louis, MO, USA
| | - Klaus F X Mayer
- Plant Genome and Systems Biology, Helmholtz Center Munich, 85764, Neuherberg, Germany
- WZW, Technical University Munich, Munich, Germany
| | | | - Josep M Casacuberta
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Bellaterra, Cerdanyola del Vallès, 08193, Barcelona, Spain
| | - Klaas Vandepoele
- VIB Center for Plant Systems Biology, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schaenzlestr. 18, 79104, Freiburg, Germany
| | - Andrew C Cuming
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Florian Maumus
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Jérome Salse
- INRA, UMR 1095 Genetics, Diversity and Ecophysiology of Cereals (GDEC), 5 Chemin de Beaulieu, 63100, Clermont-Ferrand, France
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Stefan A Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schaenzlestr. 18, 79104, Freiburg, Germany
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93
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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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94
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Köhler C, Springer N. Plant epigenomics-deciphering the mechanisms of epigenetic inheritance and plasticity in plants. Genome Biol 2017; 18:132. [PMID: 28683755 PMCID: PMC5501107 DOI: 10.1186/s13059-017-1260-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Claudia Köhler
- Uppsala BioCenter, Department of Plant Biology and Forest Genetics, The Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Almas Allé 5, SE-750 07, Uppsala, Sweden.
| | - Nathan Springer
- College of Biological Sciences, University of Minnesota, 306 Biological Sciences, 1445 Gortner Avenue, St Paul, MN, 55108, USA.
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95
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96
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Gouil Q, Baulcombe DC. DNA Methylation Signatures of the Plant Chromomethyltransferases. PLoS Genet 2016; 12:e1006526. [PMID: 27997534 PMCID: PMC5221884 DOI: 10.1371/journal.pgen.1006526] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 01/09/2017] [Accepted: 12/07/2016] [Indexed: 12/22/2022] Open
Abstract
DNA methylation in plants is traditionally partitioned into CG, CHG and CHH contexts (with H any nucleotide but G). By investigating DNA methylation patterns in trinucleotide contexts in four angiosperm species, we show that such a representation hides spatial and functional partitioning of different methylation pathways and is incomplete. CG methylation (mCG) is largely context-independent whereas, at CHG motifs, there is under-representation of mCCG in pericentric regions of A. thaliana and tomato and throughout the chromosomes of maize and rice. In A. thaliana the biased representation of mCCG in heterochromatin is related to specificities of H3K9 methyltransferase SUVH family members. At CHH motifs there is an over-representation of different variant forms of mCHH that, similarly to mCCG hypomethylation, is partitioned into the pericentric regions of the two dicots but dispersed in the monocot chromosomes. The over-represented mCHH motifs in A. thaliana associate with specific types of transposon including both class I and II elements. At mCHH the contextual bias is due to the involvement of various chromomethyltransferases whereas the context-independent CHH methylation in A. thaliana and tomato is mediated by the RNA-directed DNA methylation process that is most active in the gene-rich euchromatin. This analysis therefore reveals that the sequence context of the methylome of plant genomes is informative about the mechanisms associated with maintenance of methylation and the overlying chromatin structure. Dense cytosine DNA methylation (mC) in eukaryotes is associated with closed chromatin and gene silencing. In plants it is well known that the sequence context of the mC (either mCG, mCHG or mCHH) provides a clue as to which of several mechanisms is involved but now, based on detailed analyses of the DNA methylome in wild type and mutants of four plant species, we reveal that there is additional information in the mC sequence context. Low mCCG and over-representation of mCAA and mCTA or mCAT in A. thaliana and tomato differentiates regions of the chromosomes near the centromere where methylation is dominated by chromomethyltransferases from the chromosome arms in which mCHH is context-independent and predominantly RNA-directed. Rice and maize have similar sequence context-dependent DNA methylation but the corresponding chromosome domains are not spatially separate as in the dicots. The discovery of the subcomponents of plant methylomes based on sequence context will allow greater resolution in past and future analyses of plant methylomes.
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Affiliation(s)
- Quentin Gouil
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - David C. Baulcombe
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
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97
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Abstract
Despite major progress in dissecting the molecular pathways that control DNA methylation patterns in plants, little is known about the mechanisms that shape plant methylomes over evolutionary time. Drawing on recent intra- and interspecific epigenomic studies, we show that methylome evolution over long timescales is largely a byproduct of genomic changes. By contrast, methylome evolution over short timescales appears to be driven mainly by spontaneous epimutational events. We argue that novel methods based on analyses of the methylation site frequency spectrum (mSFS) of natural populations can provide deeper insights into the evolutionary forces that act at each timescale.
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Affiliation(s)
- Amaryllis Vidalis
- Population Epigenetics and Epigenomics, Technical University of Munich, Liesel-Beckman-Str. 2, 85354, Freising, Germany
| | - Daniel Živković
- Population Genetics, Technical University of Munich, Liesel-Beckman-Str. 2, 85354, Freising, Germany
| | - René Wardenaar
- Groningen Bioinformatics Centre, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - David Roquis
- Population Epigenetics and Epigenomics, Technical University of Munich, Liesel-Beckman-Str. 2, 85354, Freising, Germany
| | - Aurélien Tellier
- Population Genetics, Technical University of Munich, Liesel-Beckman-Str. 2, 85354, Freising, Germany.
| | - Frank Johannes
- Population Epigenetics and Epigenomics, Technical University of Munich, Liesel-Beckman-Str. 2, 85354, Freising, Germany. .,Institute for Advanced Study, Technical University of Munich, Lichtenbergstr. 2a, 85748, Garching, Germany.
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98
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Abstract
In plants, CG DNA methylation is prevalent in the transcribed regions of many constitutively expressed genes (gene body methylation; gbM), but the origin and function of gbM remain unknown. Here we report the discovery that Eutrema salsugineum has lost gbM from its genome, to our knowledge the first instance for an angiosperm. Of all known DNA methyltransferases, only CHROMOMETHYLASE 3 (CMT3) is missing from E. salsugineum Identification of an additional angiosperm, Conringia planisiliqua, which independently lost CMT3 and gbM, supports that CMT3 is required for the establishment of gbM. Detailed analyses of gene expression, the histone variant H2A.Z, and various histone modifications in E. salsugineum and in Arabidopsis thaliana epigenetic recombinant inbred lines found no evidence in support of any role for gbM in regulating transcription or affecting the composition and modification of chromatin over evolutionary timescales.
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