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Au PCK, Dennis ES, Wang MB. Analysis of Argonaute 4-Associated Long Non-Coding RNA in Arabidopsis thaliana Sheds Novel Insights into Gene Regulation through RNA-Directed DNA Methylation. Genes (Basel) 2017; 8:E198. [PMID: 28783101 PMCID: PMC5575662 DOI: 10.3390/genes8080198] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 08/01/2017] [Accepted: 08/02/2017] [Indexed: 12/20/2022] Open
Abstract
RNA-directed DNA methylation (RdDM) is a plant-specific de novo DNA methylation mechanism that requires long noncoding RNA (lncRNA) as scaffold to define target genomic loci. While the role of RdDM in maintaining genome stability is well established, how it regulates protein-coding genes remains poorly understood and few RdDM target genes have been identified. In this study, we obtained sequences of RdDM-associated lncRNAs using nuclear RNA immunoprecipitation against ARGONAUTE 4 (AGO4), a key component of RdDM that binds specifically with the lncRNA. Comparison of these lncRNAs with gene expression data of RdDM mutants identified novel RdDM target genes. Surprisingly, a large proportion of these target genes were repressed in RdDM mutants suggesting that they are normally activated by RdDM. These RdDM-activated genes are more enriched for gene body lncRNA than the RdDM-repressed genes. Histone modification and RNA analyses of several RdDM-activated stress response genes detected increased levels of active histone mark and short RNA transcript in the lncRNA-overlapping gene body regions in the ago4 mutant despite the repressed expression of these genes. These results suggest that RdDM, or AGO4, may play a role in maintaining or activating stress response gene expression by directing gene body chromatin modification preventing cryptic transcription.
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Affiliation(s)
- Phil Chi Khang Au
- Commonwealth Scientific and Industrial Research Organisation Agriculture, Canberra, Australian Capital Territory 2601, Australia.
| | - Elizabeth S Dennis
- Commonwealth Scientific and Industrial Research Organisation Agriculture, Canberra, Australian Capital Territory 2601, Australia.
| | - Ming-Bo Wang
- Commonwealth Scientific and Industrial Research Organisation Agriculture, Canberra, Australian Capital Territory 2601, Australia.
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2
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Wang XL, Song SH, Wu YS, Li YL, Chen TT, Huang ZY, Liu S, Dunwell TL, Pfeifer GP, Dunwell JM, Wamaedeesa R, Ullah I, Wang Y, Hu SN. Genome-wide mapping of 5-hydroxymethylcytosine in three rice cultivars reveals its preferential localization in transcriptionally silent transposable element genes. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:6651-63. [PMID: 26272901 PMCID: PMC4715260 DOI: 10.1093/jxb/erv372] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
5-Hydroxymethylcytosine (5hmC), a modified form of cytosine that is considered the sixth nucleobase in DNA, has been detected in mammals and is believed to play an important role in gene regulation. In this study, 5hmC modification was detected in rice by employing a dot-blot assay, and its levels was further quantified in DNA from different rice tissues using liquid chromatography-multistage mass spectrometry (LC-MS/MS/MS). The results showed large intertissue variation in 5hmC levels. The genome-wide profiles of 5hmC modification in three different rice cultivars were also obtained using a sensitive chemical labelling followed by a next-generation sequencing method. Thousands of 5hmC peaks were identified, and a comparison of the distributions of 5hmC among different rice cultivars revealed the specificity and conservation of 5hmC modification. The identified 5hmC peaks were significantly enriched in heterochromatin regions, and mainly located in transposable elements (TEs), especially around retrotransposons. The correlation analysis of 5hmC and gene expression data revealed a close association between 5hmC and silent TEs. These findings provide a resource for plant DNA 5hmC epigenetic studies and expand our knowledge of 5hmC modification.
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Affiliation(s)
- Xi-liang Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China Graduate University of Chinese Academy of Sciences, Yuquan Road, Beijing 100039, China
| | - Shu-hui Song
- Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yong-Sheng Wu
- Mudanjiang Youbo Pharmaceutical Co., Ltd, Heilongjiang 157011, China
| | - Yu-Li Li
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China Graduate University of Chinese Academy of Sciences, Yuquan Road, Beijing 100039, China
| | - Ting-ting Chen
- Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhi-yuan Huang
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China
| | - Shuo Liu
- Environmental Toxicology Graduate Program, University of California, Riverside, CA 92521, USA
| | | | - Gerd P Pfeifer
- Beckman Research Institute, City of Hope Medical Centre, Duarte, CA 91010, USA
| | - Jim M Dunwell
- School of Agriculture, Policy and Development, University of Reading, Earley Gate, Reading RG6 6AR, UK
| | - Raheema Wamaedeesa
- School of Agriculture, Policy and Development, University of Reading, Earley Gate, Reading RG6 6AR, UK
| | - Ihsan Ullah
- School of Agriculture, Policy and Development, University of Reading, Earley Gate, Reading RG6 6AR, UK Agricultural Biotechnology Research Institute, Faisalabad 38000, Pakistan
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program, University of California, Riverside, CA 92521, USA Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Song-nian Hu
- Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
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3
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Stępiński D. Functional ultrastructure of the plant nucleolus. PROTOPLASMA 2014; 251:1285-306. [PMID: 24756369 PMCID: PMC4209244 DOI: 10.1007/s00709-014-0648-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 04/08/2014] [Indexed: 05/23/2023]
Abstract
Nucleoli are nuclear domains present in almost all eukaryotic cells. They not only specialize in the production of ribosomal subunits but also play roles in many fundamental cellular activities. Concerning ribosome biosynthesis, particular stages of this process, i.e., ribosomal DNA transcription, primary RNA transcript processing, and ribosome assembly proceed in precisely defined nucleolar subdomains. Although eukaryotic nucleoli are conservative in respect of their main function, clear morphological differences between these structures can be noticed between individual kingdoms. In most cases, a plant nucleolus shows well-ordered structure in which four main ultrastructural components can be distinguished: fibrillar centers, dense fibrillar component, granular component, and nucleolar vacuoles. Nucleolar chromatin is an additional crucial structural component of this organelle. Nucleolonema, although it is not always an unequivocally distinguished nucleolar domain, has often been described as a well-grounded morphological element, especially of plant nucleoli. The ratios and morphology of particular subcompartments of a nucleolus can change depending on its metabolic activity which in turn is correlated with the physiological state of a cell, cell type, cell cycle phase, as well as with environmental influence. Precise attribution of functions to particular nucleolar subregions in the process of ribosome biosynthesis is now possible using various approaches. The presented description of plant nucleolar morphology summarizes previous knowledge regarding the function of nucleoli as well as of their particular subdomains not only in the course of ribosome biosynthesis.
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Affiliation(s)
- Dariusz Stępiński
- Department of Cytophysiology, Faculty of Biology and Environmental Protection, University of Łódź, Pomorska 141/143, 90-236, Łódź, Poland,
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4
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Kim MY, Zilberman D. DNA methylation as a system of plant genomic immunity. TRENDS IN PLANT SCIENCE 2014; 19:320-6. [PMID: 24618094 DOI: 10.1016/j.tplants.2014.01.014] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Revised: 01/28/2014] [Accepted: 01/31/2014] [Indexed: 05/06/2023]
Abstract
Transposons are selfish genetic sequences that can increase their copy number and inflict substantial damage on their hosts. To combat these genomic parasites, plants have evolved multiple pathways to identify and silence transposons by methylating their DNA. Plants have also evolved mechanisms to limit the collateral damage from the antitransposon machinery. In this review, we examine recent developments that have elucidated many of the molecular workings of these pathways. We also highlight the evidence that the methylation and demethylation pathways interact, indicating that plants have a highly sophisticated, integrated system of transposon defense that has an important role in the regulation of gene expression.
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Affiliation(s)
- M Yvonne Kim
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Daniel Zilberman
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.
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5
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Xu C, Tian J, Mo B. siRNA-mediated DNA methylation and H3K9 dimethylation in plants. Protein Cell 2013; 4:656-63. [PMID: 23943321 DOI: 10.1007/s13238-013-3052-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 07/04/2013] [Indexed: 12/25/2022] Open
Abstract
Heterochromatic siRNAs regulate transcriptional gene silencing by inducing DNA methylation and histone H3K9 dimethylation. Recent advances have revealed the distinct phases involved in siRNA mediated silencing pathway, although the precise functions of a number of factors remain undesignated, putative mechanisms for the connection between DNA and histone methylation have been investigated, and much effort has been invested to understand the biological functions of siRNA-mediated epigenetic modification. In this review, we summarize the mechanism of siRNA-mediated epigenetic modification, which involves the production of siRNA and the recruitments of DNA and histone methytransferases to the target sequences assisted by complementary pairing between 24-nt siRNAs and nascent scaffold RNAs, the roles of siRNA-mediated epigenetic modification in maintaining genome stability and regulating gene expression have been discussed, newly identified players of the siRNA mediated silencing pathway have also been introduced.
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Affiliation(s)
- Chi Xu
- College of Life Science, Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Jing Tian
- College of Life Science, Shenzhen Key Laboratory of Marine Biological Resources and Ecological Environment, Shenzhen University, Shenzhen, 518060, China
| | - Beixin Mo
- College of Life Science, Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, 518060, China.
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K?í?ová K, Depicker A, Kova?ík A. Epigenetic switches of tobacco transgenes associate with transient redistribution of histone marks in callus culture. Epigenetics 2013; 8:666-76. [PMID: 23770973 PMCID: PMC3857346 DOI: 10.4161/epi.24613] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 03/28/2013] [Accepted: 04/08/2013] [Indexed: 11/19/2022] Open
Abstract
In plants, silencing is usually accompanied by DNA methylation and heterochromatic histone marks. We studied these epigenetic modifications in different epialleles of 35S promoter (P35S)-driven tobacco transgenes. In locus 1, the T-DNA was organized as an inverted repeat, and the residing neomycin phosphotransferase II reporter gene (P35S-nptII) was silenced at the posttranscriptional (PTGS) level. Transcriptionally silenced (TGS) epialleles were generated by trans-acting RNA signals in hybrids or in a callus culture. PTGS to TGS conversion in callus culture was accompanied by loss of the euchromatic H3K4me3 mark in the transcribed region of locus 1, but this change was not transmitted to the regenerated plants from these calli. In contrast, cytosine methylation that spread from the transcribed region into the promoter was maintained in regenerants. Also, the TGS epialleles generated by trans-acting siRNAs did not change their active histone modifications. Thus, both TGS and PTGS epialleles exhibit euchromatic (H3K4me3 and H3K9ac) histone modifications despite heavy DNA methylation in the promoter and transcribed region, respectively. However, in the TGS locus (271), abundant heterochromatic H3K9me2 marks and DNA methylation were present on P35S. Heterochromatic histone modifications are not automatically installed on transcriptionally silenced loci in tobacco, suggesting that repressive histone marks and cytosine methylation may be uncoupled. However, transient loss of euchromatic modifications may guide de novo DNA methylation leading to formation of stable repressed epialleles with recovered eukaryotic marks. Compilation of available data on epigenetic modification of inactivated P35S in different systems is provided.
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Affiliation(s)
- Kate?ina K?í?ová
- Institute of Biophysics, Academy of Sciences; Královopolská, Brno, Czech Republic
| | - Ann Depicker
- Department of Plant Systems Biology; VIB; Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics; Ghent University; Gent, Belgium
| | - Ale? Kova?ík
- Institute of Biophysics, Academy of Sciences; Královopolská, Brno, Czech Republic
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Stępiński D. Levels of DNA methylation and histone methylation and acetylation change in root tip cells of soybean seedlings grown at different temperatures. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2012; 61:9-17. [PMID: 23023582 DOI: 10.1016/j.plaphy.2012.09.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 09/01/2012] [Indexed: 06/01/2023]
Abstract
In order to check whether changes in DNA and histone modifications occur in the nuclei of root tip cells of soybean seedlings grown 1) under control conditions (25 °C), 2) subjected to chilling stress (10 °C) and 3) recovered (25 °C) after chilling, measurements of fluorescence intensity with the use of antibodies to heterochromatin as well as to euchromatin markers were carried out. Moreover, the number and sizes of chromocentres were analyzed. The studies showed that during chilling stress the fluorescence intensity for the markers characteristic of heterochromatin increased while for the markers of euchromatin decreased in comparison to the control. After the recovery the converse situation was observed, i.e. increase in fluorescence intensity for euchromatin markers and decrease in heterochromatin markers. The number of chromocentres remained unchanged in the nuclei of all three studied variants. However, differences in the sizes of chromocentres were observed - the highest number of big chromocentres and simultaneously the lowest number of small chromocentres were in the nuclei of stressed plants. Conversely - in the nuclei of recovered plants there were the lowest number of big chromocentres and the highest number of small ones. The treatment of seedlings with the inhibitors of DNA methylation (5-aza-dC) and histone deacetylation (NaBu) also caused changes in fluorescence intensity and chromocentre sizes in soybean nuclei. These results suggest that DNA and histone modification patterns can be altered in soybean nuclei by different growth temperatures and by appropriate inhibitors influencing epigenetic chromatic modifications.
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Affiliation(s)
- Dariusz Stępiński
- Department of Cytophysiology, Faculty of Biology and Environmental Protection, University of Łódź, Pomorska 141/143, 90-236 Łódź, Poland.
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Coleman-Derr D, Zilberman D. Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. PLoS Genet 2012; 8:e1002988. [PMID: 23071449 PMCID: PMC3469445 DOI: 10.1371/journal.pgen.1002988] [Citation(s) in RCA: 258] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2012] [Accepted: 08/10/2012] [Indexed: 01/07/2023] Open
Abstract
The regulation of eukaryotic chromatin relies on interactions between many epigenetic factors, including histone modifications, DNA methylation, and the incorporation of histone variants. H2A.Z, one of the most conserved but enigmatic histone variants that is enriched at the transcriptional start sites of genes, has been implicated in a variety of chromosomal processes. Recently, we reported a genome-wide anticorrelation between H2A.Z and DNA methylation, an epigenetic hallmark of heterochromatin that has also been found in the bodies of active genes in plants and animals. Here, we investigate the basis of this anticorrelation using a novel h2a.z loss-of-function line in Arabidopsis thaliana. Through genome-wide bisulfite sequencing, we demonstrate that loss of H2A.Z in Arabidopsis has only a minor effect on the level or profile of DNA methylation in genes, and we propose that the global anticorrelation between DNA methylation and H2A.Z is primarily caused by the exclusion of H2A.Z from methylated DNA. RNA sequencing and genomic mapping of H2A.Z show that H2A.Z enrichment across gene bodies, rather than at the TSS, is correlated with lower transcription levels and higher measures of gene responsiveness. Loss of H2A.Z causes misregulation of many genes that are disproportionately associated with response to environmental and developmental stimuli. We propose that H2A.Z deposition in gene bodies promotes variability in levels and patterns of gene expression, and that a major function of genic DNA methylation is to exclude H2A.Z from constitutively expressed genes. Eukaryotes package their DNA to fit within the nucleus using well-conserved proteins, called histones, that form the building blocks of nucleosomes, the fundamental units of chromatin. Histone variants are specialized versions of these proteins that change the chromatin landscape by altering the biochemical properties and interacting partners of the nucleosome. H2A.Z, a conserved eukaryotic histone variant, is preferentially enriched at the beginnings of genes, though the significance of this enrichment remains unknown. We and others have shown that H2A.Z is conspicuously absent from methylated DNA across the genome in plants and animals. Typically considered a mark of epigenetic silencing, DNA methylation has more recently been discovered in the bodies of many genes. Here, we present evidence that the genome-wide anticorrelation between DNA methylation and H2A.Z enrichment in Arabidopsis is the result of DNA methylation acting to prevent H2A.Z incorporation. We demonstrate that the presence of H2A.Z within gene bodies is correlated with lower transcription levels and higher variability in expression patterns across tissue types and environmental conditions, and we propose that a major function of gene-body DNA methylation is to exclude H2A.Z from the bodies of highly and constitutively expressed genes.
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Affiliation(s)
| | - Daniel Zilberman
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
- * E-mail:
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9
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Sasaki T, Kobayashi A, Saze H, Kakutani T. RNAi-independent de novo DNA methylation revealed in Arabidopsis mutants of chromatin remodeling gene DDM1. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 70:750-758. [PMID: 22269081 DOI: 10.1111/j.1365-313x.2012.04911.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Methylation of histone H3 lysine 9 (H3K9me) and small RNAs are associated with constitutively silent chromatin in diverse eukaryotes including plants. In plants, silent transposons are also marked by cytosine methylation, especially at non-CpG sites. Transposon-specific non-CpG methylation in plants is controlled by small RNAs and H3K9me. Although it is often assumed that small RNA directs H3K9me, interaction between small RNA and H3K9me has not been directly demonstrated in plants. We have previously shown that a mutation in the chromatin remodeling gene DDM1 (DECREASE IN DNA METHYLATION 1) induces a global decrease but a local increase of cytosine methylation and accumulation of small RNA at a locus called BONSAI. Here we show that de novo BONSAI methylation does not depend on RNAi but does depend on H3K9me. In mutants of H3K9 methyltransferase gene KRYPTONITE or the H3K9me-dependent DNA methyltransferase gene CHROMOMETHYALSE3, the ddm1-induced de novo cytosine methylation was abolished for all three contexts (CpG, CpHpG and CpHpH). Furthermore, RNAi mutants showed strong developmental defects when combined with the ddm1 mutation. Our results revealed unexpected interactions of epigenetic modifications that may be conserved among diverse eukaryotes.
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Affiliation(s)
- Taku Sasaki
- Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
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10
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You W, Tyczewska A, Spencer M, Daxinger L, Schmid MW, Grossniklaus U, Simon SA, Meyers BC, Matzke AJM, Matzke M. Atypical DNA methylation of genes encoding cysteine-rich peptides in Arabidopsis thaliana. BMC PLANT BIOLOGY 2012; 12:51. [PMID: 22512782 PMCID: PMC3422182 DOI: 10.1186/1471-2229-12-51] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Accepted: 04/19/2012] [Indexed: 05/20/2023]
Abstract
BACKGROUND In plants, transposons and non-protein-coding repeats are epigenetically silenced by CG and non-CG methylation. This pattern of methylation is mediated in part by small RNAs and two specialized RNA polymerases, termed Pol IV and Pol V, in a process called RNA-directed DNA methylation. By contrast, many protein-coding genes transcribed by Pol II contain in their gene bodies exclusively CG methylation that is independent of small RNAs and Pol IV/Pol V activities. It is unclear how the different methylation machineries distinguish between transposons and genes. Here we report on a group of atypical genes that display in their coding region a transposon-like methylation pattern, which is associated with gene silencing in sporophytic tissues. RESULTS We performed a methylation-sensitive amplification polymorphism analysis to search for targets of RNA-directed DNA methylation in Arabidopsis thaliana and identified several members of a gene family encoding cysteine-rich peptides (CRPs). In leaves, the CRP genes are silent and their coding regions contain dense, transposon-like methylation in CG, CHG and CHH contexts, which depends partly on the Pol IV/Pol V pathway and small RNAs. Methylation in the coding region is reduced, however, in the synergid cells of the female gametophyte, where the CRP genes are specifically expressed. Further demonstrating that expressed CRP genes lack gene body methylation, a CRP4-GFP fusion gene under the control of the constitutive 35 S promoter remains unmethylated in leaves and is transcribed to produce a translatable mRNA. By contrast, a CRP4-GFP fusion gene under the control of a CRP4 promoter fragment acquires CG and non-CG methylation in the CRP coding region in leaves similar to the silent endogenous CRP4 gene. CONCLUSIONS Unlike CG methylation in gene bodies, which does not dramatically affect Pol II transcription, combined CG and non-CG methylation in CRP coding regions is likely to contribute to gene silencing in leaves because loss of this methylation in synergid cells is associated with CRP gene expression. We discuss this unusual methylation pattern and its alteration in synergid cells as well as the possible retrogene origin and evolutionary significance of CRP genes that are methylated like transposons.
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Affiliation(s)
- Wanhui You
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria
| | - Agata Tyczewska
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Matthew Spencer
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria
| | - Lucia Daxinger
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria
- Epigenetics Laboratory, Queensland Institute of Medical Research, Herston, Brisbane, Queensland, Australia
| | - Marc W Schmid
- Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Ueli Grossniklaus
- Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Stacey A Simon
- Department of Plant and Soil Sciences, and Delaware Biotechnology Institute, University of Delaware, Newark, USA
| | - Blake C Meyers
- Department of Plant and Soil Sciences, and Delaware Biotechnology Institute, University of Delaware, Newark, USA
| | - Antonius JM Matzke
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria
| | - Marjori Matzke
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria
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Saze H, Kakutani T. Differentiation of epigenetic modifications between transposons and genes. CURRENT OPINION IN PLANT BIOLOGY 2011; 14:81-7. [PMID: 20869294 DOI: 10.1016/j.pbi.2010.08.017] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2010] [Accepted: 08/30/2010] [Indexed: 05/23/2023]
Abstract
Transposable elements (TEs) and repeats are methylated and silenced epigenetically in a variety of organisms including plants. Recent results in Arabidopsis suggest that the TE silencing can be reprogrammed by small RNA during gametogenesis. On the other hand, TE-specific DNA methylation independent of small RNA can be induced by H3K9 methylation through mechanisms conserved between plants and fungi. Methylation of CG sites is found not only in TEs but also in the body of constitutively transcribed genes. Although the function of gene-body methylation is still elusive, the distribution and control of this type of DNA methylation are very similar between plants and animals. Possible interactions of these multiple layers of epigenetic marks and their evolution are discussed.
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Affiliation(s)
- Hidetoshi Saze
- Department of Integrated Genetics, National Institute of Genetics, Yata 1111, Mishima 411-8540, Shizuoka, Japan
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