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Griess O, Domb K, Katz A, Harris KD, Heskiau KG, Ohad N, Zemach A. Knockout of DDM1 in Physcomitrium patens disrupts DNA methylation with a minute effect on transposon regulation and development. PLoS One 2023; 18:e0279688. [PMID: 36888585 PMCID: PMC9994747 DOI: 10.1371/journal.pone.0279688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 12/13/2022] [Indexed: 03/09/2023] Open
Abstract
The Snf2 chromatin remodeler, DECREASE IN DNA METHYLATION 1 (DDM1) facilitates DNA methylation. In flowering plants, DDM1 mediates methylation in heterochromatin, which is targeted primarily by MET1 and CMT methylases and is necessary for silencing transposons and for proper development. DNA methylation mechanisms evolved throughout plant evolution, whereas the role of DDM1 in early terrestrial plants remains elusive. Here, we studied the function of DDM1 in the moss, Physcomitrium (Physcomitrella) patens, which has robust DNA methylation that suppresses transposons and is mediated by a MET1, a CMT, and a DNMT3 methylases. To elucidate the role of DDM1 in P. patens, we have generated a knockout mutant and found DNA methylation to be strongly disrupted at any of its sequence contexts. Symmetric CG and CHG sequences were affected stronger than asymmetric CHH sites. Furthermore, despite their separate targeting mechanisms, CG (MET) and CHG (CMT) methylation were similarly depleted by about 75%. CHH (DNMT3) methylation was overall reduced by about 25%, with an evident hyper-methylation activity within lowly-methylated euchromatic transposon sequences. Despite the strong hypomethylation effect, only a minute number of transposons were transcriptionally activated in Ppddm1. Finally, Ppddm1 was found to develop normally throughout the plant life cycle. These results demonstrate that DNA methylation is strongly dependent on DDM1 in a non-flowering plant; that DDM1 is required for plant-DNMT3 (CHH) methylases, though to a lower extent than for MET1 and CMT enzymes; and that distinct and separate methylation pathways (e.g. MET1-CG and CMT-CHG), can be equally regulated by the chromatin and that DDM1 plays a role in it. Finally, our data suggest that the biological significance of DDM1 in terms of transposon regulation and plant development, is species dependent.
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Affiliation(s)
- Ofir Griess
- School of Plant Sciences and Food Security, Tel-Aviv University, Tel- Aviv, Israel
| | - Katherine Domb
- School of Plant Sciences and Food Security, Tel-Aviv University, Tel- Aviv, Israel
| | - Aviva Katz
- School of Plant Sciences and Food Security, Tel-Aviv University, Tel- Aviv, Israel
| | - Keith D. Harris
- School of Plant Sciences and Food Security, Tel-Aviv University, Tel- Aviv, Israel
| | - Karina G. Heskiau
- School of Plant Sciences and Food Security, Tel-Aviv University, Tel- Aviv, Israel
| | - Nir Ohad
- School of Plant Sciences and Food Security, Tel-Aviv University, Tel- Aviv, Israel
- * E-mail: (AZ); (NO)
| | - Assaf Zemach
- School of Plant Sciences and Food Security, Tel-Aviv University, Tel- Aviv, Israel
- * E-mail: (AZ); (NO)
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2
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Harris KD, Zemach A. Contiguous and stochastic CHH methylation patterns of plant DRM2 and CMT2 revealed by single-read methylome analysis. Genome Biol 2020; 21:194. [PMID: 32762764 PMCID: PMC7412668 DOI: 10.1186/s13059-020-02099-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 07/08/2020] [Indexed: 12/12/2022] Open
Abstract
Cytosine methylome data is commonly generated through next-generation sequencing, with analyses averaging methylation states of individual reads. We propose an alternative method of analysing single-read methylome data. Using this method, we identify patterns relating to the mechanism of two plant non-CG-methylating enzymes, CMT2 and DRM2. CMT2-methylated regions show higher stochasticity, while DRM2-methylated regions have higher variation among cells. Based on these patterns, we develop a classifier that predicts enzyme activity in different species and tissues. To facilitate further single-read analyses, we develop a genome browser, SRBrowse, optimised for visualising and analysing sequencing data at single-read resolution.
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Affiliation(s)
- Keith D Harris
- School of Plant Sciences and Food Security, Tel Aviv University, Haim Levanon, Tel Aviv, Israel
| | - Assaf Zemach
- School of Plant Sciences and Food Security, Tel Aviv University, Haim Levanon, Tel Aviv, Israel.
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3
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Tuller T, Diament A, Yahalom A, Zemach A, Atar S, Chamovitz DA. The COP9 signalosome influences the epigenetic landscape of Arabidopsis thaliana. Bioinformatics 2020; 35:2718-2723. [PMID: 30596896 DOI: 10.1093/bioinformatics/bty1053] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 10/20/2018] [Accepted: 12/21/2018] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION The COP9 signalosome is a highly conserved multi-protein complex consisting of eight subunits, which influences key developmental pathways through its regulation of protein stability and transcription. In Arabidopsis thaliana, mutations in the COP9 signalosome exhibit a number of diverse pleiotropic phenotypes. Total or partial loss of COP9 signalosome function in Arabidopsis leads to misregulation of a number of genes involved in DNA methylation, suggesting that part of the pleiotropic phenotype is due to global effects on DNA methylation. RESULTS We determined and analyzed the methylomes and transcriptomes of both partial- and total-loss-of-function Arabidopsis mutants of the COP9 signalosome. Our results support the hypothesis that the COP9 signalosome has a global genome-wide effect on methylation and that this effect is at least partially encoded in the DNA. Our analyses suggest that COP9 signalosome-dependent methylation is related to gene expression regulation in various ways. Differentially methylated regions tend to be closer in the 3D conformation of the genome to differentially expressed genes. These results suggest that the COP9 signalosome has a more comprehensive effect on gene expression than thought before, and this is partially related to regulation of methylation. The high level of COP9 signalosome conservation among eukaryotes may also suggest that COP9 signalosome regulates methylation not only in plants but also in other eukaryotes, including humans. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Tamir Tuller
- Department of Biomedical Engineering.,Sagol School of Neuroscience
| | | | - Avital Yahalom
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Assaf Zemach
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | | | - Daniel A Chamovitz
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
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4
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Harris KD, Lloyd JPB, Domb K, Zilberman D, Zemach A. DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. Epigenetics Chromatin 2019; 12:62. [PMID: 31601251 PMCID: PMC6786280 DOI: 10.1186/s13072-019-0307-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 09/25/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND DNA methylation of active genes, also known as gene body methylation, is found in many animal and plant genomes. Despite this, the transcriptional and developmental role of such methylation remains poorly understood. Here, we explore the dynamic range of DNA methylation in honey bee, a model organism for gene body methylation. RESULTS Our data show that CG methylation in gene bodies globally fluctuates during honey bee development. However, these changes cause no gene expression alterations. Intriguingly, despite the global alterations, tissue-specific CG methylation patterns of complete genes or exons are rare, implying robust maintenance of genic methylation during development. Additionally, we show that CG methylation maintenance fluctuates in somatic cells, while reaching maximum fidelity in sperm cells. Finally, unlike universally present CG methylation, we discovered non-CG methylation specifically in bee heads that resembles such methylation in mammalian brain tissue. CONCLUSIONS Based on these results, we propose that gene body CG methylation can oscillate during development if it is kept to a level adequate to preserve function. Additionally, our data suggest that heightened non-CG methylation is a conserved regulator of animal nervous systems.
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Affiliation(s)
- Keith D Harris
- School of Plant Sciences and Food Security, Tel-Aviv University, 69978, Tel-Aviv, Israel
| | - James P B Lloyd
- Center for RNA Systems Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA, 6009, Australia
| | - Katherine Domb
- School of Plant Sciences and Food Security, Tel-Aviv University, 69978, Tel-Aviv, Israel
| | - Daniel Zilberman
- Department of Cell and Developmental Biology, John Innes Center, Norwich, UK.
| | - Assaf Zemach
- School of Plant Sciences and Food Security, Tel-Aviv University, 69978, Tel-Aviv, Israel.
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Yadav NS, Khadka J, Domb K, Zemach A, Grafi G. CMT3 and SUVH4/KYP silence the exonic Evelknievel retroelement to allow for reconstitution of CMT1 mRNA. Epigenetics Chromatin 2018; 11:69. [PMID: 30446008 PMCID: PMC6238269 DOI: 10.1186/s13072-018-0240-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 11/09/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The Chromomethylase 1 (CMT1) has long been considered a nonessential gene because, in certain Arabidopsis ecotypes, the CMT1 gene is disrupted by the Evelknievel (EK) retroelement, inserted within exon 13, or contains frameshift mutations, resulting in a truncated, non-functional protein. In contrast to other transposable elements, no transcriptional activation of EK was observed under stress conditions (e.g., protoplasting). RESULTS We wanted to explore the regulatory pathway responsible for EK silencing in the Ler ecotype and its effect on CMT1 transcription. Methylome databases confirmed that EK retroelement is heavily methylated and methylation is extended toward CMT1 downstream region. Strong transcriptional activation of EK accompanied by significant reduction in non-CG methylation was found in cmt3 and kyp2, but not in ddm1 or RdDM mutants. EK activation in cmt3 and kyp2 did not interfere with upstream CMT1 expression but abolish transcription through the EK. We identified, in wild-type Ler, three spliced variants in which the entire EK is spliced out; one variant (25% of splicing incidents) facilitates proper reconstitution of an intact CMT1 mRNA. We could recover very low amount of the full-length CMT1 mRNA from WT Ler and Col, but not from cmt3 mutant. CONCLUSIONS Our findings highlight CMT3-SUVH4/KYP as the major pathway silencing the intragenic EK via inducing non-CG methylation. Furthermore, retroelement insertion within exons (e.g., CMT1) may not lead to a complete abolishment of the gene product when the element is kept silent. Rather the element can be spliced out to bring about reconstruction of an intact, functional mRNA and possibly retrieval of an active protein.
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Affiliation(s)
- Narendra Singh Yadav
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, 84990, Midreshet Ben Gurion, Israel
| | - Janardan Khadka
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, 84990, Midreshet Ben Gurion, Israel
| | - Katherine Domb
- The School of Plant Sciences and Food Security, Tel-Aviv University, 69978, Tel Aviv, Israel
| | - Assaf Zemach
- The School of Plant Sciences and Food Security, Tel-Aviv University, 69978, Tel Aviv, Israel
| | - Gideon Grafi
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, 84990, Midreshet Ben Gurion, Israel.
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6
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Khan A, Yadav NS, Morgenstern Y, Zemach A, Grafi G. Activation of Tag1 transposable elements in Arabidopsis dedifferentiating cells and their regulation by CHROMOMETHYLASE 3-mediated CHG methylation. Biochim Biophys Acta 2016; 1859:1289-98. [PMID: 27475038 DOI: 10.1016/j.bbagrm.2016.07.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Revised: 07/13/2016] [Accepted: 07/25/2016] [Indexed: 12/11/2022]
Abstract
Dedifferentiation, that is, the acquisition of stem cell-like state, commonly induced by stress (e.g., protoplasting), is characterized by open chromatin conformation, a chromatin state that could lead to activation of transposable elements (TEs). Here, we studied the activation of the Arabidopsis class II TE Tag1, in which two copies, situated close to each other (near genes) on chromosome 1 are found in Landsberg erecta (Ler) but not in Columbia (Col). We first transformed protoplasts with a construct in which a truncated Tag1 (ΔTag1 non-autonomous) blocks the expression of a reporter gene AtMBD5-GFP and found a relatively high ectopic excision of ΔTag1 accompanied by expression of AtMBD5-GFP in protoplasts derived from Ler compared to Col; further increase was observed in ddm1 (decrease in DNA methylation1) protoplasts (Ler background). Ectopic excision was associated with transcription of the endogenous Tag1 and changes in histone H3 methylation at the promoter region. Focusing on the endogenous Tag1 elements we found low level of excision in Ler protoplasts, which was slightly and strongly enhanced in ddm1 and cmt3 (chromomethylase3) protoplasts, respectively, concomitantly with reduction in Tag1 gene body (GB) CHG methylation and increased Tag1 transcription; strong activation of Tag1 was also observed in cmt3 leaves. Notably, in cmt3, but not in ddm1, Tag1 elements were excised out from their original sites and transposed elsewhere in the genome. Our results suggest that dedifferentiation is associated with Tag1 activation and that CMT3 rather than DDM1 plays a central role in restraining Tag1 activation via inducing GB CHG methylation.
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Affiliation(s)
- Asif Khan
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben Gurion 84990, Israel
| | - Narendra Singh Yadav
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben Gurion 84990, Israel
| | - Yaakov Morgenstern
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben Gurion 84990, Israel
| | - Assaf Zemach
- Department of Molecular Biology and Ecology of Plants, Tel-Aviv University, 69978 Tel Aviv, Israel
| | - Gideon Grafi
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben Gurion 84990, Israel.
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7
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Shemer O, Landau U, Candela H, Zemach A, Eshed Williams L. Competency for shoot regeneration from Arabidopsis root explants is regulated by DNA methylation. Plant Sci 2015; 238:251-61. [PMID: 26259192 DOI: 10.1016/j.plantsci.2015.06.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 06/08/2015] [Accepted: 06/14/2015] [Indexed: 05/11/2023]
Abstract
Plants exhibit high capacity to regenerate in three alternative pathways: tissue repair, somatic embryogenesis and de novo organogenesis. For most plants, de novo organ initiation can be easily achieved in tissue culture by exposing explants to auxin and/or cytokinin, yet the competence to regenerate varies among species and within tissues from the same plant. In Arabidopsis, root explants incubated directly on cytokinin-rich shoot inducing medium (SIM-direct), are incapable of regenerating shoots, and a pre-incubation step on auxin-rich callus inducing medium (CIM) is required to acquire competency to regenerate on the SIM. However the mechanism underlying competency acquisition still remains elusive. Here we show that the chromomethylase 3 (cmt3) mutant which exhibits significant reduction in CHG methylation, shows high capacity to regenerate on SIM-direct and that regeneration occurs via direct organogenesis. In WT, WUSCHEL (WUS) promoter, an essential gene for shoot formation, is highly methylated, and its expression on SIM requires pre-incubation on CIM. However, in cmt3, WUS expression induced by SIM-direct. We propose that pre-incubation on CIM is required for the re-activation of cell division. Following the transfer of roots to SIM, the intensive cell division activity continues, and in the presence of cytokinin leads to a dilution in DNA methylation that allows certain genes required for shoot regeneration to respond to SIM, thereby advancing shoot formation.
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Affiliation(s)
- Or Shemer
- The Robert H. Smith Institute of Plant Sciences & Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Udi Landau
- The Robert H. Smith Institute of Plant Sciences & Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Héctor Candela
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | - Assaf Zemach
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv 69978, Israel
| | - Leor Eshed Williams
- The Robert H. Smith Institute of Plant Sciences & Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.
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8
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Ibarra CA, Feng X, Schoft VK, Hsieh TF, Uzawa R, Rodrigues JA, Zemach A, Chumak N, Machlicova A, Nishimura T, Rojas D, Fischer RL, Tamaru H, Zilberman D. Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science 2012; 337:1360-1364. [PMID: 22984074 PMCID: PMC4034762 DOI: 10.1126/science.1224839] [Citation(s) in RCA: 375] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The Arabidopsis thaliana central cell, the companion cell of the egg, undergoes DNA demethylation before fertilization, but the targeting preferences, mechanism, and biological significance of this process remain unclear. Here, we show that active DNA demethylation mediated by the DEMETER DNA glycosylase accounts for all of the demethylation in the central cell and preferentially targets small, AT-rich, and nucleosome-depleted euchromatic transposable elements. The vegetative cell, the companion cell of sperm, also undergoes DEMETER-dependent demethylation of similar sequences, and lack of DEMETER in vegetative cells causes reduced small RNA-directed DNA methylation of transposons in sperm. Our results demonstrate that demethylation in companion cells reinforces transposon methylation in plant gametes and likely contributes to stable silencing of transposable elements across generations.
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Affiliation(s)
- Christian A. Ibarra
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Xiaoqi Feng
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Vera K. Schoft
- Gregor Mendel Institute, Austrian Academy of Sciences, 1030 Vienna, Austria
| | - Tzung-Fu Hsieh
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Rie Uzawa
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Jessica A. Rodrigues
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Assaf Zemach
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Nina Chumak
- Gregor Mendel Institute, Austrian Academy of Sciences, 1030 Vienna, Austria
| | - Adriana Machlicova
- Gregor Mendel Institute, Austrian Academy of Sciences, 1030 Vienna, Austria
| | - Toshiro Nishimura
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Denisse Rojas
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Robert L. Fischer
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Hisashi Tamaru
- Gregor Mendel Institute, Austrian Academy of Sciences, 1030 Vienna, Austria
| | - Daniel Zilberman
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
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9
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10
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Abstract
Eukaryotic cytosine methylation represses transcription but also occurs in the bodies of active genes, and the extent of methylation biology conservation is unclear. We quantified DNA methylation in 17 eukaryotic genomes and found that gene body methylation is conserved between plants and animals, whereas selective methylation of transposons is not. We show that methylation of plant transposons in the CHG context extends to green algae and that exclusion of histone H2A.Z from methylated DNA is conserved between plants and animals, and we present evidence for RNA-directed DNA methylation of fungal genes. Our data demonstrate that extant DNA methylation systems are mosaics of conserved and derived features, and indicate that gene body methylation is an ancient property of eukaryotic genomes.
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Affiliation(s)
- Assaf Zemach
- Department of Plant and Microbial Biology, 211 Koshland Hall, University of California, Berkeley, CA 94720, USA
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11
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Zemach A, Paul LK, Stambolsky P, Efroni I, Rotter V, Grafi G. The C-terminal domain of the Arabidopsis AtMBD7 protein confers strong chromatin binding activity. Exp Cell Res 2009; 315:3554-62. [PMID: 19647732 DOI: 10.1016/j.yexcr.2009.07.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Revised: 07/26/2009] [Accepted: 07/27/2009] [Indexed: 12/01/2022]
Abstract
The Arabidopsis MBD7 (AtMBD7) - a naturally occurring poly MBD protein - was previously found to be functional in binding methylated-CpG dinucleotides in vitro and localized to highly methylated chromocenters in vivo. Furthermore, AtMBD7 has significantly lower mobility within the nucleus conferred by cooperative activity of its three MBD motifs. Here we show that besides the MBD motifs, AtMBD7 possesses a strong chromatin binding domain located at its C-terminus designated sticky-C (StkC). Mutational analysis showed that a glutamic acid residue near the C-terminus is essential though not sufficient for the StkC function. Further analysis demonstrated that this motif can render nuclear proteins highly immobile both in plant and animal cells, without affecting their native subnuclear localization. Thus, the C-terminal, StkC motif plays an important role in fastening AtMBD7 to its chromosomal, CpG-methylated sites. It may be possible to utilize this motif for fastening nuclear proteins to their chromosomal sites both in plant and animal cells for research and gene therapy applications.
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Affiliation(s)
- Assaf Zemach
- Department of Plant Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
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12
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Abstract
Parent-of-origin-specific (imprinted) gene expression is regulated in Arabidopsis thaliana endosperm by cytosine demethylation of the maternal genome mediated by the DNA glycosylase DEMETER, but the extent of the methylation changes is not known. Here, we show that virtually the entire endosperm genome is demethylated, coupled with extensive local non-CG hypermethylation of small interfering RNA-targeted sequences. Mutation of DEMETER partially restores endosperm CG methylation to levels found in other tissues, indicating that CG demethylation is specific to maternal sequences. Endosperm demethylation is accompanied by CHH hypermethylation of embryo transposable elements. Our findings demonstrate extensive reconfiguration of the endosperm methylation landscape that likely reinforces transposon silencing in the embryo.
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Affiliation(s)
- Tzung-Fu Hsieh
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
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13
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Abstract
Three methyl-CpG-binding domain (MBD) proteins in Arabidopsis, AtMBD5, AtMBD6, and AtMBD7, are functional in binding methylated CpG dinucleotides in vitro and localize to the highly CpG-methylated chromocenters in vivo. These proteins differ, however, in their subnuclear localization pattern; AtMBD5 and AtMBD6, each containing a single MBD motif, show preference for two perinucleolar chromocenters, whereas AtMBD7, a naturally occurring poly-MBD protein containing three MBD motifs, localizes to all chromocenters. Here we studied the significance of multiple MBD motifs for subnuclear localization and mobility in living cells. We found that the number of MBD motifs determines the subnuclear localization of the MBD protein. Furthermore, live kinetic experiments showed that AtMBD7-green fluorescent protein (GFP) has lower mobility than AtMBD5-GFP and AtMBD6-GFP, which is conferred by cooperative activity of its three MBD motifs. Thus, the number of MBD motifs appears to affect not only binding affinity and mobility within the nucleus, but also the subnuclear localization of the protein. Our results suggest that poly-MBD proteins can directly affect chromatin structure by inducing intra- and inter-chromatin compaction via bridging over multiple methylated CpG sites.
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Affiliation(s)
- Assaf Zemach
- Department of Plant Sciences, The Weizmann Institute of Science, Rehovot, Israel.
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14
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Grafi G, Ben-Meir H, Avivi Y, Moshe M, Dahan Y, Zemach A. Histone methylation controls telomerase-independent telomere lengthening in cells undergoing dedifferentiation. Dev Biol 2007; 306:838-46. [PMID: 17448460 DOI: 10.1016/j.ydbio.2007.03.023] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2007] [Revised: 03/09/2007] [Accepted: 03/18/2007] [Indexed: 11/21/2022]
Abstract
Cellular dedifferentiation underlies topical issues in biology such as regeneration and nuclear cloning and has common features in plants and animals. In plants, this process characterizes the transition of differentiated leaf cells to protoplasts (plant cells devoid of cell walls) and is accompanied by global chromatin reorganization associated with reprogramming of gene expression. A screen for mutants defective in proliferation and callus formation identified kyp-2-a mutant in the KRYPTONITE (KYP)/SUVH4 gene encoding a histone H3 lysine 9 (H3K9) methyltransferase. Analysis of telomere length revealed stochastic telomerase-independent lengthening of telomeres in wild type but not in kyp-2 protoplasts. In kyp-2 mutant, telomeric repeats were no longer associated with dimethylated H3K9. The Arabidopsis telomerase reverse transcriptase (tert) mutant displayed accelerated proliferation despite its short telomeres, though it also showed accelerated cell death. Microarray analysis uncovered several components of the ubiquitin proteolytic system, which are downregulated in kyp-2 compared to wild-type protoplasts. Thus, our results suggest that histone methylation activity is required for the establishment/maintenance of the dedifferentiated state and/or reentry into the cell cycle, at least partly, through activation of genes whose products are involved in the ubiquitin proteolytic pathway. In addition, our results illuminate the complexity of cellular dedifferentiation, particularly the occurrence of DNA recombination that can lead to genome instability.
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Affiliation(s)
- Gideon Grafi
- Albert Katz Department of Dryland Biotechnologies, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus 84990, Israel.
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15
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Grafi G, Zemach A, Pitto L. Methyl-CpG-binding domain (MBD) proteins in plants. ACTA ACUST UNITED AC 2007; 1769:287-94. [PMID: 17407793 DOI: 10.1016/j.bbaexp.2007.02.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2006] [Revised: 02/01/2007] [Accepted: 02/16/2007] [Indexed: 11/18/2022]
Abstract
Cytosine methylation is the most prevalent epigenetic modification of plant nuclear DNA, which occurs in symmetrical CpG or CpNpG as well as in non-symmetrical contexts. Intensive studies demonstrated the central role played by cytosine methylation in genome organization, gene expression and in plant growth and development. However, the way by which the methyl group is interpreted into a functional state has only recently begun to be explored with the isolation and characterization of methylated DNA binding proteins capable of binding 5-methylcytosine. These proteins belong to an evolutionary conserved protein family initially described in animals termed methyl-CpG-binding domain (MBD) proteins. Here, we highlight recent advances and present new prospects concerning plant MBD proteins and their possible role in controlling chromatin structure mediated by CpG methylation.
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Affiliation(s)
- Gideon Grafi
- Albert Katz Department of Dryland Biotechnologies, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion 84990, Israel.
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Zemach A, Grafi G. Methyl-CpG-binding domain proteins in plants: interpreters of DNA methylation. Trends Plant Sci 2007; 12:80-5. [PMID: 17208509 DOI: 10.1016/j.tplants.2006.12.004] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2006] [Revised: 11/06/2006] [Accepted: 12/20/2006] [Indexed: 05/09/2023]
Abstract
The effect of DNA methylation on various aspects of plant cellular and developmental processes has been well documented over the past 35 years. However, the underlying molecular mechanism interpreting the methylation signal has only recently been explored with the isolation and characterization of the Arabidopsis methyl-CpG-binding domain (MBD) proteins. In this review, we highlight recent advances and present new models concerning Arabidopsis MBD proteins and their possible role in controlling chromatin structure mediated by CpG methylation.
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Affiliation(s)
- Assaf Zemach
- Department of Plant Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
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Zemach A, Li Y, Ben-Meir H, Oliva M, Mosquna A, Kiss V, Avivi Y, Ohad N, Grafi G. Different domains control the localization and mobility of LIKE HETEROCHROMATIN PROTEIN1 in Arabidopsis nuclei. Plant Cell 2006; 18:133-45. [PMID: 16361394 PMCID: PMC1323489 DOI: 10.1105/tpc.105.036855] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Plants possess a single gene for the structurally related HETEROCHROMATIN PROTEIN1 (HP1), termed LIKE-HP1 (LHP1). We investigated the subnuclear localization, binding properties, and dynamics of LHP1 proteins in Arabidopsis thaliana cells. Transient expression assays showed that tomato (Solanum lycopersicum) LHP1 fused to green fluorescent protein (GFP; Sl LHP1-GFP) and Arabidopsis LHP1 (At LHP1-GFP) localized to heterochromatic chromocenters and showed punctuated distribution within the nucleus; tomato but not Arabidopsis LHP1 was also localized within the nucleolus. Mutations of aromatic cage residues that recognize methyl K9 of histone H3 abolished their punctuated distribution and localization to chromocenters. Sl LHP1-GFP plants displayed cell type-dependent subnuclear localization. The diverse localization pattern of tomato LHP1 did not require the chromo shadow domain (CSD), whereas the chromodomain alone was insufficient for localization to chromocenters; a nucleolar localization signal was identified within the hinge region. Fluorescence recovery after photobleaching showed that Sl LHP1 is a highly mobile protein whose localization and retention are controlled by distinct domains; retention at the nucleolus and chromocenters is conferred by the CSD. Our results imply that LHP1 recruitment to chromatin is mediated, at least in part, through interaction with methyl K9 and that LHP1 controls different nuclear processes via transient binding to its nuclear sites.
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Affiliation(s)
- Assaf Zemach
- Department of Plant Sciences, Weizman Institute of Science, Rehovot, Israel
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Zemach A, Li Y, Wayburn B, Ben-Meir H, Kiss V, Avivi Y, Kalchenko V, Jacobsen SE, Grafi G. DDM1 binds Arabidopsis methyl-CpG binding domain proteins and affects their subnuclear localization. Plant Cell 2005; 17:1549-58. [PMID: 15805479 PMCID: PMC1091773 DOI: 10.1105/tpc.105.031567] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2005] [Accepted: 03/14/2005] [Indexed: 05/21/2023]
Abstract
Methyl-CpG binding domain (MBD) proteins in Arabidopsis thaliana bind in vitro methylated CpG sites. Here, we aimed to characterize the binding properties of AtMBDs to chromatin in Arabidopsis nuclei. By expressing in wild-type cells AtMBDs fused to green fluorescent protein (GFP), we showed that AtMBD7 was evenly distributed at all chromocenters, whereas AtMBD5 and 6 showed preference for two perinucleolar chromocenters adjacent to nucleolar organizing regions. AtMBD2, previously shown to be incapable of binding in vitro-methylated CpG, was dispersed within the nucleus, excluding chromocenters and the nucleolus. Recruitment of AtMBD5, 6, and 7 to chromocenters was disrupted in ddm1 and met1 mutant cells, where a significant reduction in cytosine methylation occurs. In these mutant cells, however, AtMBD2 accumulated at chromocenters. No effect on localization was observed in the chromomethylase3 mutant showing reduced CpNpG methylation or in kyp-2 displaying a reduction in Lys 9 histone H3 methylation. Transient expression of DDM1 fused to GFP showed that DDM1 shares common sites with AtMBD proteins. Glutathione S-transferase pull-down assays demonstrated that AtMBDs bind DDM1; the MBD motif was sufficient for this interaction. Our results suggest that the subnuclear localization of AtMBD is not solely dependent on CpG methylation; DDM1 may facilitate localization of AtMBDs at specific nuclear domains.
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Affiliation(s)
- Assaf Zemach
- Department of Plant Sciences, Weizman Institute of Science, Rehovot 76100, Israel
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Abstract
Cytosine methylation at symmetrical CpG and CpNpG sequences plays a key role in the epigenetic control of plant growth and development; yet, the way by which the methylation signal is interpreted into a functional state has not been elucidated. In animals, the methylation signal is recognized by methyl-CpG-binding domain (MBD) proteins that specifically bind methylated CpG dinucleotides. In Arabidopsis thaliana, 12 putative MBD proteins were identified and classified into seven subclasses. Here, we characterized six MBD proteins representing four subclasses (II, III, IV, and VI) of the Arabidopsis MBD family. We found that AtMBD7 (subclass VI), a unique protein containing a double MBD motif, as well as AtMBD5 and AtMBD6 (subclass IV), bind specifically symmetrically methylated CpG sites. The MBD motif derived from AtMBD6, but not from AtMBD2, was sufficient for binding methylated CpG dinucleotides. AtMBD6 precipitated histone deacetylase (HDAC) activity from the leaf nuclear extract. The examined AtMBD proteins neither bound methylated CpNpG sequences nor did they display DNA demethylase activity. Our results suggest that AtMBD5, AtMBD6, and AtMBD7 are likely to function in Arabidopsis plants as mediators of the CpG methylation, linking DNA methylation-induced gene silencing with histone deacetylation.
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Affiliation(s)
- Assaf Zemach
- Department of Plant Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
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Fass E, Shahar S, Zhao J, Zemach A, Avivi Y, Grafi G. Phosphorylation of histone h3 at serine 10 cannot account directly for the detachment of human heterochromatin protein 1gamma from mitotic chromosomes in plant cells. J Biol Chem 2002; 277:30921-7. [PMID: 12060650 DOI: 10.1074/jbc.m112250200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Heterochromatin protein 1 (HP1) controls heterochromatin formation in animal cells, at least partly through interaction with lysine 9 (Lys-9)-methylated histone H3. We aimed to determine whether a structurally conserved human HP1 protein exhibits conserved heterochromatin localization in plant cells and studied its relation to modified histone H3. We generated transgenic tobacco plants and cycling cells expressing the human HP1gamma fused to green fluorescent protein (GFP) and followed its association with chromatin. Plants expressing GFP-HP1gamma showed no phenotypic perturbations. We found that GFP-HP1gamma is preferentially associated with the transcriptionally "inactive" heterochromatin fraction, a fraction enriched in Lys-9-methylated histone H3. During mitosis GFP-HP1gamma is detached from chromosomes concomitantly with phosphorylation of histone H3 at serine 10 and reassembles as cells exit mitosis. However, this phosphorylation cannot directly account for the dissociation of GFP-HP1gamma from mitotic chromosomes inasmuch as phosphorylation does not interfere with binding to HP1gamma. It is, therefore, possible that phosphorylation at serine 10 creates a "code" that is read by as yet an unknown factor(s), eventually leading to detachment of GFP-HP1gamma from mitotic chromosomes. Together, our results suggest that chromatin organization in plants and animals is conserved, being controlled at least partly by the association of HP1 proteins with methylated histone H3.
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Affiliation(s)
- Ephraim Fass
- Department of Plant Sciences, The Weizmann Institute of Science, Rehovot 76100 Israel
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