301
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Kuhlmann M, Finke A, Mascher M, Mette MF. DNA methylation maintenance consolidates RNA-directed DNA methylation and transcriptional gene silencing over generations in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 80:269-81. [PMID: 25070184 DOI: 10.1111/tpj.12630] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 07/21/2014] [Accepted: 07/24/2014] [Indexed: 05/22/2023]
Abstract
In plants, 24 nucleotide short interfering RNAs serve as a signal to direct cytosine methylation at homologous DNA regions in the nucleus. If the targeted DNA has promoter function, this RNA-directed DNA methylation may result in transcriptional gene silencing. In a genetic screen for factors involved in RNA-directed transcriptional silencing of a ProNOS-NPTII reporter transgene in Arabidopsis thaliana, we captured alleles of DOMAINS REARRANGED METHYLTRANSFERASE 2, the gene encoding the DNA methyltransferase that is mainly responsible for de novo DNA methylation in the context of RNA-directed DNA methylation. Interestingly, methylation of the reporter gene ProNOS was not completely erased in these mutants, but persisted in the symmetric CG context, indicating that RNA-directed DNA methylation had been consolidated by DNA methylation maintenance. Taking advantage of the segregation of the transgenes giving rise to ProNOS short interfering RNAs and carrying the ProNOS-NPTII reporter in our experimental system, we found that ProNOS DNA methylation maintenance was first evident after two generations of ongoing RNA-directed DNA methylation, and then increased in extent with further generations. As ProNOS DNA methylation had already reached its final level in the first generation of RNA-directed DNA methylation, our findings suggest that establishment of DNA methylation at a particular region may be divided into distinct stages. An initial phase of efficient, but still fully reversible, de novo DNA methylation and transcriptional gene silencing is followed by transition to efficient maintenance of cytosine methylation in a symmetric sequence context accompanied by persistence of gene silencing.
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Affiliation(s)
- Markus Kuhlmann
- Research Group Epigenetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466, Gatersleben, Germany
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302
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Cui X, Cao X. Epigenetic regulation and functional exaptation of transposable elements in higher plants. CURRENT OPINION IN PLANT BIOLOGY 2014; 21:83-88. [PMID: 25061895 DOI: 10.1016/j.pbi.2014.07.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 06/23/2014] [Accepted: 07/02/2014] [Indexed: 05/06/2023]
Abstract
Transposable elements (TEs) are mobile genetic elements that can proliferate in their host genomes. Because of their robust amplification, TEs have long been considered 'selfish DNA', harmful insertions that can threaten host genome integrity. The idea of TEs as junk DNA comes from analysis of epigenetic silencing of their mobility in plants and animals. This idea contrasts with McClintock's characterization of TEs as 'controlling elements'. Emerging studies on the regulatory functions of TEs in plant genomes have updated McClintock's characterization, indicating exaptation of TEs for genetic regulation. In this review, we summarize recent progress in TE silencing, particularly in Arabidopsis and rice, and show that TEs provide an abundant, natural source of regulation for the host genome.
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Affiliation(s)
- Xiekui Cui
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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303
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Epigenetic dysregulation by nickel through repressive chromatin domain disruption. Proc Natl Acad Sci U S A 2014; 111:14631-6. [PMID: 25246589 DOI: 10.1073/pnas.1406923111] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Investigations into the genomic landscape of histone modifications in heterochromatic regions have revealed histone H3 lysine 9 dimethylation (H3K9me2) to be important for differentiation and maintaining cell identity. H3K9me2 is associated with gene silencing and is organized into large repressive domains that exist in close proximity to active genes, indicating the importance of maintenance of proper domain structure. Here we show that nickel, a nonmutagenic environmental carcinogen, disrupted H3K9me2 domains, resulting in the spreading of H3K9me2 into active regions, which was associated with gene silencing. We found weak CCCTC-binding factor (CTCF)-binding sites and reduced CTCF binding at the Ni-disrupted H3K9me2 domain boundaries, suggesting a loss of CTCF-mediated insulation function as a potential reason for domain disruption and spreading. We furthermore show that euchromatin islands, local regions of active chromatin within large H3K9me2 domains, can protect genes from H3K9me2-spreading-associated gene silencing. These results have major implications in understanding H3K9me2 dynamics and the consequences of chromatin domain disruption during pathogenesis.
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304
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Yelagandula R, Stroud H, Holec S, Zhou K, Feng S, Zhong X, Muthurajan UM, Nie X, Kawashima T, Groth M, Luger K, Jacobsen SE, Berger F. The histone variant H2A.W defines heterochromatin and promotes chromatin condensation in Arabidopsis. Cell 2014; 158:98-109. [PMID: 24995981 DOI: 10.1016/j.cell.2014.06.006] [Citation(s) in RCA: 197] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 03/14/2014] [Accepted: 05/14/2014] [Indexed: 11/18/2022]
Abstract
Histone variants play crucial roles in gene expression, genome integrity, and chromosome segregation. We report that the four H2A variants in Arabidopsis define different genomic features, contributing to overall genomic organization. The histone variant H2A.W marks heterochromatin specifically and acts in synergy with heterochromatic marks H3K9me2 and DNA methylation to maintain transposon silencing. In vitro, H2A.W enhances chromatin condensation by promoting fiber-to-fiber interactions via its conserved C-terminal motif. In vivo, H2A.W is required for heterochromatin condensation, demonstrating that H2A.W plays critical roles in heterochromatin organization. Similarities in conserved motifs between H2A.W and another H2A variant in metazoans suggest that plants and animals share common mechanisms for heterochromatin condensation.
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Affiliation(s)
- Ramesh Yelagandula
- Temasek Lifesciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore, Singapore; Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543 Singapore, Singapore
| | - Hume Stroud
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Sarah Holec
- Temasek Lifesciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore, Singapore
| | - Keda Zhou
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Suhua Feng
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Xuehua Zhong
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Uma M Muthurajan
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Xin Nie
- Temasek Lifesciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore, Singapore; Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543 Singapore, Singapore
| | - Tomokazu Kawashima
- Temasek Lifesciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore, Singapore
| | - Martin Groth
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Karolin Luger
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA; Howard Hughes Medical Institute, Colorado State University, Fort Collins, CO 80523, USA
| | - Steven E Jacobsen
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Frédéric Berger
- Temasek Lifesciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore, Singapore; Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543 Singapore, Singapore.
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305
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West PT, Li Q, Ji L, Eichten SR, Song J, Vaughn MW, Schmitz RJ, Springer NM. Genomic distribution of H3K9me2 and DNA methylation in a maize genome. PLoS One 2014; 9:e105267. [PMID: 25122127 PMCID: PMC4133378 DOI: 10.1371/journal.pone.0105267] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 07/18/2014] [Indexed: 11/24/2022] Open
Abstract
DNA methylation and dimethylation of lysine 9 of histone H3 (H3K9me2) are two chromatin modifications that can be associated with gene expression or recombination rate. The maize genome provides a complex landscape of interspersed genes and transposons. The genome-wide distribution of DNA methylation and H3K9me2 were investigated in seedling tissue for the maize inbred B73 and compared to patterns of these modifications observed in Arabidopsis thaliana. Most maize transposons are highly enriched for DNA methylation in CG and CHG contexts and for H3K9me2. In contrast to findings in Arabidopsis, maize CHH levels in transposons are generally low but some sub-families of transposons are enriched for CHH methylation and these families exhibit low levels of H3K9me2. The profile of modifications over genes reveals that DNA methylation and H3K9me2 is quite low near the beginning and end of genes. Although elevated CG and CHG methylation are found within gene bodies, CHH and H3K9me2 remain low. Maize has much higher levels of CHG methylation within gene bodies than observed in Arabidopsis and this is partially attributable to the presence of transposons within introns for some maize genes. These transposons are associated with high levels of CHG methylation and H3K9me2 but do not appear to prevent transcriptional elongation. Although the general trend is for a strong depletion of H3K9me2 and CHG near the transcription start site there are some putative genes that have high levels of these chromatin modifications. This study provides a clear view of the relationship between DNA methylation and H3K9me2 in the maize genome and how the distribution of these modifications is shaped by the interplay of genes and transposons.
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Affiliation(s)
- Patrick T. West
- Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Qing Li
- Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Lexiang Ji
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
| | - Steven R. Eichten
- Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Jawon Song
- Texas Advanced Computing Center, University of Texas-Austin, Austin, Texas, United States of America
| | - Matthew W. Vaughn
- Texas Advanced Computing Center, University of Texas-Austin, Austin, Texas, United States of America
| | - Robert J. Schmitz
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Nathan M. Springer
- Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota, United States of America
- * E-mail:
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306
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Alqarni SSM, Murthy A, Zhang W, Przewloka MR, Silva APG, Watson AA, Lejon S, Pei XY, Smits AH, Kloet SL, Wang H, Shepherd NE, Stokes PH, Blobel GA, Vermeulen M, Glover DM, Mackay JP, Laue ED. Insight into the architecture of the NuRD complex: structure of the RbAp48-MTA1 subcomplex. J Biol Chem 2014; 289:21844-55. [PMID: 24920672 PMCID: PMC4139204 DOI: 10.1074/jbc.m114.558940] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 05/30/2014] [Indexed: 12/22/2022] Open
Abstract
The nucleosome remodeling and deacetylase (NuRD) complex is a widely conserved transcriptional co-regulator that harbors both nucleosome remodeling and histone deacetylase activities. It plays a critical role in the early stages of ES cell differentiation and the reprogramming of somatic to induced pluripotent stem cells. Abnormalities in several NuRD proteins are associated with cancer and aging. We have investigated the architecture of NuRD by determining the structure of a subcomplex comprising RbAp48 and MTA1. Surprisingly, RbAp48 recognizes MTA1 using the same site that it uses to bind histone H4, showing that assembly into NuRD modulates RbAp46/48 interactions with histones. Taken together with other results, our data show that the MTA proteins act as scaffolds for NuRD complex assembly. We further show that the RbAp48-MTA1 interaction is essential for the in vivo integration of RbAp46/48 into the NuRD complex.
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Affiliation(s)
- Saad S M Alqarni
- From the School of Molecular Bioscience, University of Sydney, New South Wales 2006, Australia
| | - Andal Murthy
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Wei Zhang
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Marcin R Przewloka
- Department of Genetics, University of Cambridge, CB2 3EH, United Kingdom
| | - Ana P G Silva
- From the School of Molecular Bioscience, University of Sydney, New South Wales 2006, Australia
| | - Aleksandra A Watson
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Sara Lejon
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Xue Y Pei
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Arne H Smits
- Department of Molecular Cancer Research, UMC Utrecht, Universiteitsweg 100, 3584CG Utrecht, The Netherlands, and
| | - Susan L Kloet
- Department of Molecular Cancer Research, UMC Utrecht, Universiteitsweg 100, 3584CG Utrecht, The Netherlands, and
| | - Hongxin Wang
- Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104
| | - Nicholas E Shepherd
- From the School of Molecular Bioscience, University of Sydney, New South Wales 2006, Australia
| | - Philippa H Stokes
- From the School of Molecular Bioscience, University of Sydney, New South Wales 2006, Australia
| | - Gerd A Blobel
- Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104
| | - Michiel Vermeulen
- Department of Molecular Cancer Research, UMC Utrecht, Universiteitsweg 100, 3584CG Utrecht, The Netherlands, and
| | - David M Glover
- Department of Genetics, University of Cambridge, CB2 3EH, United Kingdom
| | - Joel P Mackay
- From the School of Molecular Bioscience, University of Sydney, New South Wales 2006, Australia,
| | - Ernest D Laue
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom,
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307
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Cheng X. Structural and functional coordination of DNA and histone methylation. Cold Spring Harb Perspect Biol 2014; 6:6/8/a018747. [PMID: 25085914 DOI: 10.1101/cshperspect.a018747] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
One of the most fundamental questions in the control of gene expression in mammals is how epigenetic methylation patterns of DNA and histones are established, erased, and recognized. This central process in controlling gene expression includes coordinated covalent modifications of DNA and its associated histones. This article focuses on structural aspects of enzymatic activities of histone (arginine and lysine) methylation and demethylation and functional links between the methylation status of the DNA and histones. An interconnected network of methyltransferases, demethylases, and accessory proteins is responsible for changing or maintaining the modification status of specific regions of chromatin.
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Affiliation(s)
- Xiaodong Cheng
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
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308
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Kawashima T, Berger F. Epigenetic reprogramming in plant sexual reproduction. Nat Rev Genet 2014; 15:613-24. [DOI: 10.1038/nrg3685] [Citation(s) in RCA: 193] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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309
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Du J, Johnson LM, Groth M, Feng S, Hale CJ, Li S, Vashisht AA, Wohlschlegel JA, Patel DJ, Jacobsen SE. Mechanism of DNA methylation-directed histone methylation by KRYPTONITE. Mol Cell 2014; 55:495-504. [PMID: 25018018 DOI: 10.1016/j.molcel.2014.06.009] [Citation(s) in RCA: 134] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 05/12/2014] [Accepted: 06/02/2014] [Indexed: 01/08/2023]
Abstract
In Arabidopsis, CHG DNA methylation is controlled by the H3K9 methylation mark through a self-reinforcing loop between DNA methyltransferase CHROMOMETHYLASE3 (CMT3) and H3K9 histone methyltransferase KRYPTONITE/SUVH4 (KYP). We report on the structure of KYP in complex with methylated DNA, substrate H3 peptide, and cofactor SAH, thereby defining the spatial positioning of the SRA domain relative to the SET domain. The methylated DNA is bound by the SRA domain with the 5mC flipped out of the DNA, while the H3(1-15) peptide substrate binds between the SET and post-SET domains, with the ε-ammonium of K9 positioned adjacent to bound SAH. These structural insights, complemented by functional data on key mutants of residues lining the 5mC and H3K9-binding pockets within KYP, establish how methylated DNA recruits KYP to the histone substrate. Together, the structures of KYP and previously reported CMT3 complexes provide insights into molecular mechanisms linking DNA and histone methylation.
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Affiliation(s)
- Jiamu Du
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Lianna M Johnson
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Martin Groth
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA.,Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Suhua Feng
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA.,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California at Los Angeles, Los Angeles, CA 90095, USA.,Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Christopher J Hale
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Sisi Li
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Ajay A Vashisht
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - James A Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Steven E Jacobsen
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA.,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California at Los Angeles, Los Angeles, CA 90095, USA.,Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, CA 90095, USA
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310
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Dinh TT, Gao L, Liu X, Li D, Li S, Zhao Y, O'Leary M, Le B, Schmitz RJ, Manavella P, Li S, Weigel D, Pontes O, Ecker JR, Chen X. DNA topoisomerase 1α promotes transcriptional silencing of transposable elements through DNA methylation and histone lysine 9 dimethylation in Arabidopsis. PLoS Genet 2014; 10:e1004446. [PMID: 24992598 PMCID: PMC4080997 DOI: 10.1371/journal.pgen.1004446] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Accepted: 05/05/2014] [Indexed: 11/18/2022] Open
Abstract
RNA-directed DNA methylation (RdDM) and histone H3 lysine 9 dimethylation (H3K9me2) are related transcriptional silencing mechanisms that target transposable elements (TEs) and repeats to maintain genome stability in plants. RdDM is mediated by small and long noncoding RNAs produced by the plant-specific RNA polymerases Pol IV and Pol V, respectively. Through a chemical genetics screen with a luciferase-based DNA methylation reporter, LUCL, we found that camptothecin, a compound with anti-cancer properties that targets DNA topoisomerase 1α (TOP1α) was able to de-repress LUCL by reducing its DNA methylation and H3K9me2 levels. Further studies with Arabidopsis top1α mutants showed that TOP1α silences endogenous RdDM loci by facilitating the production of Pol V-dependent long non-coding RNAs, AGONAUTE4 recruitment and H3K9me2 deposition at TEs and repeats. This study assigned a new role in epigenetic silencing to an enzyme that affects DNA topology. DNA topoisomerase is an enzyme that releases the torsional stress in DNA generated during DNA replication or transcription. Here, we uncovered an unexpected role of DNA topoisomerase 1α (TOP1α) in the maintenance of genome stability. Eukaryotic genomes are usually littered with transposable elements (TEs) and repeats, which pose threats to genome stability due to their tendency to move or recombine. Mechanisms are in place to silence these elements, such as RNA-directed DNA methylation (RdDM) and histone H3 lysine 9 dimethylation (H3K9me2) in plants. Two plant-specific RNA polymerases, Pol IV and Pol V, generate small and long noncoding RNAs, respectively, from TEs and repeats. These RNAs then recruit protein factors to deposit DNA methylation or H3K9me2 to silence the loci. In this study, we found that treatment of plants with camptothecin, a TOP1α inhibitor, or loss of function in TOP1α, led to the de-repression of RdDM target loci, which was accompanied by loss of H3K9me2 or DNA methylation. The role of TOP1α in RdDM could be attributed to its promotion of Pol V, but not Pol IV, transcription to generate long noncoding RNAs.
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Affiliation(s)
- Thanh Theresa Dinh
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
- ChemGen IGERT program, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Lei Gao
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Xigang Liu
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Dongming Li
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Shengben Li
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Yuanyuan Zhao
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Michael O'Leary
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Brandon Le
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Robert J. Schmitz
- Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - Pablo Manavella
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Shaofang Li
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Olga Pontes
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Joseph R. Ecker
- Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California, United States of America
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
- Howard Hughes Medical Institute, University of California Riverside, Riverside, California, United States of America
- * E-mail:
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311
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Eichten SR, Schmitz RJ, Springer NM. Epigenetics: Beyond Chromatin Modifications and Complex Genetic Regulation. PLANT PHYSIOLOGY 2014; 165:933-947. [PMID: 24872382 PMCID: PMC4081347 DOI: 10.1104/pp.113.234211] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Chromatin modifications and epigenetics may play important roles in many plant processes, including developmental regulation, responses to environmental stimuli, and local adaptation. Chromatin modifications describe biochemical changes to chromatin state, such as alterations in the specific type or placement of histones, modifications of DNA or histones, or changes in the specific proteins or RNAs that associate with a genomic region. The term epigenetic is often used to describe a variety of unexpected patterns of gene regulation or inheritance. Here, we specifically define epigenetics to include the key aspects of heritability (stable transmission of gene expression states through mitotic or meiotic cell divisions) and independence from DNA sequence changes. We argue against generically equating chromatin and epigenetics; although many examples of epigenetics involve chromatin changes, those chromatin changes are not always heritable or may be influenced by genetic changes. Careful use of the terms chromatin modifications and epigenetics can help separate the biochemical mechanisms of regulation from the inheritance patterns of altered chromatin states. Here, we also highlight examples in which chromatin modifications and epigenetics affect important plant processes.
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Affiliation(s)
- Steven R Eichten
- Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108 (S.R.E., N.M.S.); andDepartment of Genetics, University of Georgia, Athens, Georgia 30602 (R.J.S.)
| | - Robert J Schmitz
- Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108 (S.R.E., N.M.S.); andDepartment of Genetics, University of Georgia, Athens, Georgia 30602 (R.J.S.)
| | - Nathan M Springer
- Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108 (S.R.E., N.M.S.); andDepartment of Genetics, University of Georgia, Athens, Georgia 30602 (R.J.S.)
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312
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Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. Cell 2014; 156:1286-1297. [PMID: 24630728 DOI: 10.1016/j.cell.2014.01.029] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 10/25/2013] [Accepted: 01/10/2014] [Indexed: 11/24/2022]
Abstract
Dnmt1 epigenetically propagates symmetrical CG methylation in many eukaryotes. Their genomes are typically depleted of CG dinucleotides because of imperfect repair of deaminated methylcytosines. Here, we extensively survey diverse species lacking Dnmt1 and show that, surprisingly, symmetrical CG methylation is nonetheless frequently present and catalyzed by a different DNA methyltransferase family, Dnmt5. Numerous Dnmt5-containing organisms that diverged more than a billion years ago exhibit clustered methylation, specifically in nucleosome linkers. Clustered methylation occurs at unprecedented densities and directly disfavors nucleosomes, contributing to nucleosome positioning between clusters. Dense methylation is enabled by a regime of genomic sequence evolution that enriches CG dinucleotides and drives the highest CG frequencies known. Species with linker methylation have small, transcriptionally active nuclei that approach the physical limits of chromatin compaction. These features constitute a previously unappreciated genome architecture, in which dense methylation influences nucleosome positions, likely facilitating nuclear processes under extreme spatial constraints.
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313
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Abstract
Cytosine DNA methylation is an epigenetic modification in eukaryotes that maintains genome integrity and regulates gene expression. The DNA methylation patterns in plants are more complex than those in animals, and plants and animals have common as well as distinct pathways in regulating DNA methylation. Recent studies involving genetic, molecular, biochemical and genomic approaches have greatly expanded our knowledge of DNA methylation in plants. The roles of many proteins as well as non-coding RNAs in DNA methylation have been uncovered.
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Affiliation(s)
- Yuanyuan Zhao
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521 ; Howard Hughes Medical Institute, University of California, Riverside, CA 92521
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314
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Zhong X, Du J, Hale CJ, Gallego-Bartolome J, Feng S, Vashisht AA, Chory J, Wohlschlegel JA, Patel DJ, Jacobsen SE. Molecular mechanism of action of plant DRM de novo DNA methyltransferases. Cell 2014; 157:1050-60. [PMID: 24855943 PMCID: PMC4123750 DOI: 10.1016/j.cell.2014.03.056] [Citation(s) in RCA: 197] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 02/20/2014] [Accepted: 03/17/2014] [Indexed: 01/01/2023]
Abstract
DNA methylation is a conserved epigenetic gene-regulation mechanism. DOMAINS REARRANGED METHYLTRANSFERASE (DRM) is a key de novo methyltransferase in plants, but how DRM acts mechanistically is poorly understood. Here, we report the crystal structure of the methyltransferase domain of tobacco DRM (NtDRM) and reveal a molecular basis for its rearranged structure. NtDRM forms a functional homodimer critical for catalytic activity. We also show that Arabidopsis DRM2 exists in complex with the small interfering RNA (siRNA) effector ARGONAUTE4 (AGO4) and preferentially methylates one DNA strand, likely the strand acting as the template for RNA polymerase V-mediated noncoding RNA transcripts. This strand-biased DNA methylation is also positively correlated with strand-biased siRNA accumulation. These data suggest a model in which DRM2 is guided to target loci by AGO4-siRNA and involves base-pairing of associated siRNAs with nascent RNA transcripts.
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Affiliation(s)
- Xuehua Zhong
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jiamu Du
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Christopher J Hale
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Javier Gallego-Bartolome
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Suhua Feng
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute and Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ajay A Vashisht
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Joanne Chory
- Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - James A Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.
| | - Steven E Jacobsen
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute and Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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315
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Transcriptional gene silencing by Arabidopsis microrchidia homologues involves the formation of heteromers. Proc Natl Acad Sci U S A 2014; 111:7474-9. [PMID: 24799676 DOI: 10.1073/pnas.1406611111] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Epigenetic gene silencing is of central importance to maintain genome integrity and is mediated by an elaborate interplay between DNA methylation, histone posttranslational modifications, and chromatin remodeling complexes. DNA methylation and repressive histone marks usually correlate with transcriptionally silent heterochromatin, however there are exceptions to this relationship. In Arabidopsis, mutation of Morpheus Molecule 1 (MOM1) causes transcriptional derepression of heterochromatin independently of changes in DNA methylation. More recently, two Arabidopsis homologues of mouse microrchidia (MORC) genes have also been implicated in gene silencing and heterochromatin condensation without altering genome-wide DNA methylation patterns. In this study, we show that Arabidopsis microrchidia (AtMORC6) physically interacts with AtMORC1 and with its close homologue, AtMORC2, in two mutually exclusive protein complexes. RNA-sequencing analyses of high-order mutants indicate that AtMORC1 and AtMORC2 act redundantly to repress a common set of loci. We also examined genetic interactions between AtMORC6 and MOM1 pathways. Although AtMORC6 and MOM1 control the silencing of a very similar set of genomic loci, we observed synergistic transcriptional regulation in the mom1/atmorc6 double mutant, suggesting that these epigenetic regulators act mainly by different silencing mechanisms.
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316
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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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317
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Du J, Patel DJ. Structural biology-based insights into combinatorial readout and crosstalk among epigenetic marks. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:719-27. [PMID: 24747177 DOI: 10.1016/j.bbagrm.2014.04.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 03/20/2014] [Accepted: 04/11/2014] [Indexed: 12/11/2022]
Abstract
Epigenetic mechanisms control gene regulation by writing, reading and erasing specific epigenetic marks. Within the context of multi-disciplinary approaches applied to investigate epigenetic regulation in diverse systems, structural biology techniques have provided insights at the molecular level of key interactions between upstream regulators and downstream effectors. The early structural efforts focused on studies at the single domain-single mark level have been rapidly extended to research at the multiple domain-multiple mark level, thereby providing additional insights into connections within the complicated epigenetic regulatory network. This review focuses on recent results from structural studies on combinatorial readout and crosstalk among epigenetic marks. It starts with an overview of multiple readout of histone marks associated with both single and dual histone tails, as well as the potential crosstalk between them. Next, this review further expands on the simultaneous readout by epigenetic modules of histone and DNA marks, thereby establishing connections between histone lysine methylation and DNA methylation at the nucleosomal level. Finally, the review discusses the role of pre-existing epigenetic marks in directing the writing/erasing of certain epigenetic marks. This article is part of a Special Issue entitled: Molecular mechanisms of histone modification function.
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Affiliation(s)
- Jiamu Du
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA; Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China.
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.
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318
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Blevins T, Pontvianne F, Cocklin R, Podicheti R, Chandrasekhara C, Yerneni S, Braun C, Lee B, Rusch D, Mockaitis K, Tang H, Pikaard CS. A two-step process for epigenetic inheritance in Arabidopsis. Mol Cell 2014; 54:30-42. [PMID: 24657166 DOI: 10.1016/j.molcel.2014.02.019] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 12/08/2013] [Accepted: 02/13/2014] [Indexed: 10/25/2022]
Abstract
In Arabidopsis, multisubunit RNA polymerases IV and V orchestrate RNA-directed DNA methylation (RdDM) and transcriptional silencing, but what identifies the loci to be silenced is unclear. We show that heritable silent locus identity at a specific subset of RdDM targets requires HISTONE DEACETYLASE 6 (HDA6) acting upstream of Pol IV recruitment and siRNA biogenesis. At these loci, epigenetic memory conferring silent locus identity is erased in hda6 mutants such that restoration of HDA6 activity cannot restore siRNA biogenesis or silencing. Silent locus identity is similarly lost in mutants for the cytosine maintenance methyltransferase, MET1. By contrast, pol IV or pol V mutants disrupt silencing without erasing silent locus identity, allowing restoration of Pol IV or Pol V function to restore silencing. Collectively, these observations indicate that silent locus specification and silencing are separable steps that together account for epigenetic inheritance of the silenced state.
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Affiliation(s)
- Todd Blevins
- Howard Hughes Medical Institute, Indiana University, Bloomington, IN 47405, USA; Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Frédéric Pontvianne
- Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Ross Cocklin
- Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Ram Podicheti
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA; School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA
| | - Chinmayi Chandrasekhara
- Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Satwica Yerneni
- School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA
| | - Chris Braun
- School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA
| | - Brandon Lee
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Doug Rusch
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA
| | - Keithanne Mockaitis
- Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA; Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA
| | - Haixu Tang
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA; School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA
| | - Craig S Pikaard
- Howard Hughes Medical Institute, Indiana University, Bloomington, IN 47405, USA; Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA.
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319
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Guerrero-Bosagna C, Skinner MK. Environmental epigenetics and effects on male fertility. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 791:67-81. [PMID: 23955673 DOI: 10.1007/978-1-4614-7783-9_5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Environmental exposures to factors such as toxicants or nutrition can have impacts on testis biology and male fertility. The ability of these factors to influence epigenetic mechanisms in early life exposures or from ancestral exposures will be reviewed. A growing number of examples suggest environmental epigenetics will be a critical factor to consider in male reproduction.
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Affiliation(s)
- Carlos Guerrero-Bosagna
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
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320
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Niederhuth CE, Schmitz RJ. Covering your bases: inheritance of DNA methylation in plant genomes. MOLECULAR PLANT 2014; 7:472-80. [PMID: 24270503 PMCID: PMC3941479 DOI: 10.1093/mp/sst165] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 11/11/2013] [Indexed: 05/24/2023]
Abstract
Cytosine methylation is an important base modification that is inherited across mitotic and meiotic cell divisions in plant genomes. Heritable methylation variants can contribute to within-species phenotypic variation. Few methylation variants were known until recently, making it possible to begin to address major unanswered questions: the extent of natural methylation variation within plant genomes, its effects on phenotypic variation, its degree of dependence on genotype, and how it fits into an evolutionary context. Techniques like whole-genome bisulfite sequencing (WGBS) make it possible to determine cytosine methylation states at single-base resolution across entire genomes and populations. Application of this method to natural and novel experimental populations is revealing answers to these long-standing questions about the role of DNA methylation in plant genomes.
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Affiliation(s)
| | - Robert J. Schmitz
- To whom correspondence should be addressed. E-mail , fax 706 542 3910, tel. 706-5421882
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321
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Garg R, Kumari R, Tiwari S, Goyal S. Genomic survey, gene expression analysis and structural modeling suggest diverse roles of DNA methyltransferases in legumes. PLoS One 2014; 9:e88947. [PMID: 24586452 PMCID: PMC3934875 DOI: 10.1371/journal.pone.0088947] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 01/15/2014] [Indexed: 11/18/2022] Open
Abstract
DNA methylation plays a crucial role in development through inheritable gene silencing. Plants possess three types of DNA methyltransferases (MTases), namely Methyltransferase (MET), Chromomethylase (CMT) and Domains Rearranged Methyltransferase (DRM), which maintain methylation at CG, CHG and CHH sites. DNA MTases have not been studied in legumes so far. Here, we report the identification and analysis of putative DNA MTases in five legumes, including chickpea, soybean, pigeonpea, Medicago and Lotus. MTases in legumes could be classified in known MET, CMT, DRM and DNA nucleotide methyltransferases (DNMT2) subfamilies based on their domain organization. First three MTases represent DNA MTases, whereas DNMT2 represents a transfer RNA (tRNA) MTase. Structural comparison of all the MTases in plants with known MTases in mammalian and plant systems have been reported to assign structural features in context of biological functions of these proteins. The structure analysis clearly specified regions crucial for protein-protein interactions and regions important for nucleosome binding in various domains of CMT and MET proteins. In addition, structural model of DRM suggested that circular permutation of motifs does not have any effect on overall structure of DNA methyltransferase domain. These results provide valuable insights into role of various domains in molecular recognition and should facilitate mechanistic understanding of their function in mediating specific methylation patterns. Further, the comprehensive gene expression analyses of MTases in legumes provided evidence of their role in various developmental processes throughout the plant life cycle and response to various abiotic stresses. Overall, our study will be very helpful in establishing the specific functions of DNA MTases in legumes.
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Affiliation(s)
- Rohini Garg
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
- * E-mail:
| | - Romika Kumari
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Sneha Tiwari
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Shweta Goyal
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
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322
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Dangwal M, Kapoor S, Kapoor M. The PpCMT chromomethylase affects cell growth and interacts with the homolog of LIKE HETEROCHROMATIN PROTEIN 1 in the moss Physcomitrella patens. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 77:589-603. [PMID: 24329971 DOI: 10.1111/tpj.12406] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 11/30/2013] [Accepted: 12/03/2013] [Indexed: 05/06/2023]
Abstract
Chromomethylases (CMTs) are plant-specific cytosine DNA methyltransferases that are involved in maintenance of CpNpG methylation. In seed plants, histone methylation and interaction of CMT with LIKE HETEROCHROMATIN PROTEIN 1 (LHP1) is essential for recruitment of CMT to target sites. LHP1 has been characterized as a putative component of the POLYCOMB REPRESSIVE COMPLEX1 (PRC1) in plants, and functions downstream of PRC2 to maintain genes in repressed state for orchestrated development. In the present study, we show that targeted disruption of PpCMT results in an approximately 50% reduction in global cytosine methylation levels. This affects growth of apical cells, predominantly growth of side branch initials emerging from chloronema cells. In some places, these cells develop thick walls with plasmolyzed cellular contents. Transcript accumulation patterns of genes involved in apical cell extension and metabolism of hemicelluloses, such as xyloglucans, in the primary cell walls decreased many fold in ppcmt mutant lines, as determined by real-time PCR. Using yeast two-hybrid method and bimolecular fluorescence complementation assay, we show that PpCMT and PpLHP1 interact through their chromo domains, while PpLHP1 homodimerizes through its chromo shadow domain. The results presented in this study provide insight into the role of the single chromomethylase, PpCMT, in proliferation of protonema filaments, and shed light on the evolutionary conservation of proteins interacting with these methylases in the early land plant, Physcomitrella patens.
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Affiliation(s)
- Meenakshi Dangwal
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi, 110078, India
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323
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Liu ZW, Shao CR, Zhang CJ, Zhou JX, Zhang SW, Li L, Chen S, Huang HW, Cai T, He XJ. The SET domain proteins SUVH2 and SUVH9 are required for Pol V occupancy at RNA-directed DNA methylation loci. PLoS Genet 2014; 10:e1003948. [PMID: 24465213 PMCID: PMC3898904 DOI: 10.1371/journal.pgen.1003948] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 09/25/2013] [Indexed: 12/05/2022] Open
Abstract
RNA-directed DNA methylation (RdDM) is required for transcriptional silencing of transposons and other DNA repeats in Arabidopsis thaliana. Although previous research has demonstrated that the SET domain-containing SU(VAR)3–9 homologs SUVH2 and SUVH9 are involved in the RdDM pathway, the underlying mechanism remains unknown. Our results indicated that SUVH2 and/or SUVH9 not only interact with the chromatin-remodeling complex termed DDR (DMS3, DRD1, and RDM1) but also with the newly characterized complex composed of two conserved Microrchidia (MORC) family proteins, MORC1 and MORC6. The effect of suvh2suvh9 on Pol IV-dependent siRNA accumulation and DNA methylation is comparable to that of the Pol V mutant nrpe1 and the DDR complex mutant dms3, suggesting that SUVH2 and SUVH9 are functionally associated with RdDM. Our CHIP assay demonstrated that SUVH2 and SUVH9 are required for the occupancy of Pol V at RdDM loci and facilitate the production of Pol V-dependent noncoding RNAs. Moreover, SUVH2 and SUVH9 are also involved in the occupancy of DMS3 at RdDM loci. The putative catalytic active site in the SET domain of SUVH2 is dispensable for the function of SUVH2 in RdDM and H3K9 dimethylation. We propose that SUVH2 and SUVH9 bind to methylated DNA and facilitate the recruitment of Pol V to RdDM loci by associating with the DDR complex and the MORC complex. Small RNA-induced transcriptional silencing at transposable elements and other DNA repeats is an evolutionarily conserved mechanism in plants, fungi, and animals. In Arabidopsis thaliana, an RNA-directed DNA methylation pathway is involved in transcriptional silencing. Noncoding RNAs produced by the plant-specific DNA-dependent RNA polymerase V are required for RNA-directed DNA methylation. A chromatin-remodeling complex was previously demonstrated to be required for the occupancy of DNA-dependent RNA polymerase V at RNA-directed DNA methylation loci. Our results suggest that two putative histone methyltransferases are inactive in their enzymatic activity and act as adaptor proteins to facilitate the recruitment of DNA-dependent RNA polymerase V to chromatin by associating with the chromatin-remodeling complex. In combination with previous studies, we propose that the inactive histone methyltransferases bind to methylated DNA, thereby linking DNA methylation to Pol V transcription at RNA-directed DNA methylation loci.
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Affiliation(s)
- Zhang-Wei Liu
- National Institute of Biological Sciences, Beijing, China
| | | | - Cui-Jun Zhang
- National Institute of Biological Sciences, Beijing, China
| | - Jin-Xing Zhou
- National Institute of Biological Sciences, Beijing, China
| | - Su-Wei Zhang
- National Institute of Biological Sciences, Beijing, China
| | - Lin Li
- National Institute of Biological Sciences, Beijing, China
| | - She Chen
- National Institute of Biological Sciences, Beijing, China
| | - Huan-Wei Huang
- National Institute of Biological Sciences, Beijing, China
| | - Tao Cai
- National Institute of Biological Sciences, Beijing, China
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing, China
- * E-mail:
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324
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Borges F, Martienssen RA. Establishing epigenetic variation during genome reprogramming. RNA Biol 2014; 10:490-4. [PMID: 23774895 DOI: 10.4161/rna.24085] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Transgenerational reprogramming of DNA methylation is important for transposon silencing and epigenetic inheritance. A stochastic regulation of methylation states in the germline may lead to epigenetic variation and the formation of epialleles that contribute to phenotypic variation. In Arabidopsis thaliana inbred lines, the frequency of single base variation of DNA methylation is much higher than genetic mutation and, interestingly, variable epialleles are pre-methylated in the male germline. However, these same alleles are targeted for demethylation in the pollen vegetative nucleus, by a mechanism that seems to contribute to the accumulation of small RNAs that reinforce transcriptional gene silencing in the gametes. These observations are paving the way toward understanding the extent of epigenetic reprogramming in higher plants, and the mechanisms regulating the stability of acquired epigenetic states across generations.
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Affiliation(s)
- Filipe Borges
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
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325
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Coustham V, Vlad D, Deremetz A, Gy I, Cubillos FA, Kerdaffrec E, Loudet O, Bouché N. SHOOT GROWTH1 maintains Arabidopsis epigenomes by regulating IBM1. PLoS One 2014; 9:e84687. [PMID: 24404182 PMCID: PMC3880313 DOI: 10.1371/journal.pone.0084687] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 11/26/2013] [Indexed: 11/17/2022] Open
Abstract
Maintaining correct DNA and histone methylation patterns is essential for the development of all eukaryotes. In Arabidopsis, we identified SHOOT GROWTH1 (SG1), a novel protein involved in the control of gene methylation. SG1 contains both a Bromo-Adjacent Homology (BAH) domain found in several chromatin regulators and an RNA-Recognition Motif (RRM). The sg1 mutations are associated with drastic pleiotropic phenotypes. The mutants degenerate after few generations and are similar to mutants of the histone demethylase INCREASE IN BONSAI METHYLATION1 (IBM1). A methylome analysis of sg1 mutants revealed a large number of gene bodies hypermethylated in the cytosine CHG context, associated with an increase in di-methylation of lysine 9 on histone H3 tail (H3K9me2), an epigenetic mark normally found in silenced transposons. The sg1 phenotype is suppressed by mutations in genes encoding the DNA methyltransferase CHROMOMETHYLASE3 (CMT3) or the histone methyltransferase KRYPTONITE (KYP), indicating that SG1 functions antagonistically to CMT3 or KYP. We further show that the IBM1 transcript is not correctly processed in sg1, and that the functional IBM1 transcript complements sg1. Altogether, our results suggest a function for SG1 in the maintenance of genome integrity by regulating IBM1.
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Affiliation(s)
- Vincent Coustham
- INRA, UMR1318, Institut Jean-Pierre Bourgin, RD10, Versailles, France ; AgroParisTech, Institut Jean-Pierre Bourgin, RD10, Versailles, France
| | - Daniela Vlad
- INRA, UMR1318, Institut Jean-Pierre Bourgin, RD10, Versailles, France ; AgroParisTech, Institut Jean-Pierre Bourgin, RD10, Versailles, France
| | - Aurélie Deremetz
- INRA, UMR1318, Institut Jean-Pierre Bourgin, RD10, Versailles, France ; AgroParisTech, Institut Jean-Pierre Bourgin, RD10, Versailles, France
| | - Isabelle Gy
- INRA, UMR1318, Institut Jean-Pierre Bourgin, RD10, Versailles, France ; AgroParisTech, Institut Jean-Pierre Bourgin, RD10, Versailles, France
| | - Francisco A Cubillos
- INRA, UMR1318, Institut Jean-Pierre Bourgin, RD10, Versailles, France ; AgroParisTech, Institut Jean-Pierre Bourgin, RD10, Versailles, France
| | - Envel Kerdaffrec
- INRA, UMR1318, Institut Jean-Pierre Bourgin, RD10, Versailles, France ; AgroParisTech, Institut Jean-Pierre Bourgin, RD10, Versailles, France
| | - Olivier Loudet
- INRA, UMR1318, Institut Jean-Pierre Bourgin, RD10, Versailles, France ; AgroParisTech, Institut Jean-Pierre Bourgin, RD10, Versailles, France
| | - Nicolas Bouché
- INRA, UMR1318, Institut Jean-Pierre Bourgin, RD10, Versailles, France ; AgroParisTech, Institut Jean-Pierre Bourgin, RD10, Versailles, France
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326
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Hou PQ, Lee YI, Hsu KT, Lin YT, Wu WZ, Lin JY, Nam TN, Fu SF. Functional characterization of Nicotiana benthamiana chromomethylase 3 in developmental programs by virus-induced gene silencing. PHYSIOLOGIA PLANTARUM 2014; 150:119-32. [PMID: 23683172 DOI: 10.1111/ppl.12071] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Revised: 05/02/2013] [Accepted: 05/03/2013] [Indexed: 05/11/2023]
Abstract
DNA methylation is essential for normal developmental processes and genome stability. DNA methyltransferases are key enzymes catalyzing DNA methylation. Chromomethylase (CMT) genes are specific to the plant kingdom and encode chromodomain-containing methyltransferases. However, the function of CMT genes in plants remains elusive. In this study, we isolated and characterized a CMT gene from Nicotiana benthamiana, designated NbCMT3. Alignment of the NbCMT3 amino acid sequence with other plant CMT3s showed conservation of bromo-adjacent-homology and methyltransferase catalytic domains. We investigated the expression patterns of NbCMT3 and its function in developmental programs. NbCMT3 was expressed predominately in proliferating tissues such as apical shoots and young leaves. NbCMT3 protein showed a nuclear location, which could be related to its putative cellular functions. Knocking down NbCMT3 expression by virus-induced gene silencing revealed its vital role(s) in leaf morphogenesis. The formation of palisade cells was defective in NbCMT3-silenced plants as compared with controls. NbCMT3 has a role in developmental programs.
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Affiliation(s)
- Pin-Quan Hou
- Department of Biology, National Chunghua University of Education, No.1, Jin-De Road, 500, Changhua, Taiwan
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327
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Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis. Nat Struct Mol Biol 2013; 21:64-72. [PMID: 24336224 PMCID: PMC4103798 DOI: 10.1038/nsmb.2735] [Citation(s) in RCA: 559] [Impact Index Per Article: 50.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Accepted: 11/14/2013] [Indexed: 11/09/2022]
Abstract
DNA methylation occurs in CG and non-CG sequence contexts. Non-CG methylation is abundant in plants, and is mediated by CHROMOMETHYLASE (CMT) and DOMAINS REARRANGED METHYLTRANSFERASE (DRM) proteins; however its roles remain poorly understood. Here we characterize the roles of non-CG methylation in Arabidopsis thaliana. We show that a poorly characterized methyltransferase, CMT2, is a functional methyltransferase in vitro and in vivo. CMT2 preferentially binds histone H3 lysine 9 (H3K9) dimethylation and methylates non-CG cytosines that are regulated by H3K9 methylation. We revealed the contributions and redundancies between each non-CG methyltransferase in DNA methylation patterning and in regulating transcription. We also demonstrate extensive dependencies of small RNA accumulation and H3K9 methylation patterning on non-CG methylation, suggesting self-reinforcing mechanisms between these epigenetic factors. The results suggest that non-CG methylation patterns are critical in shaping the histone modification and small non-coding RNA landscapes.
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328
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Identification of Arabidopsis SUMO-interacting proteins that regulate chromatin activity and developmental transitions. Proc Natl Acad Sci U S A 2013; 110:19956-61. [PMID: 24255109 DOI: 10.1073/pnas.1319985110] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Posttranslational modification of proteins by small ubiquitin-like modifier (SUMO) plays essential roles in eukaryotic growth and development. Many covalently modified SUMO targets have been identified; however, the extent and significance of noncovalent interactions of SUMO with cellular proteins is poorly understood. Here, large-scale yeast two-hybrid screens repeatedly identified a surprisingly small number of proteins that interacted with three Arabidopsis SUMO isoforms. These SUMO-interacting proteins are nuclear and fall into two main categories: six histone or DNA methyltransferses or demethylases and six proteins that we show to be the evolutionary and functional homologs of SUMO-targeted ubiquitin ligases (STUbLs). The selectivity of the screen for several methylases and demethylases suggests that SUMO interaction with these proteins has a significant impact on chromatin methylation. Furthermore, the Arabidopsis STUbLs (AT-STUbLs) complemented to varying degrees the growth defects of the Schizosaccharomyces pombe STUbL mutant rfp1/rfp2, and three of them also complemented the genome integrity defects of this mutant, demonstrating that these proteins show STUbL activity. We show that one of the AT-STUbLs least related to the S. pombe protein, AT-STUbL4, has acquired a plant-specific function in the floral transition. It reduces protein levels of CYCLING DOF FACTOR 2, hence increasing transcript levels of CONSTANS and promoting flowering through the photoperiodic pathway.
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329
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Abstract
This review focuses on a structure-based analysis of histone posttranslational modification (PTM) readout, where the PTMs serve as docking sites for reader modules as part of larger complexes displaying chromatin modifier and remodeling activities, with the capacity to alter chromatin architecture and templated processes. Individual topics addressed include the diversity of reader-binding pocket architectures and common principles underlying readout of methyl-lysine and methyl-arginine marks, their unmodified counterparts, as well as acetyl-lysine and phosphoserine marks. The review also discusses the impact of multivalent readout of combinations of PTMs localized at specific genomic sites by linked binding modules on processes ranging from gene transcription to repair. Additional topics include cross talk between histone PTMs, histone mimics, epigenetic-based diseases, and drug-based therapeutic intervention. The review ends by highlighting new initiatives and advances, as well as future challenges, toward the promise of enhancing our structural and mechanistic understanding of the readout of histone PTMs at the nucleosomal level.
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Affiliation(s)
- Dinshaw J Patel
- Structural Biology Department, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA.
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330
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Pecinka A, Abdelsamad A, Vu GTH. Hidden genetic nature of epigenetic natural variation in plants. TRENDS IN PLANT SCIENCE 2013; 18:625-32. [PMID: 23953885 DOI: 10.1016/j.tplants.2013.07.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 07/08/2013] [Accepted: 07/11/2013] [Indexed: 05/22/2023]
Abstract
Transcriptional gene silencing (TGS) is an epigenetic mechanism that suppresses the activity of repetitive DNA elements via accumulation of repressive chromatin marks. We discuss natural variation in TGS, with a particular focus on cases that affect the function of protein-coding genes and lead to developmental or physiological changes. Comparison of the examples described has revealed that most natural variation is associated with genetic determinants, such as gene rearrangements, inverted repeats, and transposon insertions that triggered TGS. Recent technical advances have enabled the study of epigenetic natural variation at a whole-genome scale and revealed patterns of inter- and intraspecific epigenetic variation. Future studies exploring non-model species may reveal species-specific evolutionary adaptations at the level of chromatin configuration.
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Affiliation(s)
- Ales Pecinka
- Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany.
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331
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Turck F, Coupland G. Natural variation in epigenetic gene regulation and its effects on plant developmental traits. Evolution 2013; 68:620-31. [PMID: 24117443 DOI: 10.1111/evo.12286] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 09/30/2013] [Indexed: 01/02/2023]
Abstract
In plants, epigenetic variation contributes to phenotypic differences in developmental traits. At the mechanistic level, this variation is conferred by DNA methylation and histone modifications. We describe several examples in which changes in gene expression caused by variation in DNA methylation lead to alterations in plant development. In these examples, the presence of repeated sequences or transposons within the promoters of the affected genes are associated with DNA methylation and gene inactivation. Small interfering RNAs expressed from these sequences recruit DNA methylation to the gene. Some of these methylated alleles are unstable giving rise to revertant sectors during mitosis and to progeny in which the methylated state is lost. However, others are stable for many generations and persist through speciation. These examples indicate that although DNA methylation influences gene expression, this is frequently dependent on classical changes to DNA sequence such as transposon insertions. By contrast, forms of histone methylation cause repression of gene expression that is stably inherited through mitosis but that can also be erased over time or during meiosis. A striking example involves the induction of flowering by exposure to low winter temperatures in Arabidopsis thaliana and its relatives. Histone methylation participates in repression of expression of an inhibitor of flowering during cold. In annual, semelparous species such as A. thaliana, this histone methylation is stably inherited through mitosis after return from cold to warm temperatures allowing the plant to flower continuously during spring and summer until it senesces. However, in perennial, iteroparous relatives the histone modification rapidly disappears when temperatures rise, allowing expression of the floral inhibitor to increase and limiting flowering to a short interval. In this case, epigenetic histone modifications control a key adaptive trait, and their pattern changes rapidly during evolution associated with life-history strategy. We discuss these examples of epigenetic developmental traits with emphasis on the underlying mechanisms, their stability, and adaptive value.
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Affiliation(s)
- Franziska Turck
- Max Planck Institute for Plant Breeding Research, Carl von Linne Weg 10, D-50829, Cologne, Germany.
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332
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Schmitz RJ, He Y, Valdés-López O, Khan SM, Joshi T, Urich MA, Nery JR, Diers B, Xu D, Stacey G, Ecker JR. Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population. Genome Res 2013; 23:1663-74. [PMID: 23739894 PMCID: PMC3787263 DOI: 10.1101/gr.152538.112] [Citation(s) in RCA: 169] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Accepted: 06/05/2013] [Indexed: 01/22/2023]
Abstract
Cytosine DNA methylation is one avenue for passing information through cell divisions. Here, we present epigenomic analyses of soybean recombinant inbred lines (RILs) and their parents. Identification of differentially methylated regions (DMRs) revealed that DMRs mostly cosegregated with the genotype from which they were derived, but examples of the uncoupling of genotype and epigenotype were identified. Linkage mapping of methylation states assessed from whole-genome bisulfite sequencing of 83 RILs uncovered widespread evidence for local methylQTL. This epigenomics approach provides a comprehensive study of the patterns and heritability of methylation variants in a complex genetic population over multiple generations, paving the way for understanding how methylation variants contribute to phenotypic variation.
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Affiliation(s)
- Robert J. Schmitz
- Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Yupeng He
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
- Bioinformatics Program, University of California at San Diego, La Jolla, California 92093, USA
| | - Oswaldo Valdés-López
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, USA
| | - Saad M. Khan
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, USA
- Informatics Institute, University of Missouri, Columbia, Missouri 65211, USA
| | - Trupti Joshi
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, USA
- Informatics Institute, University of Missouri, Columbia, Missouri 65211, USA
- Department of Computer Science, University of Missouri, Columbia, Missouri 65211, USA
- National Center for Soybean Biotechnology, University of Missouri, Columbia, Missouri 65211, USA
| | - Mark A. Urich
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Joseph R. Nery
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Brian Diers
- Department of Crop Sciences, University of Illinois, Urbana, Illinois 61801, USA
| | - Dong Xu
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, USA
- Informatics Institute, University of Missouri, Columbia, Missouri 65211, USA
- Department of Computer Science, University of Missouri, Columbia, Missouri 65211, USA
- National Center for Soybean Biotechnology, University of Missouri, Columbia, Missouri 65211, USA
| | - Gary Stacey
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, USA
- National Center for Soybean Biotechnology, University of Missouri, Columbia, Missouri 65211, USA
- Divisions of Plant Science and Biochemistry, University of Missouri, Columbia, Missouri 65211, USA
| | - Joseph R. Ecker
- Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
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333
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RNA-binding protein regulates plant DNA methylation by controlling mRNA processing at the intronic heterochromatin-containing gene IBM1. Proc Natl Acad Sci U S A 2013; 110:15467-72. [PMID: 24003136 DOI: 10.1073/pnas.1315399110] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
DNA methylation-dependent heterochromatin formation is a conserved mechanism of epigenetic silencing of transposons and other repeat elements in many higher eukaryotes. Genes adjacent to repetitive elements are often also subjected to this epigenetic silencing. Consequently, plants have evolved antisilencing mechanisms such as active DNA demethylation mediated by the REPRESSOR OF SILENCING 1 (ROS1) family of 5-methylcytosine DNA glycosylases to protect these genes from silencing. Some transposons and other repeat elements have found residence in the introns of genes. It is unclear how these intronic repeat elements-containing genes are regulated. We report here the identification of ANTI-SILENCING 1 (ASI1), a bromo-adjacent homology domain and RNA recognition motif-containing protein, from a forward genetic screen for cellular antisilencing factors in Arabidopsis thaliana. ASI1 is required to prevent promoter DNA hypermethylation and transcriptional silencing of some transgenes. Genome-wide DNA methylation analysis reveals that ASI1 has a similar role to that of the histone H3K9 demethylase INCREASE IN BONSAI METHYLATION 1 (IBM1) in preventing CHG methylation in the bodies of thousands of genes. We found that ASI1 is an RNA-binding protein and ensures the proper expression of IBM1 full-length transcript by associating with an intronic heterochromatic repeat element of IBM1. Through mRNA sequencing, we identified many genes containing intronic transposon elements that require ASI1 for proper expression. Our results suggest that ASI1 associates with intronic heterochromatin and binds the gene transcripts to promote their 3' distal polyadenylation. The study thus reveals a unique mechanism by which higher eukaryotes deal with the collateral effect of silencing intronic repeat elements.
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334
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Zhang H, Wang B, Duan CG, Zhu JK. Chemical probes in plant epigenetics studies. PLANT SIGNALING & BEHAVIOR 2013; 8:25364. [PMID: 23838953 PMCID: PMC4002629 DOI: 10.4161/psb.25364] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 06/11/2013] [Indexed: 06/01/2023]
Abstract
Transcription potential is determined by the accessibility of DNA sequences within the context of chromatin, which is coordinately controlled by various epigenetic modifications. Chemical inhibition of epigenetic regulators provides a quick and effective approach to investigate the roles of epigenetic modifications in controlling many biological processes, especially for species in which genetic information is limited. This mini-review provides a brief overview of epigenetic regulators in the model organism Arabidopsis thaliana and summarizes compounds that have been applied in plant epigenetics studies, with highlights in the applications of these chemical probes in mechanistic and functional investigations.
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Affiliation(s)
- Huiming Zhang
- Department of Horticulture and Landscape Architecture; Purdue University; West Lafayette, IN USA
| | - Bangshing Wang
- Department of Horticulture and Landscape Architecture; Purdue University; West Lafayette, IN USA
| | - Cheng-Guo Duan
- Department of Horticulture and Landscape Architecture; Purdue University; West Lafayette, IN USA
| | - Jian-Kang Zhu
- Department of Horticulture and Landscape Architecture; Purdue University; West Lafayette, IN USA
- Shanghai Center for Plant Stress Biology; Shanghai Institutes of Biological Sciences; Chinese Academy of Sciences; Shanghai, PR China
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335
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Abstract
Imprinted gene expression--the biased expression of alleles dependent on their parent of origin--is an important type of epigenetic gene regulation in flowering plants and mammals. In plants, genes are imprinted primarily in the endosperm, the triploid placenta-like tissue that surrounds and nourishes the embryo during its development. Differential allelic expression is correlated with active DNA demethylation by DNA glycosylases and repressive targeting by the Polycomb group proteins. Imprinted gene expression is one consequence of a large-scale remodeling to the epigenome, primarily directed at transposable elements, that occurs in gametes and seeds. This remodeling could be important for maintaining the epigenome in the embryo as well as for establishing gene imprinting.
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Affiliation(s)
- Mary Gehring
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142;
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336
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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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337
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Saze H, Kitayama J, Takashima K, Miura S, Harukawa Y, Ito T, Kakutani T. Mechanism for full-length RNA processing of Arabidopsis genes containing intragenic heterochromatin. Nat Commun 2013; 4:2301. [DOI: 10.1038/ncomms3301] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 07/12/2013] [Indexed: 01/20/2023] Open
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338
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Zhou HR, Zhang FF, Ma ZY, Huang HW, Jiang L, Cai T, Zhu JK, Zhang C, He XJ. Folate polyglutamylation is involved in chromatin silencing by maintaining global DNA methylation and histone H3K9 dimethylation in Arabidopsis. THE PLANT CELL 2013; 25:2545-59. [PMID: 23881414 PMCID: PMC3753382 DOI: 10.1105/tpc.113.114678] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2013] [Revised: 06/09/2013] [Accepted: 07/10/2013] [Indexed: 05/17/2023]
Abstract
DNA methylation and repressive histone Histone3 Lysine9 (H3K9) dimethylation correlate with chromatin silencing in plants and mammals. To identify factors required for DNA methylation and H3K9 dimethylation, we screened for suppressors of the repressor of silencing1 (ros1) mutation, which causes silencing of the expression of the RD29A (RESPONSE TO DESSICATION 29A) promoter-driven luciferase transgene (RD29A-LUC) and the 35S promoter-driven NPTII (NEOMYCIN PHOSPHOTRANSFERASE II) transgene (35S-NPTII). We identified the folylpolyglutamate synthetase FPGS1 and the known factor DECREASED DNA METHYLATION1 (DDM1). The fpgs1 and ddm1 mutations release the silencing of both RD29A-LUC and 35S-NPTII. Genome-wide analysis indicated that the fpgs1 mutation reduces DNA methylation and releases chromatin silencing at a genome-wide scale. The effect of fpgs1 on chromatin silencing is correlated with reduced levels of DNA methylation and H3K9 dimethylation. Supplementation of fpgs1 mutants with 5-formyltetrahydrofolate, a stable form of folate, rescues the defects in DNA methylation, histone H3K9 dimethylation, and chromatin silencing. The competitive inhibitor of methyltransferases, S-adenosylhomocysteine, is markedly upregulated in fpgs1, by which fpgs1 reduces S-adenosylmethionine accessibility to methyltransferases and accordingly affects DNA and histone methylation. These results suggest that FPGS1-mediated folate polyglutamylation is required for DNA methylation and H3K9 dimethylation through its function in one-carbon metabolism. Our study makes an important contribution to understanding the complex interplay among metabolism, development, and epigenetic regulation.
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Affiliation(s)
- Hao-Ran Zhou
- National Institute of Biological Sciences, Beijing 102206, China
- Graduate School of Peking Union Medical College, Beijing 100730, China
| | - Fang-Fang Zhang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Ze-Yang Ma
- National Institute of Biological Sciences, Beijing 102206, China
| | - Huan-Wei Huang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Ling Jiang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Tao Cai
- National Institute of Biological Sciences, Beijing 102206, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology and Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907
| | - Chuyi Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing 102206, China
- Graduate School of Peking Union Medical College, Beijing 100730, China
- Address correspondence to
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339
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González RM, Ricardi MM, Iusem ND. Epigenetic marks in an adaptive water stress-responsive gene in tomato roots under normal and drought conditions. Epigenetics 2013; 8:864-72. [PMID: 23807313 PMCID: PMC3883789 DOI: 10.4161/epi.25524] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Tolerance to water deficits was evolutionarily relevant to the conquest of land by primitive plants. In this context, epigenetic events may have played important roles in the establishment of drought stress responses. We decided to inspect epigenetic marks in the plant organ that is crucial in the sensing of drought stress: the root. Using tomato as a crop model plant, we detected the methylated epialleles of Asr2, a protein-coding gene widespread in the plant kingdom and thought to alleviate restricted water availability. We found 3 contexts (CG, CNG, and CNN) of methylated cytosines in the regulatory region of Solanum lycopersicum Asr2 but only one context (CG) in the gene body. To test the hypothesis of a link between epigenetics marks and the adaptation of plants to drought, we explored the cytosine methylation status of Asr2 in the root resulting from water-deficit stress conditions. We found that a brief exposure to simulated drought conditions caused the removal of methyl marks in the regulatory region at 77 of the 142 CNN sites. In addition, the study of histone modifications around this model gene in the roots revealed that the distal regulatory region was rich in H3K27me3 but that its abundance did not change as a consequence of stress. Additionally, under normal conditions, both the regulatory and coding regions contained the typically repressive H3K9me2 mark, which was lost after 30 min of water deprivation. As analogously conjectured for the paralogous gene Asr1, rapidly acquired new Asr2 epialleles in somatic cells due to desiccation might be stable enough and heritable through the germ line across generations, thereby efficiently contributing to constitutive, adaptive gene expression during the evolution of desiccation-tolerant populations or species.
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Affiliation(s)
- Rodrigo M González
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIByNE); CONICET; Buenos Aires, Argentina
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340
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The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell 2013; 153:193-205. [PMID: 23540698 DOI: 10.1016/j.cell.2013.02.033] [Citation(s) in RCA: 728] [Impact Index Per Article: 66.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2012] [Revised: 12/01/2012] [Accepted: 02/11/2013] [Indexed: 11/20/2022]
Abstract
Nucleosome remodelers of the DDM1/Lsh family are required for DNA methylation of transposable elements, but the reason for this is unknown. How DDM1 interacts with other methylation pathways, such as small-RNA-directed DNA methylation (RdDM), which is thought to mediate plant asymmetric methylation through DRM enzymes, is also unclear. Here, we show that most asymmetric methylation is facilitated by DDM1 and mediated by the methyltransferase CMT2 separately from RdDM. We find that heterochromatic sequences preferentially require DDM1 for DNA methylation and that this preference depends on linker histone H1. RdDM is instead inhibited by heterochromatin and absolutely requires the nucleosome remodeler DRD1. Together, DDM1 and RdDM mediate nearly all transposon methylation and collaborate to repress transposition and regulate the methylation and expression of genes. Our results indicate that DDM1 provides DNA methyltransferases access to H1-containing heterochromatin to allow stable silencing of transposable elements in cooperation with the RdDM pathway.
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341
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Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1. Nature 2013; 498:385-9. [PMID: 23636332 DOI: 10.1038/nature12178] [Citation(s) in RCA: 250] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2012] [Accepted: 04/12/2013] [Indexed: 12/31/2022]
Abstract
DNA methylation is an epigenetic modification that has critical roles in gene silencing, development and genome integrity. In Arabidopsis, DNA methylation is established by DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2) and targeted by 24-nucleotide small interfering RNAs (siRNAs) through a pathway termed RNA-directed DNA methylation (RdDM). This pathway requires two plant-specific RNA polymerases: Pol-IV, which functions to initiate siRNA biogenesis, and Pol-V, which functions to generate scaffold transcripts that recruit downstream RdDM factors. To understand the mechanisms controlling Pol-IV targeting we investigated the function of SAWADEE HOMEODOMAIN HOMOLOG 1 (SHH1), a Pol-IV-interacting protein. Here we show that SHH1 acts upstream in the RdDM pathway to enable siRNA production from a large subset of the most active RdDM targets, and that SHH1 is required for Pol-IV occupancy at these same loci. We also show that the SHH1 SAWADEE domain is a novel chromatin-binding module that adopts a unique tandem Tudor-like fold and functions as a dual lysine reader, probing for both unmethylated K4 and methylated K9 modifications on the histone 3 (H3) tail. Finally, we show that key residues within both lysine-binding pockets of SHH1 are required in vivo to maintain siRNA and DNA methylation levels as well as Pol-IV occupancy at RdDM targets, demonstrating a central role for methylated H3K9 binding in SHH1 function and providing the first insights into the mechanism of Pol-IV targeting. Given the parallels between methylation systems in plants and mammals, a further understanding of this early targeting step may aid our ability to control the expression of endogenous and newly introduced genes, which has broad implications for agriculture and gene therapy.
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342
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DTF1 is a core component of RNA-directed DNA methylation and may assist in the recruitment of Pol IV. Proc Natl Acad Sci U S A 2013; 110:8290-5. [PMID: 23637343 DOI: 10.1073/pnas.1300585110] [Citation(s) in RCA: 128] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
DNA methylation is an important epigenetic mark in many eukaryotic organisms. De novo DNA methylation in plants can be achieved by the RNA-directed DNA methylation (RdDM) pathway, where the plant-specific DNA-dependent RNA polymerase IV (Pol IV) transcribes target sequences to initiate 24-nt siRNA production and action. The putative DNA binding protein DTF1/SHH1 of Arabidopsis has been shown to associate with Pol IV and is required for 24-nt siRNA accumulation and transcriptional silencing at several RdDM target loci. However, the extent and mechanism of DTF1 function in RdDM is unclear. We show here that DTF1 is necessary for the accumulation of the majority of Pol IV-dependent 24-nt siRNAs. It is also required for a large proportion of Pol IV-dependent de novo DNA methylation. Interestingly, there is a group of RdDM target loci where 24-nt siRNA accumulation but not DNA methylation is dependent on DTF1. DTF1 interacts directly with the chromatin remodeling protein CLASSY 1 (CLSY1), and both DTF1 and CLSY1 are associated in vivo with Pol IV but not Pol V, which functions downstream in the RdDM effector complex. DTF1 and DTF2 (a DTF1-like protein) contain a SAWADEE domain, which was found to bind specifically to histone H3 containing H3K9 methylation. Taken together, our results show that DTF1 is a core component of the RdDM pathway, and suggest that DTF1 interacts with CLSY1 to assist in the recruitment of Pol IV to RdDM target loci where H3K9 methylation may be an important feature. Our results also suggest the involvement of DTF1 in an important negative feedback mechanism for DNA methylation at some RdDM target loci.
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343
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Borges F, Calarco JP, Martienssen RA. Reprogramming the epigenome in Arabidopsis pollen. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2013; 77:1-5. [PMID: 23619015 DOI: 10.1101/sqb.2013.77.014969] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Epigenetic reprogramming in Arabidopsis thaliana occurs in developing pollen. The male gametophyte is derived from haploid microspores via two postmeiotic cell divisions to give rise to the gametes (sperm cells, SC) and the vegetative cell (VC). The purification of individual cell types during pollen development coupled with genome-wide DNA methylation analysis and small RNA sequencing has revealed a dynamic regulation of the epigenome during gametogenesis. Interestingly, imprinted loci and previously identified variable epialleles are hypermethylated in the germline; however, their stability after fertilization appears to require targeted demethylation in the neighboring vegetative cell nucleus, possibly by releasing mobile small RNAs that reinforce transcriptional gene silencing and DNA methylation in the gametes. These results have led to a new model for the establishment and transgenerational maintenance of epigenetic marks in flowering plants.
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Affiliation(s)
- F Borges
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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344
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Li P, Demirci F, Mahalingam G, Demirci C, Nakano M, Meyers BC. An integrated workflow for DNA methylation analysis. J Genet Genomics 2013; 40:249-60. [PMID: 23706300 DOI: 10.1016/j.jgg.2013.03.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 03/25/2013] [Accepted: 03/25/2013] [Indexed: 10/27/2022]
Abstract
The analysis of cytosine methylation provides a new way to assess and describe epigenetic regulation at a whole-genome level in many eukaryotes. DNA methylation has a demonstrated role in the genome stability and protection, regulation of gene expression and many other aspects of genome function and maintenance. BS-seq is a relatively unbiased method for profiling the DNA methylation, with a resolution capable of measuring methylation at individual cytosines. Here we describe, as an example, a workflow to handle DNA methylation analysis, from BS-seq library preparation to the data visualization. We describe some applications for the analysis and interpretation of these data. Our laboratory provides public access to plant DNA methylation data via visualization tools available at our "Next-Gen Sequence" websites (http://mpss.udel.edu), along with small RNA, RNA-seq and other data types.
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Affiliation(s)
- Pingchuan Li
- Department of Plant & Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
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345
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Nikolov M, Fischle W. Systematic analysis of histone modification readout. ACTA ACUST UNITED AC 2013; 9:182-94. [DOI: 10.1039/c2mb25328c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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