1
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Xie G, Du X, Hu H, Du J. Molecular mechanisms of the RNA polymerases in plant RNA-directed DNA methylation. Trends Biochem Sci 2024; 49:247-256. [PMID: 38072749 DOI: 10.1016/j.tibs.2023.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 11/16/2023] [Accepted: 11/21/2023] [Indexed: 03/10/2024]
Abstract
In plants, two atypical DNA-dependent RNA polymerases, RNA polymerase IV (Pol IV) and Pol V, and an RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) together produce noncoding RNAs (ncRNAs) to guide the plant-specific RNA-directed DNA methylation (RdDM). Although both Pol IV and Pol V have evolved from the canonical Pol II, they have adapted to different roles in RdDM. The mechanisms of their adaptation are key to understanding plant DNA methylation and the divergent evolution of polymerases. In this review, we summarize insights that have emerged from recent structural studies of Pol IV, Pol V, and RDR2 and discuss their structural features critical for efficient ncRNA production in RdDM.
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Affiliation(s)
- Guohui Xie
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xuan Du
- Department of Biochemistry and Molecular Biology, International Cancer Center, Shenzhen University Medical School, Shenzhen 518060, China
| | - Hongmiao Hu
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Jiamu Du
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China; Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen 518055, China.
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2
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Felgines L, Rymen B, Martins LM, Xu G, Matteoli C, Himber C, Zhou M, Eis J, Coruh C, Böhrer M, Kuhn L, Chicher J, Pandey V, Hammann P, Wohlschlegel J, Waltz F, Law JA, Blevins T. CLSY docking to Pol IV requires a conserved domain critical for small RNA biogenesis and transposon silencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.26.573199. [PMID: 38234754 PMCID: PMC10793415 DOI: 10.1101/2023.12.26.573199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Eukaryotes must balance the need for gene transcription by RNA polymerase II (Pol II) against the danger of mutations caused by transposable element (TE) proliferation. In plants, these gene expression and TE silencing activities are divided between different RNA polymerases. Specifically, RNA polymerase IV (Pol IV), which evolved from Pol II, transcribes TEs to generate small interfering RNAs (siRNAs) that guide DNA methylation and block TE transcription by Pol II. While the Pol IV complex is recruited to TEs via SNF2-like CLASSY (CLSY) proteins, how Pol IV partners with the CLSYs remains unknown. Here we identified a conserved CYC-YPMF motif that is specific to Pol IV and is positioned on the complex exterior. Furthermore, we found that this motif is essential for the co-purification of all four CLSYs with Pol IV, but that only one CLSY is present in any given Pol IV complex. These findings support a "one CLSY per Pol IV" model where the CYC-YPMF motif acts as a CLSY-docking site. Indeed, mutations in and around this motif phenocopy pol iv null mutants. Together, these findings provide structural and functional insights into a critical protein feature that distinguishes Pol IV from other RNA polymerases, allowing it to promote genome stability by targeting TEs for silencing.
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3
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Yang DL, Huang K, Deng D, Zeng Y, Wang Z, Zhang Y. DNA-dependent RNA polymerases in plants. THE PLANT CELL 2023; 35:3641-3661. [PMID: 37453082 PMCID: PMC10533338 DOI: 10.1093/plcell/koad195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 06/09/2023] [Accepted: 05/29/2023] [Indexed: 07/18/2023]
Abstract
DNA-dependent RNA polymerases (Pols) transfer the genetic information stored in genomic DNA to RNA in all organisms. In eukaryotes, the typical products of nuclear Pol I, Pol II, and Pol III are ribosomal RNAs, mRNAs, and transfer RNAs, respectively. Intriguingly, plants possess two additional Pols, Pol IV and Pol V, which produce small RNAs and long noncoding RNAs, respectively, mainly for silencing transposable elements. The five plant Pols share some subunits, but their distinct functions stem from unique subunits that interact with specific regulatory factors in their transcription cycles. Here, we summarize recent advances in our understanding of plant nucleus-localized Pols, including their evolution, function, structures, and transcription cycles.
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Affiliation(s)
- Dong-Lei Yang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Kun Huang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Deyin Deng
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Lin’an, Hangzhou 311300, China
| | - Yuan Zeng
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Zhenxing Wang
- College of Horticulture, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Yu Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
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4
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Renken K, Mendoza SM, Diaz S, Slotkin RK, Hancock CN. Pol V produced RNA facilitates transposable element excision site repair in Arabidopsis. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000793. [PMID: 37273575 PMCID: PMC10236241 DOI: 10.17912/micropub.biology.000793] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 06/06/2023]
Abstract
The plant-specific RNA Polymerase V (Pol V) plays a key role in gene silencing, but its role in repair of double stranded DNA breaks is unclear. Excision of the transposable element mPing creates double stranded breaks that are repaired by NHEJ. We measured mPing excision site repair in multiple DNA methylation mutants including pol V using an mPing : GFP reporter. Two independent mutant alleles of pol V showed less GFP expression, indicating that the Pol V protein plays a role in excision site repair. Sequence analysis of the pol V excision sites indicated an elevated rate of large deletions consistent with less efficient repair. These results clarify the role of Pol V, but not other RNA-directed DNA methylation proteins (Pol IV) or maintenance DNA methylation pathways ( MET1 ), in the repair of double-strand DNA breaks.
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Affiliation(s)
- Kaili Renken
- Biology and Geology, University of South Carolina Aiken, Aiken, South Carolina, United States
| | - Sarah M. Mendoza
- Biology and Geology, University of South Carolina Aiken, Aiken, South Carolina, United States
| | - Stephanie Diaz
- Biology and Geology, University of South Carolina Aiken, Aiken, South Carolina, United States
- Cardiovascular Disease Initiative, Bayer and Broad Institute of MIT and Harvard
| | - R. Keith Slotkin
- Donald Danforth Plant Science Center, St Louis, Missouri, United States
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, United States
| | - C. Nathan Hancock
- Biology and Geology, University of South Carolina Aiken, Aiken, South Carolina, United States
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5
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Abstract
Plants have an extraordinary diversity of transcription machineries, including five nuclear DNA-dependent RNA polymerases. Four of these enzymes are dedicated to the production of long noncoding RNAs (lncRNAs), which are ribonucleic acids with functions independent of their protein-coding potential. lncRNAs display a broad range of lengths and structures, but they are distinct from the small RNA guides of RNA interference (RNAi) pathways. lncRNAs frequently serve as structural, catalytic, or regulatory molecules for gene expression. They can affect all elements of genes, including promoters, untranslated regions, exons, introns, and terminators, controlling gene expression at various levels, including modifying chromatin accessibility, transcription, splicing, and translation. Certain lncRNAs protect genome integrity, while others respond to environmental cues like temperature, drought, nutrients, and pathogens. In this review, we explain the challenge of defining lncRNAs, introduce the machineries responsible for their production, and organize this knowledge by viewing the functions of lncRNAs throughout the structure of a typical plant gene.
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Affiliation(s)
- Andrzej T Wierzbicki
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA;
| | - Todd Blevins
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, F-67084 Strasbourg, France;
| | - Szymon Swiezewski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland;
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6
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Broad noncoding transcription suggests genome surveillance by RNA polymerase V. Proc Natl Acad Sci U S A 2020; 117:30799-30804. [PMID: 33199612 DOI: 10.1073/pnas.2014419117] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Eukaryotic genomes are pervasively transcribed, yet most transcribed sequences lack conservation or known biological functions. In Arabidopsis thaliana, RNA polymerase V (Pol V) produces noncoding transcripts, which base pair with small interfering RNA (siRNA) and allow specific establishment of RNA-directed DNA methylation (RdDM) on transposable elements. Here, we show that Pol V transcribes much more broadly than previously expected, including subsets of both heterochromatic and euchromatic regions. At already established RdDM targets, Pol V and siRNA work together to maintain silencing. In contrast, some euchromatic sequences do not give rise to siRNA but are covered by low levels of Pol V transcription, which is needed to establish RdDM de novo if a transposon is reactivated. We propose a model where Pol V surveils the genome to make it competent to silence newly activated or integrated transposons. This indicates that pervasive transcription of nonconserved sequences may serve an essential role in maintenance of genome integrity.
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7
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Panda K, Slotkin RK. Long-Read cDNA Sequencing Enables a "Gene-Like" Transcript Annotation of Transposable Elements. THE PLANT CELL 2020; 32:2687-2698. [PMID: 32647069 PMCID: PMC7474280 DOI: 10.1105/tpc.20.00115] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 06/11/2020] [Accepted: 06/25/2020] [Indexed: 05/05/2023]
Abstract
Transcript-based annotations of genes facilitate both genome-wide analyses and detailed single-locus research. In contrast, transposable element (TE) annotations are rudimentary, consisting of information only on TE location and type. The repetitiveness and limited annotation of TEs prevent the ability to distinguish between potentially functional expressed elements and degraded copies. To improve genome-wide TE bioinformatics, we performed long-read sequencing of cDNAs from Arabidopsis (Arabidopsis thaliana) lines deficient in multiple layers of TE repression. These uniquely mapping transcripts were used to identify the set of TEs able to generate polyadenylated RNAs and create a new transcript-based annotation of TEs that we have layered upon the existing high-quality community standard annotation. We used this annotation to reduce the bioinformatic complexity associated with multimapping reads from short-read RNA sequencing experiments, and we show that this improvement is expanded in a TE-rich genome such as maize (Zea mays). Our TE annotation also enables the testing of specific standing hypotheses in the TE field. We demonstrate that inaccurate TE splicing does not trigger small RNA production, and the cell more strongly targets DNA methylation to TEs that have the potential to make mRNAs. This work provides a transcript-based TE annotation for Arabidopsis and maize, which serves as a blueprint to reduce the bioinformatic complexity associated with repetitive TEs in any organism.
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Affiliation(s)
- Kaushik Panda
- Donald Danforth Plant Science Center, St. Louis, 63132 Missouri
| | - R Keith Slotkin
- Donald Danforth Plant Science Center, St. Louis, 63132 Missouri
- Division of Biological Sciences, University of Missouri, Columbia, 63132 Missouri
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8
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Lu Y, Dai J, Yang L, La Y, Zhou S, Qiang S, Wang Q, Tan F, Wu Y, Kong W, La H. Involvement of MEM1 in DNA demethylation in Arabidopsis. PLANT MOLECULAR BIOLOGY 2020; 102:307-322. [PMID: 31902068 DOI: 10.1007/s11103-019-00949-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 12/16/2019] [Indexed: 06/10/2023]
Abstract
MEM1 participates in ROS1-mediated DNA demethylation pathway, and acts functionally as ROS3 to counteract the effects of RdDM pathway.mem1mutation leads to large numbers of hyper-DMRs inArabidopsisgenome. In higher plants, DNA methylation performs important functions in silencing transcribed genes and transposable elements (TEs). Active DNA demethylation mediated by REPRESSOR OF SILENCING 1 (ROS1) is able to antagonize the action of DNA methylation caused by RNA-directed DNA methylation (RdDM) pathway, which plays critical roles in keeping DNA methylation at a proper level. In this study, a new mutant named mem1 (for methylation elevated mutant 1) was isolated from a genetic screen of T-DNA insertional mutant population for lines with elevated DNA methylation at a particular locus through Chop-PCR method. MEM1 possesses a Zf-C3HC domain, and is localized in nucleus as well as highly expressed in cotyledons. Whole-genome bisulfite sequencing data showed that knockout mutation of MEM1 leads to 4519 CG, 1793 CHG and 12739 CHH hyper-DMRs (for differentially methylated regions). Further analysis indicated that there are 2751, 2216 and 2042 overlapped CG hyper-DMRs between mem1-1and three mutants, i.e. ros1-4, rdd and ros3-2, respectively; 797, 2514, and 6766 overlapped CHH hyper-DMRs were observed between mem1-1 and three such mutants, respectively; mem1 nrpd1-3 and mem1 rdm1 double mutants showed nearly complete or partial loss of hypermethylation at 4 tested loci, suggesting that MEM1 performs similar functions as DNA glycosylase/lyases in counteracting excessive DNA methylation, and MEM1 plays important roles as REPRESSOR OF SILENCING 3 (ROS3) in erasing CHH methylation caused by the RdDM pathway. Together, these data demonstrate the involvement of MEM1 in ROS1-mediated DNA demethylation pathway and functional connections between MEM1 and ROS3.
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Affiliation(s)
- Yanke Lu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Jie Dai
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Liu Yang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Yumei La
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Shaoxia Zhou
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Sheng Qiang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Qianqian Wang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Feng Tan
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Yufeng Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Weiwen Kong
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Honggui La
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
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9
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Xu M, Mazur MJ, Tao X, Kormelink R. Cellular RNA Hubs: Friends and Foes of Plant Viruses. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:40-54. [PMID: 31415225 DOI: 10.1094/mpmi-06-19-0161-fi] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
RNA granules are dynamic cellular foci that are widely spread in eukaryotic cells and play essential roles in cell growth and development, and immune and stress responses. Different types of granules can be distinguished, each with a specific function and playing a role in, for example, RNA transcription, modification, processing, decay, translation, and arrest. By means of communication and exchange of (shared) components, they form a large regulatory network in cells. Viruses have been reported to interact with one or more of these either cytoplasmic or nuclear granules, and act either proviral, to enable and support viral infection and facilitate viral movement, or antiviral, protecting or clearing hosts from viral infection. This review describes an overview and recent progress on cytoplasmic and nuclear RNA granules and their interplay with virus infection, first in animal systems and as a prelude to the status and current developments on plant viruses, which have been less well studied on this thus far.
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Affiliation(s)
- Min Xu
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- Laboratory of Virology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Magdalena J Mazur
- Laboratory of Virology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Xiaorong Tao
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Richard Kormelink
- Laboratory of Virology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
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10
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Genome-wide association mapping for seed protein content in finger millet (Eleusine coracana) global collection through genotyping by sequencing. J Cereal Sci 2020. [DOI: 10.1016/j.jcs.2019.102888] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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11
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Ferrafiat L, Pflieger D, Singh J, Thieme M, Böhrer M, Himber C, Gerbaud A, Bucher E, Pikaard CS, Blevins T. The NRPD1 N-terminus contains a Pol IV-specific motif that is critical for genome surveillance in Arabidopsis. Nucleic Acids Res 2019; 47:9037-9052. [PMID: 31372633 PMCID: PMC6753494 DOI: 10.1093/nar/gkz618] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 07/03/2019] [Accepted: 07/11/2019] [Indexed: 12/29/2022] Open
Abstract
RNA-guided surveillance systems constrain the activity of transposable elements (TEs) in host genomes. In plants, RNA polymerase IV (Pol IV) transcribes TEs into primary transcripts from which RDR2 synthesizes double-stranded RNA precursors for small interfering RNAs (siRNAs) that guide TE methylation and silencing. How the core subunits of Pol IV, homologs of RNA polymerase II subunits, diverged to support siRNA biogenesis in a TE-rich, repressive chromatin context is not well understood. Here we studied the N-terminus of Pol IV’s largest subunit, NRPD1. Arabidopsis lines harboring missense mutations in this N-terminus produce wild-type (WT) levels of NRPD1, which co-purifies with other Pol IV subunits and RDR2. Our in vitro transcription and genomic analyses reveal that the NRPD1 N-terminus is critical for robust Pol IV-dependent transcription, siRNA production and DNA methylation. However, residual RNA-directed DNA methylation observed in one mutant genotype indicates that Pol IV can operate uncoupled from the high siRNA levels typically observed in WT plants. This mutation disrupts a motif uniquely conserved in Pol IV, crippling the enzyme's ability to inhibit retrotransposon mobilization. We propose that the NRPD1 N-terminus motif evolved to regulate Pol IV function in genome surveillance.
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Affiliation(s)
- Laura Ferrafiat
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, F-67084 Strasbourg, France
| | - David Pflieger
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, F-67084 Strasbourg, France
| | - Jasleen Singh
- Howard Hughes Medical Institute, Indiana University, Bloomington, IN 47405, USA.,Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Michael Thieme
- Botanisches Institut, Universität Basel, CH-4056 Basel, Switzerland
| | - Marcel Böhrer
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, F-67084 Strasbourg, France
| | - Christophe Himber
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, F-67084 Strasbourg, France
| | - Aude Gerbaud
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, F-67084 Strasbourg, France
| | - Etienne Bucher
- Botanisches Institut, Universität Basel, CH-4056 Basel, Switzerland
| | - Craig S Pikaard
- Howard Hughes Medical Institute, Indiana University, Bloomington, IN 47405, USA.,Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Todd Blevins
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, F-67084 Strasbourg, France
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12
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Ji L, Mathioni SM, Johnson S, Tucker D, Bewick AJ, Do Kim K, Daron J, Slotkin RK, Jackson SA, Parrott WA, Meyers BC, Schmitz RJ. Genome-Wide Reinforcement of DNA Methylation Occurs during Somatic Embryogenesis in Soybean. THE PLANT CELL 2019; 31:2315-2331. [PMID: 31439802 PMCID: PMC6790092 DOI: 10.1105/tpc.19.00255] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/29/2019] [Accepted: 08/19/2019] [Indexed: 05/06/2023]
Abstract
Somatic embryogenesis is an important tissue culture technique that sometimes leads to phenotypic variation via genetic and/or epigenetic changes. To understand the genomic and epigenomic impacts of somatic embryogenesis, we characterized soybean (Glycine max) epigenomes sampled from embryos at 10 different stages ranging from 6 weeks to 13 years of continuous culture. We identified genome-wide increases in DNA methylation from cultured samples, especially at CHH sites. The hypermethylation almost exclusively occurred in regions previously possessing non-CG methylation and was accompanied by increases in the expression of genes encoding the RNA-directed DNA methylation (RdDM) machinery. The epigenomic changes were similar between somatic and zygotic embryogenesis. Following the initial global wave of hypermethylation, rare decay events of maintenance methylation were observed, and the extent of the decay increased with time in culture. These losses in DNA methylation were accompanied by downregulation of genes encoding the RdDM machinery and transcriptome reprogramming reminiscent of transcriptomes during late-stage seed development. These results reveal a process for reinforcing already silenced regions to maintain genome integrity during somatic embryogenesis over the short term, which eventually decays at certain loci over longer time scales.
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Affiliation(s)
- Lexiang Ji
- Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602
| | | | - Sarah Johnson
- Institute for Plant Breeding Genetics and Genomics, University of Georgia, Athens, Georgia 30602
| | - Donna Tucker
- Institute for Plant Breeding Genetics and Genomics, University of Georgia, Athens, Georgia 30602
| | - Adam J Bewick
- Department of Genetics, University of Georgia, Athens, Georgia 30602
| | - Kyung Do Kim
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602
| | - Josquin Daron
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210
| | - R Keith Slotkin
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602
| | - Wayne A Parrott
- Institute for Plant Breeding Genetics and Genomics, University of Georgia, Athens, Georgia 30602
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
- Division of Plant Sciences, University of Missouri, Columbia, Missouri 63132
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, Georgia 30602
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13
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Marchais A, Chevalier C, Voinnet O. Extensive profiling in Arabidopsis reveals abundant polysome-associated 24-nt small RNAs including AGO5-dependent pseudogene-derived siRNAs. RNA (NEW YORK, N.Y.) 2019; 25:1098-1117. [PMID: 31138671 PMCID: PMC6800511 DOI: 10.1261/rna.069294.118] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 04/07/2019] [Indexed: 05/19/2023]
Abstract
In a reductionist perspective, plant silencing small (s)RNAs are often classified as mediating nuclear transcriptional gene silencing (TGS) or cytosolic posttranscriptional gene silencing (PTGS). Among the PTGS diagnostics is the association of AGOs and their sRNA cargos with the translation apparatus. In Arabidopsis, this is observed for AGO1 loaded with micro(mi)RNAs and, accordingly, translational-repression (TR) is one layer of plant miRNA action. Using AGO1:miRNA-mediated TR as a paradigm, we explored, with two unrelated polysome-isolation methods, which, among the ten Arabidopsis AGOs and numerous sRNA classes, interact with translation. We found that representatives of all three AGO-clades associate with polysomes, including the TGS-effector AGO4 and stereotypical 24-nt sRNAs that normally mediate TGS of transposons/repeats. Strikingly, approximately half of these annotated 24-nt siRNAs displayed unique matches in coding regions/introns of genes, and in pseudogenes, but not in transposons/repeats commonly found in their vicinity. Protein-coding gene-derived 24-nt sRNAs correlate with gene-body methylation. Those derived from pseudogenes belong to two main clusters defined by their parental-gene expression patterns, and are vastly enriched in AGO5, itself found on polysomes. Based on their tight expression pattern in developing and mature siliques, their biogenesis, and genomic/epigenomic features of their loci-of-origin, we discuss potential roles for these hitherto unknown polysome-enriched, pseudogene-derived siRNAs.
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Affiliation(s)
- Antonin Marchais
- Department of Biology, Swiss Federal Institute of Technology (ETH), 8092 Zürich, Switzerland
| | - Clément Chevalier
- Department of Biology, Swiss Federal Institute of Technology (ETH), 8092 Zürich, Switzerland
| | - Olivier Voinnet
- Department of Biology, Swiss Federal Institute of Technology (ETH), 8092 Zürich, Switzerland
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14
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Choudury SG, Shahid S, Cuerda-Gil D, Panda K, Cullen A, Ashraf Q, Sigman MJ, McCue AD, Slotkin RK. The RNA Export Factor ALY1 Enables Genome-Wide RNA-Directed DNA Methylation. THE PLANT CELL 2019; 31:759-774. [PMID: 30814259 PMCID: PMC6501602 DOI: 10.1105/tpc.18.00624] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 01/23/2019] [Accepted: 02/22/2019] [Indexed: 05/07/2023]
Abstract
RNA-directed DNA methylation (RdDM) is a set of mechanisms by which transcriptionally repressive DNA and histone methylation are targeted to viruses, transposable elements, and some transgenes. We identified an Arabidopsis (Arabidopsis thaliana) mutant in which all forms of RdDM are deficient, leading to transcriptional activation of some transposable elements and the inability to initiate transgene silencing. The corresponding gene, ALY1, encodes an RNA binding nuclear export protein. Arabidopsis ALY proteins function together to export many messenger RNAs (mRNAs), but we found that ALY1 is unique among this family for its ability to enable RdDM. Through the identification of ALY1 direct targets via RNA immunoprecipitation sequencing, coupled with mRNA sequencing of nuclear and cytoplasmic fractions, we identified mRNAs of known RdDM factors that fail to efficiently export from the nucleus in aly1 mutants. We found that loss of RdDM in aly1 is a result of deficient nuclear export of the ARGONAUTE6 mRNA and subsequent decreases in ARGONAUTE6 protein, a key effector of RdDM. One aly1 allele was more severe due to an additional loss of RNA Polymerase V function, which is also necessary for RdDM. Together, our data reconcile the broad role of ALY1 in mRNA export with the specific loss of RdDM through the activities of ARGONAUTE6 and RNA Polymerase V.
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Affiliation(s)
- Sarah G Choudury
- Molecular, Cellular and Developmental Biology Graduate Program, The Ohio State University, Columbus, Ohio 43210
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
| | - Saima Shahid
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
| | - Diego Cuerda-Gil
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
| | - Kaushik Panda
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
| | - Alissa Cullen
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
| | - Quratulayn Ashraf
- Molecular, Cellular and Developmental Biology Graduate Program, The Ohio State University, Columbus, Ohio 43210
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
| | - Meredith J Sigman
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
| | - Andrea D McCue
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
| | - R Keith Slotkin
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211
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15
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Trujillo JT, Seetharam AS, Hufford MB, Beilstein MA, Mosher RA. Evidence for a Unique DNA-Dependent RNA Polymerase in Cereal Crops. Mol Biol Evol 2018; 35:2454-2462. [PMID: 30053133 PMCID: PMC6188566 DOI: 10.1093/molbev/msy146] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Gene duplication is an important driver for the evolution of new genes and protein functions. Duplication of DNA-dependent RNA polymerase (Pol) II subunits within plants led to the emergence of RNA Pol IV and V complexes, each of which possess unique functions necessary for RNA-directed DNA Methylation. Comprehensive identification of Pol V subunit orthologs across the monocot radiation revealed a duplication of the largest two subunits within the grasses (Poaceae), including critical cereal crops. These paralogous Pol subunits display sequence conservation within catalytic domains, but their carboxy terminal domains differ in length and character of the Ago-binding platform, suggesting unique functional interactions. Phylogenetic analysis of the catalytic region indicates positive selection on one paralog following duplication, consistent with retention via neofunctionalization. Positive selection on residue pairs that are predicted to interact between subunits suggests that paralogous subunits have evolved specific assembly partners. Additional Pol subunits as well as Pol-interacting proteins also possess grass-specific paralogs, supporting the hypothesis that a novel Pol complex with distinct function has evolved in the grass family, Poaceae.
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Affiliation(s)
- Joshua T Trujillo
- Department of Molecular & Cellular Biology, The University of Arizona, Tucson, AZ
| | | | - Matthew B Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA
| | - Mark A Beilstein
- Department of Molecular & Cellular Biology, The University of Arizona, Tucson, AZ
- The School of Plant Sciences, The University of Arizona, Tucson, AZ
| | - Rebecca A Mosher
- Department of Molecular & Cellular Biology, The University of Arizona, Tucson, AZ
- The School of Plant Sciences, The University of Arizona, Tucson, AZ
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16
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Eimer H, Sureshkumar S, Singh Yadav A, Kraupner-Taylor C, Bandaranayake C, Seleznev A, Thomason T, Fletcher SJ, Gordon SF, Carroll BJ, Balasubramanian S. RNA-Dependent Epigenetic Silencing Directs Transcriptional Downregulation Caused by Intronic Repeat Expansions. Cell 2018; 174:1095-1105.e11. [PMID: 30057112 DOI: 10.1016/j.cell.2018.06.044] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 04/20/2018] [Accepted: 06/22/2018] [Indexed: 01/07/2023]
Abstract
Transcriptional downregulation caused by intronic triplet repeat expansions underlies diseases such as Friedreich's ataxia. This downregulation of gene expression is coupled with epigenetic changes, but the underlying mechanisms are unknown. Here, we show that an intronic GAA/TTC triplet expansion within the IIL1 gene of Arabidopsis thaliana results in accumulation of 24-nt short interfering RNAs (siRNAs) and repressive histone marks at the IIL1 locus, which in turn causes its transcriptional downregulation and an associated phenotype. Knocking down DICER LIKE-3 (DCL3), which produces 24-nt siRNAs, suppressed transcriptional downregulation of IIL1 and the triplet expansion-associated phenotype. Furthermore, knocking down additional components of the RNA-dependent DNA methylation (RdDM) pathway also suppressed both transcriptional downregulation of IIL1 and the repeat expansion-associated phenotype. Thus, our results show that triplet repeat expansions can lead to local siRNA biogenesis, which in turn downregulates transcription through an RdDM-dependent epigenetic modification.
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Affiliation(s)
- Hannes Eimer
- School of Biological Sciences, Monash University, Clayton Campus, VIC 3800, Australia
| | - Sridevi Sureshkumar
- School of Biological Sciences, Monash University, Clayton Campus, VIC 3800, Australia
| | - Avilash Singh Yadav
- School of Biological Sciences, Monash University, Clayton Campus, VIC 3800, Australia
| | | | - Champa Bandaranayake
- School of Biological Sciences, Monash University, Clayton Campus, VIC 3800, Australia
| | - Andrei Seleznev
- School of Biological Sciences, Monash University, Clayton Campus, VIC 3800, Australia
| | - Tamblyn Thomason
- School of Biological Sciences, Monash University, Clayton Campus, VIC 3800, Australia
| | - Stephen J Fletcher
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia QLD 4072, Australia
| | | | - Bernard J Carroll
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia QLD 4072, Australia
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17
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McKinlay A, Podicheti R, Wendte JM, Cocklin R, Rusch DB. RNA polymerases IV and V influence the 3' boundaries of Polymerase II transcription units in Arabidopsis. RNA Biol 2017; 15:269-279. [PMID: 29199514 DOI: 10.1080/15476286.2017.1409930] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Nuclear multisubunit RNA polymerases IV and V (Pol IV and Pol V) evolved in plants as specialized forms of Pol II. Their functions are best understood in the context of RNA-directed DNA methylation (RdDM), a process in which Pol IV-dependent 24 nt siRNAs direct the de novo cytosine methylation of regions transcribed by Pol V. Pol V has additional functions, independent of Pol IV and 24 nt siRNA biogenesis, in maintaining the repression of transposons and genomic repeats whose silencing depends on maintenance cytosine methylation. Here we report that Pol IV and Pol V play unexpected roles in defining the 3' boundaries of Pol II transcription units. Nuclear run-on assays reveal that in the absence of Pol IV or Pol V, Pol II occupancy downstream of poly A sites increases for approximately 12% of protein-coding genes. This effect is most pronounced for convergently transcribed gene pairs. Although Pols IV and V are detected near transcript ends of the affected Pol II - transcribed genes, their role in limiting Pol II read-through is independent of siRNA biogenesis or cytosine methylation for the majority of these genes. Interestingly, we observed that splicing was less efficient in pol IV or pol V mutant plants, compared to wild-type plants, suggesting that Pol IV or Pol V might affect pre-mRNA processing. We speculate that Pols IV and V (and/or their associated factors) play roles in Pol II transcription termination and pre-mRNA splicing by influencing polymerase elongation rates and/or release at collision sites for convergent genes.
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Affiliation(s)
- Anastasia McKinlay
- a Department of Biology , Indiana University , Bloomington , Indiana , USA
| | - Ram Podicheti
- b Center for Genomics and Bioinformatics, Indiana University , Bloomington , Indiana , USA.,c School of Informatics and Computing, Indiana University , Bloomington , IN , USA
| | - Jered M Wendte
- a Department of Biology , Indiana University , Bloomington , Indiana , USA
| | - Ross Cocklin
- a Department of Biology , Indiana University , Bloomington , Indiana , USA.,d Howard Hughes Medical Institute, Indiana University , Bloomington , Indiana
| | - Douglas B Rusch
- b Center for Genomics and Bioinformatics, Indiana University , Bloomington , Indiana , USA
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18
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Lahmy S, Pontier D, Bies-Etheve N, Laudié M, Feng S, Jobet E, Hale CJ, Cooke R, Hakimi MA, Angelov D, Jacobsen SE, Lagrange T. Evidence for ARGONAUTE4-DNA interactions in RNA-directed DNA methylation in plants. Genes Dev 2016; 30:2565-2570. [PMID: 27986858 PMCID: PMC5204349 DOI: 10.1101/gad.289553.116] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 11/17/2016] [Indexed: 12/29/2022]
Abstract
RNA polymerase V (Pol V) long noncoding RNAs (lncRNAs) have been proposed to guide ARGONAUTE4 (AGO4) to chromatin in RNA-directed DNA methylation (RdDM) in plants. Here, we provide evidence, based on laser UV-assisted zero-length cross-linking, for functionally relevant AGO4-DNA interaction at RdDM targets. We further demonstrate that Pol V lncRNAs or the act of their transcription are required to lock Pol V holoenzyme into a stable DNA-bound state that allows AGO4 recruitment via redundant glycine-tryptophan/tryptophan-glycine AGO hook motifs present on both Pol V and its associated factor, SPT5L. We propose a model in which AGO4-DNA interaction could be responsible for the unique specificities of RdDM.
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Affiliation(s)
- Sylvie Lahmy
- Laboratoire Génome et Développement des Plantes (LGDP), UMR5096, Centre National de la Recherche Scientifique (CNRS), Université de Perpignan via Domitia (UPVD), 66860 Perpignan, France
| | - Dominique Pontier
- Laboratoire Génome et Développement des Plantes (LGDP), UMR5096, Centre National de la Recherche Scientifique (CNRS), Université de Perpignan via Domitia (UPVD), 66860 Perpignan, France
| | - Natacha Bies-Etheve
- Laboratoire Génome et Développement des Plantes (LGDP), UMR5096, Centre National de la Recherche Scientifique (CNRS), Université de Perpignan via Domitia (UPVD), 66860 Perpignan, France
| | - Michèle Laudié
- Laboratoire Génome et Développement des Plantes (LGDP), UMR5096, Centre National de la Recherche Scientifique (CNRS), Université de Perpignan via Domitia (UPVD), 66860 Perpignan, France
| | - Suhua Feng
- Department of Molecular, Cell, and Developmental Biology, University of California at Los Angeles, Los Angeles, California 90095, USA.,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Edouard Jobet
- Laboratoire Génome et Développement des Plantes (LGDP), UMR5096, Centre National de la Recherche Scientifique (CNRS), Université de Perpignan via Domitia (UPVD), 66860 Perpignan, France
| | - Christopher J Hale
- Department of Molecular, Cell, and Developmental Biology, University of California at Los Angeles, Los Angeles, California 90095, USA.,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California at Los Angeles, Los Angeles, California 90095, USA.,Department of Pathology, Center for Precision Diagnostics, University of Washington, Seattle, Washington 98195, USA
| | - Richard Cooke
- Laboratoire Génome et Développement des Plantes (LGDP), UMR5096, Centre National de la Recherche Scientifique (CNRS), Université de Perpignan via Domitia (UPVD), 66860 Perpignan, France
| | - Mohamed-Ali Hakimi
- Institute for Advanced Biosciences (IAB), UMR5309, CNRS, U1209, Institut National de la Santé et de la Recherche Médicale (INSERM), Grenoble Alpes University, 38000 Grenoble, France
| | - Dimitar Angelov
- Laboratoire de Biologie et Modélisation de la Cellule (LBMC), UMR 5239, CNRS/École Normale Supérieure de Lyon (ENSL)/Université Claude Bernard Lyon 1 (UCBL), 69007 Lyon, France.,Institut NeuroMyogène (INMG), UMR 5310, CNRS/UCBL/ENSL, 69007 Lyon, France
| | - Steven E Jacobsen
- Department of Molecular, Cell, and Developmental Biology, University of California at Los Angeles, Los Angeles, California 90095, USA.,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California at Los Angeles, Los Angeles, California 90095, USA.,Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Thierry Lagrange
- Laboratoire Génome et Développement des Plantes (LGDP), UMR5096, Centre National de la Recherche Scientifique (CNRS), Université de Perpignan via Domitia (UPVD), 66860 Perpignan, France
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19
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Trujillo JT, Beilstein MA, Mosher RA. The Argonaute-binding platform of NRPE1 evolves through modulation of intrinsically disordered repeats. THE NEW PHYTOLOGIST 2016; 212:1094-1105. [PMID: 27431917 PMCID: PMC5125548 DOI: 10.1111/nph.14089] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 06/04/2016] [Indexed: 05/26/2023]
Abstract
Argonaute (Ago) proteins are important effectors in RNA silencing pathways, but they must interact with other machinery to trigger silencing. Ago hooks have emerged as a conserved motif responsible for interaction with Ago proteins, but little is known about the sequence surrounding Ago hooks that must restrict or enable interaction with specific Argonautes. Here we investigated the evolutionary dynamics of an Ago-binding platform in NRPE1, the largest subunit of RNA polymerase V. We compared NRPE1 sequences from > 50 species, including dense sampling of two plant lineages. This study demonstrates that the Ago-binding platform of NRPE1 retains Ago hooks, intrinsic disorder, and repetitive character while being highly labile at the sequence level. We reveal that loss of sequence conservation is the result of relaxed selection and frequent expansions and contractions of tandem repeat arrays. These factors allow a complete restructuring of the Ago-binding platform over 50-60 million yr. This evolutionary pattern is also detected in a second Ago-binding platform, suggesting it is a general mechanism. The presence of labile repeat arrays in all analyzed NRPE1 Ago-binding platforms indicates that selection maintains repetitive character, potentially to retain the ability to rapidly restructure the Ago-binding platform.
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Affiliation(s)
- Joshua T Trujillo
- The School of Plant Sciences, The University of Arizona, Tucson, AZ, 85721-0036, USA
| | - Mark A Beilstein
- The School of Plant Sciences, The University of Arizona, Tucson, AZ, 85721-0036, USA
| | - Rebecca A Mosher
- The School of Plant Sciences, The University of Arizona, Tucson, AZ, 85721-0036, USA
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20
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Böhmdorfer G, Sethuraman S, Rowley MJ, Krzyszton M, Rothi MH, Bouzit L, Wierzbicki AT. Long non-coding RNA produced by RNA polymerase V determines boundaries of heterochromatin. eLife 2016; 5. [PMID: 27779094 PMCID: PMC5079748 DOI: 10.7554/elife.19092] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 10/06/2016] [Indexed: 01/10/2023] Open
Abstract
RNA-mediated transcriptional gene silencing is a conserved process where small RNAs target transposons and other sequences for repression by establishing chromatin modifications. A central element of this process are long non-coding RNAs (lncRNA), which in Arabidopsis thaliana are produced by a specialized RNA polymerase known as Pol V. Here we show that non-coding transcription by Pol V is controlled by preexisting chromatin modifications located within the transcribed regions. Most Pol V transcripts are associated with AGO4 but are not sliced by AGO4. Pol V-dependent DNA methylation is established on both strands of DNA and is tightly restricted to Pol V-transcribed regions. This indicates that chromatin modifications are established in close proximity to Pol V. Finally, Pol V transcription is preferentially enriched on edges of silenced transposable elements, where Pol V transcribes into TEs. We propose that Pol V may play an important role in the determination of heterochromatin boundaries. DOI:http://dx.doi.org/10.7554/eLife.19092.001
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Affiliation(s)
- Gudrun Böhmdorfer
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, United States
| | - Shriya Sethuraman
- Bioinformatics Graduate Program, University of Michigan, Ann Arbor, United States
| | - M Jordan Rowley
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, United States
| | - Michal Krzyszton
- Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
| | - M Hafiz Rothi
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, United States
| | - Lilia Bouzit
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, United States
| | - Andrzej T Wierzbicki
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, United States
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21
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Wendte JM, Pikaard CS. The RNAs of RNA-directed DNA methylation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:140-148. [PMID: 27521981 DOI: 10.1016/j.bbagrm.2016.08.004] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/05/2016] [Accepted: 08/06/2016] [Indexed: 10/21/2022]
Abstract
RNA-directed chromatin modification that includes cytosine methylation silences transposable elements in both plants and mammals, contributing to genome defense and stability. In Arabidopsis thaliana, most RNA-directed DNA methylation (RdDM) is guided by small RNAs derived from double-stranded precursors synthesized at cytosine-methylated loci by nuclear multisubunit RNA Polymerase IV (Pol IV), in close partnership with the RNA-dependent RNA polymerase, RDR2. These small RNAs help keep transposons transcriptionally inactive. However, if transposons escape silencing, and are transcribed by multisubunit RNA polymerase II (Pol II), their mRNAs can be recognized and degraded, generating small RNAs that can also guide initial DNA methylation, thereby enabling subsequent Pol IV-RDR2 recruitment. In both pathways, the small RNAs find their target sites by interacting with longer noncoding RNAs synthesized by multisubunit RNA Polymerase V (Pol V). Despite a decade of progress, numerous questions remain concerning the initiation, synthesis, processing, size and features of the RNAs that drive RdDM. Here, we review recent insights, questions and controversies concerning RNAs produced by Pols IV and V, and their functions in RdDM. We also provide new data concerning Pol V transcript 5' and 3' ends. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.
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Affiliation(s)
- Jered M Wendte
- Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University, 915 E. Third Street, Bloomington, IN 47405, USA
| | - Craig S Pikaard
- Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University, 915 E. Third Street, Bloomington, IN 47405, USA; Howard Hughes Medical Institute, Indiana University, Bloomington, IN 47405, USA.
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22
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Blevins T, Podicheti R, Mishra V, Marasco M, Wang J, Rusch D, Tang H, Pikaard CS. Identification of Pol IV and RDR2-dependent precursors of 24 nt siRNAs guiding de novo DNA methylation in Arabidopsis. eLife 2015; 4:e09591. [PMID: 26430765 PMCID: PMC4716838 DOI: 10.7554/elife.09591] [Citation(s) in RCA: 167] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Accepted: 10/01/2015] [Indexed: 12/21/2022] Open
Abstract
In Arabidopsis thaliana, abundant 24 nucleotide small interfering RNAs (24 nt siRNA) guide the cytosine methylation and silencing of transposons and a subset of genes. 24 nt siRNA biogenesis requires nuclear RNA polymerase IV (Pol IV), RNA-dependent RNA polymerase 2 (RDR2) and DICER-like 3 (DCL3). However, siRNA precursors are mostly undefined. We identified Pol IV and RDR2-dependent RNAs (P4R2 RNAs) that accumulate in dcl3 mutants and are diced into 24 nt RNAs by DCL3 in vitro. P4R2 RNAs are mostly 26-45 nt and initiate with a purine adjacent to a pyrimidine, characteristics shared by Pol IV transcripts generated in vitro. RDR2 terminal transferase activity, also demonstrated in vitro, may account for occasional non-templated nucleotides at P4R2 RNA 3' termini. The 24 nt siRNAs primarily correspond to the 5' or 3' ends of P4R2 RNAs, suggesting a model whereby siRNAs are generated from either end of P4R2 duplexes by single dicing events.
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Affiliation(s)
- Todd Blevins
- Howard Hughes Medical Institute, Indiana University, Bloomington, United States
- Department of Biology, Indiana University, Bloomington, United States
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, United States
| | - Ram Podicheti
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, United States
- School of Informatics and Computing, Indiana University, Bloomington, United States
| | - Vibhor Mishra
- Department of Biology, Indiana University, Bloomington, United States
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, United States
| | - Michelle Marasco
- Department of Biology, Indiana University, Bloomington, United States
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, United States
| | - Jing Wang
- Department of Biology, Indiana University, Bloomington, United States
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, United States
| | - Doug Rusch
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, United States
| | - Haixu Tang
- School of Informatics and Computing, Indiana University, Bloomington, United States
| | - Craig S Pikaard
- Howard Hughes Medical Institute, Indiana University, Bloomington, United States
- Department of Biology, Indiana University, Bloomington, United States
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, United States
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23
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Zhou M, Law JA. RNA Pol IV and V in gene silencing: Rebel polymerases evolving away from Pol II's rules. CURRENT OPINION IN PLANT BIOLOGY 2015; 27:154-64. [PMID: 26344361 PMCID: PMC4618083 DOI: 10.1016/j.pbi.2015.07.005] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 07/15/2015] [Accepted: 07/19/2015] [Indexed: 05/19/2023]
Abstract
Noncoding RNAs regulate gene expression at both the transcriptional and post-transcriptional levels, and play critical roles in development, imprinting and the maintenance of genome integrity in eukaryotic organisms [1,2,3]. Therefore, it is important to understand how the production of such RNAs are controlled. In addition to the three canonical DNA dependent RNA polymerases (Pol) Pol I, II and III, two non-redundant plant-specific RNA polymerases, Pol IV and Pol V, have been identified and shown to generate noncoding RNAs that are required for transcriptional gene silencing via the RNA-directed DNA methylation (RdDM) pathway. Thus, somewhat paradoxically, transcription is required for gene silencing. This paradox extends beyond plants, as silencing pathways in yeast, fungi, flies, worms, and mammals also require transcriptional machinery [4,5]. As plants have evolved specialized RNA polymerases to carry out gene silencing in a manner that is separate from the essential roles of Pol II, their characterization offers unique insights into how RNA polymerases facilitate gene silencing. In this review, we focus on the mechanisms of Pol IV and Pol V function, including their compositions, their transcripts, and their modes of recruitment to chromatin.
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Affiliation(s)
- Ming Zhou
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Julie A Law
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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24
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Wang Y, Ma H. Step-wise and lineage-specific diversification of plant RNA polymerase genes and origin of the largest plant-specific subunits. THE NEW PHYTOLOGIST 2015; 207:1198-212. [PMID: 25921392 DOI: 10.1111/nph.13432] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 03/24/2015] [Indexed: 05/25/2023]
Abstract
Proteins often function as complexes, yet little is known about the evolution of dissimilar subunits of complexes. DNA-directed RNA polymerases (RNAPs) are multisubunit complexes, with distinct eukaryotic types for different classes of transcripts. In addition to Pol I-III, common in eukaryotes, plants have Pol IV and V for epigenetic regulation. Some RNAP subunits are specific to one type, whereas other subunits are shared by multiple types. We have conducted extensive phylogenetic and sequence analyses, and have placed RNAP gene duplication events in land plant history, thereby reconstructing the subunit compositions of the novel RNAPs during land plant evolution. We found that Pol IV/V have experienced step-wise duplication and diversification of various subunits, with increasingly distinctive subunit compositions. Also, lineage-specific duplications have further increased RNAP complexity with distinct copies in different plant families and varying divergence for subunits of different RNAPs. Further, the largest subunits of Pol IV/V probably originated from a gene fusion in the ancestral land plants. We propose a framework of plant RNAP evolution, providing an excellent model for protein complex evolution.
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Affiliation(s)
- Yaqiong Wang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 220 Handan Road, Shanghai, 200433, China
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and Institute of Biodiversity Sciences, Fudan University, Shanghai, 200433, China
| | - Hong Ma
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 220 Handan Road, Shanghai, 200433, China
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and Institute of Biodiversity Sciences, Fudan University, Shanghai, 200433, China
- Institutes of Biomedical Sciences, Fudan University, 138 Yixueyuan Road, Shanghai, 200032, China
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25
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Ream TS, Haag JR, Pontvianne F, Nicora CD, Norbeck AD, Paša-Tolić L, Pikaard CS. Subunit compositions of Arabidopsis RNA polymerases I and III reveal Pol I- and Pol III-specific forms of the AC40 subunit and alternative forms of the C53 subunit. Nucleic Acids Res 2015; 43:4163-78. [PMID: 25813043 PMCID: PMC4417161 DOI: 10.1093/nar/gkv247] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Accepted: 03/10/2015] [Indexed: 12/17/2022] Open
Abstract
Using affinity purification and mass spectrometry, we identified the subunits of Arabidopsis thaliana multisubunit RNA polymerases I and III (abbreviated as Pol I and Pol III), the first analysis of their physical compositions in plants. In all eukaryotes examined to date, AC40 and AC19 subunits are common to Pol I (a.k.a. Pol A) and Pol III (a.k.a. Pol C) and are encoded by single genes. Surprisingly, A. thaliana and related species express two distinct AC40 paralogs, one of which assembles into Pol I and the other of which assembles into Pol III. Changes at eight amino acid positions correlate with the functional divergence of Pol I- and Pol III-specific AC40 paralogs. Two genes encode homologs of the yeast C53 subunit and either protein can assemble into Pol III. By contrast, only one of two potential C17 variants, and one of two potential C31 variants were detected in Pol III. We introduce a new nomenclature system for plant Pol I and Pol III subunits in which the 12 subunits that are structurally and functionally homologous among Pols I through V are assigned equivalent numbers.
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Affiliation(s)
- Thomas S Ream
- Division of Biology and Biomedical Sciences, Washington University, St. Louis, MO 63130, USA
| | - Jeremy R Haag
- Division of Biology and Biomedical Sciences, Washington University, St. Louis, MO 63130, USA Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Frederic Pontvianne
- Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Carrie D Nicora
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Angela D Norbeck
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Ljiljana Paša-Tolić
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Craig S Pikaard
- Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA Howard Hughes Medical Institute, Indiana University, Bloomington, IN 47405, USA
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Huang Y, Kendall T, Forsythe ES, Dorantes-Acosta A, Li S, Caballero-Pérez J, Chen X, Arteaga-Vázquez M, Beilstein MA, Mosher RA. Ancient Origin and Recent Innovations of RNA Polymerase IV and V. Mol Biol Evol 2015; 32:1788-99. [PMID: 25767205 PMCID: PMC4476159 DOI: 10.1093/molbev/msv060] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Small RNA-mediated chromatin modification is a conserved feature of eukaryotes. In flowering plants, the short interfering (si)RNAs that direct transcriptional silencing are abundant and subfunctionalization has led to specialized machinery responsible for synthesis and action of these small RNAs. In particular, plants possess polymerase (Pol) IV and Pol V, multi-subunit homologs of the canonical DNA-dependent RNA Pol II, as well as specialized members of the RNA-dependent RNA Polymerase (RDR), Dicer-like (DCL), and Argonaute (AGO) families. Together these enzymes are required for production and activity of Pol IV-dependent (p4-)siRNAs, which trigger RNA-directed DNA methylation (RdDM) at homologous sequences. p4-siRNAs accumulate highly in developing endosperm, a specialized tissue found only in flowering plants, and are rare in nonflowering plants, suggesting that the evolution of flowers might coincide with the emergence of specialized RdDM machinery. Through comprehensive identification of RdDM genes from species representing the breadth of the land plant phylogeny, we describe the ancient origin of Pol IV and Pol V, suggesting that a nearly complete and functional RdDM pathway could have existed in the earliest land plants. We also uncover innovations in these enzymes that are coincident with the emergence of seed plants and flowering plants, and recent duplications that might indicate additional subfunctionalization. Phylogenetic analysis reveals rapid evolution of Pol IV and Pol V subunits relative to their Pol II counterparts and suggests that duplicates were retained and subfunctionalized through Escape from Adaptive Conflict. Evolution within the carboxy-terminal domain of the Pol V largest subunit is particularly striking, where illegitimate recombination facilitated extreme sequence divergence.
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Affiliation(s)
- Yi Huang
- The School of Plant Sciences, The University of Arizona
| | - Timmy Kendall
- The School of Plant Sciences, The University of Arizona
| | | | - Ana Dorantes-Acosta
- Instituto de Biotecnología y Ecología Aplicada (INBIOTECA), Universidad Veracruzana, Veracruz, México
| | - Shaofang Li
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside
| | | | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside
| | - Mario Arteaga-Vázquez
- Instituto de Biotecnología y Ecología Aplicada (INBIOTECA), Universidad Veracruzana, Veracruz, México
| | | | - Rebecca A Mosher
- The School of Plant Sciences, The University of Arizona The Bio5 Institute, The University of Arizona
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Functional diversification of maize RNA polymerase IV and V subtypes via alternative catalytic subunits. Cell Rep 2014; 9:378-390. [PMID: 25284785 DOI: 10.1016/j.celrep.2014.08.067] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 07/09/2014] [Accepted: 08/26/2014] [Indexed: 01/08/2023] Open
Abstract
Unlike nuclear multisubunit RNA polymerases I, II, and III, whose subunit compositions are conserved throughout eukaryotes, plant RNA polymerases IV and V are nonessential, Pol II-related enzymes whose subunit compositions are still evolving. Whereas Arabidopsis Pols IV and V differ from Pol II in four or five of their 12 subunits, respectively, and differ from one another in three subunits, proteomic analyses show that maize Pols IV and V differ from Pol II in six subunits but differ from each other only in their largest subunits. Use of alternative catalytic second subunits, which are nonredundant for development and paramutation, yields at least two subtypes of Pol IV and three subtypes of Pol V in maize. Pol IV/Pol V associations with MOP1, RMR1, AGO121, Zm_DRD1/CHR127, SHH2a, and SHH2b extend parallels between paramutation in maize and the RNA-directed DNA methylation pathway in Arabidopsis.
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He XJ, Ma ZY, Liu ZW. Non-coding RNA transcription and RNA-directed DNA methylation in Arabidopsis. MOLECULAR PLANT 2014; 7:1406-1414. [PMID: 24966349 DOI: 10.1093/mp/ssu075] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
RNA-directed DNA methylation (RdDM) is responsible for transcriptional silencing of endogenous transposable elements and introduced transgenes. This process requires non-coding RNAs produced by DNA-dependent RNA polymerases IV and V (Pol IV and Pol V). Pol IV-produced non-coding RNAs are precursors of 24-nt small interfering RNAs, whereas Pol V-produced ncRNAs directly act as scaffold RNAs. In this review, we summarize recent advances in the understanding of RdDM. In particular, we focus on the mechanisms underlying the recruitment of Pol IV and Pol V to chromatin and the targeting of RdDM.
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Affiliation(s)
- Xin-Jian He
- National Institute of Biological Sciences, Beijing 102206, China.
| | - Ze-Yang Ma
- National Institute of Biological Sciences, Beijing 102206, China
| | - Zhang-Wei Liu
- National Institute of Biological Sciences, Beijing 102206, China
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29
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Abstract
RNA-directed DNA methylation (RdDM) is the major small RNA-mediated epigenetic pathway in plants. RdDM requires a specialized transcriptional machinery that comprises two plant-specific RNA polymerases - Pol IV and Pol V - and a growing number of accessory proteins, the functions of which in the RdDM mechanism are only partially understood. Recent work has revealed variations in the canonical RdDM pathway and identified factors that recruit Pol IV and Pol V to specific target sequences. RdDM, which transcriptionally represses a subset of transposons and genes, is implicated in pathogen defence, stress responses and reproduction, as well as in interallelic and intercellular communication.
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30
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Yang LP, Fang YY, An CP, Dong L, Zhang ZH, Chen H, Xie Q, Guo HS. C2-mediated decrease in DNA methylation, accumulation of siRNAs, and increase in expression for genes involved in defense pathways in plants infected with beet severe curly top virus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 73:910-7. [PMID: 23176533 DOI: 10.1111/tpj.12081] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 11/16/2012] [Accepted: 11/20/2012] [Indexed: 05/20/2023]
Abstract
Cytosine methylation is one of epigenetic information marked on the DNA sequence. In plants, small interfering RNAs (siRNAs) target homologous genomic DNA sequences for cytosine methylation. This process, known as RNA-directed DNA methylation (RdDM), plays an important role in transposon control, regulation of gene expression and virus resistance. In this paper, we demonstrate that the C2 protein encoded by a geminivirus (beet severe curly top virus, BSCTV) mediated a decrease in DNA methylation of repeat regions in the promoters of ACD6, an upstream regulator of the salicylic acid defense pathway, and GSTF14, an endogenous gene of the glutathione S-transferase superfamily that is implicated in numerous stress responses. C2-mediated decreases in DNA methylation reduced accumulation of the siRNAs derived from the promoter repeats and enhanced the steady-state expression of both ACD6 and GSTF14 transcripts. Reduced accumulation of BSCTV-derived siRNAs was detected in BSCTV-infected plants, but not in plants infected with C2-deficient BSCTV (c2(- ) BSCTV). C2 protein exhibited no siRNA-binding activity. Instead, our results revealed that C2 protein-mediated decreases in DNA methylation appeared to affect the production of siRNAs that are required for targeting and reinforcing RdDM, a process that activated expression of defense-related genes that are normally dampened by these siRNAs in the host plants. However, C2-dependent reduction in virus-derived siRNAs also benefits the viruses by disrupting the feedback loop reinforcing DNA methylation-mediated antiviral silencing.
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Affiliation(s)
- Li-Ping Yang
- State Key Laboratory of Plant Genomics and National Center for Plant gene research (Beijing), Institute of Microbiology, Beijing, 100101, China
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31
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Haag JR, Ream TS, Marasco M, Nicora CD, Norbeck AD, Pasa-Tolic L, Pikaard CS. In vitro transcription activities of Pol IV, Pol V, and RDR2 reveal coupling of Pol IV and RDR2 for dsRNA synthesis in plant RNA silencing. Mol Cell 2012; 48:811-8. [PMID: 23142082 DOI: 10.1016/j.molcel.2012.09.027] [Citation(s) in RCA: 147] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Revised: 08/13/2012] [Accepted: 09/19/2012] [Indexed: 01/05/2023]
Abstract
In Arabidopsis, RNA-dependent DNA methylation and transcriptional silencing involves three nuclear RNA polymerases that are biochemically undefined: the presumptive DNA-dependent RNA polymerases Pol IV and Pol V and the putative RNA-dependent RNA polymerase RDR2. Here we demonstrate their RNA polymerase activities in vitro. Unlike Pol II, Pols IV and V require an RNA primer, are insensitive to α-amanitin, and differ in their ability to displace the nontemplate DNA strand during transcription. Biogenesis of 24 nt small interfering RNAs (siRNAs), which guide cytosine methylation to corresponding sequences, requires both Pol IV and RDR2, which physically associate in vivo. Whereas Pol IV does not require RDR2 for activity, RDR2 is nonfunctional in the absence of associated Pol IV. These results suggest that the physical and mechanistic coupling of Pol IV and RDR2 results in the channeled synthesis of double-stranded precursors for 24 nt siRNA biogenesis.
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Affiliation(s)
- Jeremy R Haag
- Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
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32
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Finke A, Kuhlmann M, Mette MF. IDN2 has a role downstream of siRNA formation in RNA-directed DNA methylation. Epigenetics 2012; 7:950-60. [PMID: 22810086 PMCID: PMC3427290 DOI: 10.4161/epi.21237] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In plants, a particular class of short interfering (si)RNAs can serve as a signal to induce cytosine methylation at homologous genomic regions. If the targeted DNA has promoter function, this RNA-directed DNA methylation (RdDM) can result in transcriptional gene silencing (TGS). RNA-directed transcriptional gene silencing (RdTGS) of transgenes provides a versatile system for the study of epigenetic gene regulation. We used transcription of a nopaline synthase promoter (ProNOS)-inverted repeat (IR) to provide a RNA signal that triggers de novo cytosine methylation and TGS of a homologous ProNOS copy in trans. Utilizing a ProNOS-NPTII reporter gene showing high sensitivity to silencing in this two component system, a forward genetic screen for EMS-induced no rna-directed transcriptional silencing (nrd) mutations was performed in Arabidopsis thaliana. Three nrd mutant lines were found to contain one novel loss-of-function allele of idn2/rdm12 and two of nrpd2a/nrpe2a. IDN2/RDM12 encodes a XH/XS domain protein that is able to bind double-stranded RNA with 5′ overhangs, while NRPD2a/NRPE2a encodes the common second-largest subunit of the plant specific DNA-dependent RNA polymerases IV and V involved in silencing processes. Both idn2/rdm12 and nrpd2a/nrpe2a release target transgene expression and reduce CHH context methylation at transgenic as well as endogenous RdDM target regions to similar extents. Nevertheless, accumulation of IR-derived siRNA is not affected, allowing us to present a refined model for the pathway of RdDM and RdTGS that positions function of IDN2 downstream of siRNA formation and points to an important role for its XH domain.
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Affiliation(s)
- Andreas Finke
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
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33
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Lee TF, Gurazada SGR, Zhai J, Li S, Simon SA, Matzke MA, Chen X, Meyers BC. RNA polymerase V-dependent small RNAs in Arabidopsis originate from small, intergenic loci including most SINE repeats. Epigenetics 2012; 7:781-95. [PMID: 22647529 PMCID: PMC3679228 DOI: 10.4161/epi.20290] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
In plants, heterochromatin is maintained by a small RNA-based gene silencing mechanism known as RNA-directed DNA methylation (RdDM). RdDM requires the non-redundant functions of two plant-specific DNA-dependent RNA polymerases (RNAP), RNAP IV and RNAP V. RNAP IV plays a major role in siRNA biogenesis, while RNAP V may recruit DNA methylation machinery to target endogenous loci for silencing. Although small RNA-generating regions that are dependent on both RNAP IV and RNAP V have been identified previously, the genomic loci targeted by RNAP V for siRNA accumulation and silencing have not been described extensively. To characterize the RNAP V-dependent, heterochromatic siRNA-generating regions in the Arabidopsis genome, we deeply sequenced the small RNA populations of wild-type and RNAP V null mutant (nrpe1) plants. Our results showed that RNAP V-dependent siRNA-generating loci are associated predominately with short repetitive sequences in intergenic regions. Suppression of small RNA production from short repetitive sequences was also prominent in RdDM mutants including dms4, drd1, dms3 and rdm1, reflecting the known association of these RdDM effectors with RNAP V. The genomic regions targeted by RNAP V were small, with an estimated average length of 238 bp. Our results suggest that RNAP V affects siRNA production from genomic loci with features dissimilar to known RNAP IV-dependent loci. RNAP V, along with RNAP IV and DRM1/2, may target and silence a set of small, intergenic transposable elements located in dispersed genomic regions for silencing. Silencing at these loci may be actively reinforced by RdDM.
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Affiliation(s)
- Tzuu-fen Lee
- Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
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34
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Saze H, Tsugane K, Kanno T, Nishimura T. DNA methylation in plants: relationship to small RNAs and histone modifications, and functions in transposon inactivation. PLANT & CELL PHYSIOLOGY 2012; 53:766-84. [PMID: 22302712 DOI: 10.1093/pcp/pcs008] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
DNA methylation is a type of epigenetic marking that strongly influences chromatin structure and gene expression in plants and mammals. Over the past decade, DNA methylation has been intensively investigated in order to elucidate its control mechanisms. These studies have shown that small RNAs are involved in the induction of DNA methylation, that there is a relationship between DNA methylation and histone methylation, and that the base excision repair pathway has an important role in DNA demethylation. Some aspects of DNA methylation have also been shown to be shared with mammals, suggesting that the regulatory pathways are, in part at least, evolutionarily conserved. Considerable progress has been made in elucidating the mechanisms that control DNA methylation; however, many aspects of the mechanisms that read the information encoded by DNA methylation and mediate this into downstream regulation remain uncertain, although some candidate proteins have been identified. DNA methylation has a vital role in the inactivation of transposons, suggesting that DNA methylation is a key factor in the evolution and adaptation of plants.
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Affiliation(s)
- Hidetoshi Saze
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
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35
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36
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Abstract
Given the widespread impact of RNA silencing on the Arabidopsis thaliana genome, it is indeed remarkable that this means of gene regulation went undiscovered for so long. Since the publication of landmark papers in 1998 (Fire et al., Nature 391:806-811, 1998; Waterhouse et al., Proc Natl Acad Sci U S A 95:13959-13964, 1998), intense research efforts have resulted in much progress from the speculation of Mello and colleagues that "the mechanisms underlying RNA interference probably exist for a biological purpose" (Fire et al., Nature 391:806-811, 1998). Across the eukaryotic kingdom, with the notable exception of Saccharomyces cerevisiae (Moazed, Science 326:544-550, 2009), the importance of small RNA-driven gene regulation has been recognized and implicated in central developmental processes as well as in aberrant and diseased states. Plants have by far the most complex RNA-based control of gene expression (Wang et al., Floriculture, ornamental and plant biotechnology, vol. III, 2006). Four distinct RNA silencing pathways have been recognized in plants, albeit with considerable conservation of the molecular components. These pathways are directed by various small RNA species, including microRNAs (miRNAs), trans-acting small interfering RNAs (siRNA) (ta-siRNAs), repeat-associated siRNAs (ra-siRNAs), and natural antisense transcript siRNAs (nat-siRNAs). The effective functionality of each of these pathways appear to be fundamental to the integrity of A. thaliana. Furthermore, in response to viral invasion, plants synthesize viral sRNAs as a means of defense. This process may in fact reflect the ancient origins of RNA silencing: plants may have evolved RNA silencing pathways as a defense mechanism against foreign nucleic acid species in the absence of an immune system (Wang and Metzlaff, Curr Opin Plant Biol 8:216-222, 2005). The generation of viral siRNAs is a particularly interesting illustration of RNA silencing as it provides a context to explore the potential to harness a naturally occurring system to the end goal of artificially engineering viral resistance.
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37
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Dong L, Liu M, Fang YY, Zhao JH, He XF, Ying XB, Zhang YY, Xie Q, Chua NH, Guo HS. DRD1-Pol V-dependent self-silencing of an exogenous silencer restricts the non-cell autonomous silencing of an endogenous target gene. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 68:633-45. [PMID: 21771120 PMCID: PMC3204326 DOI: 10.1111/j.1365-313x.2011.04714.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
In plants, the exogenous transgene transcribing inverted-repeat (exo-IR) sequences produces double-stranded RNAs that are processed by DCL4. The 21-nt small interfering RNAs generated function as mobile signals to trigger non-cell autonomous silencing of target endogenes in the neighboring 10-15 cells. The potential involvement of nuclear silencing pathway components in signal spreading or sensing in target cells is not clear. Here, we demonstrate that the exo-IR silencer (exo-Pdsi) is negatively autoregulated through methylation spreading, which acts in cis to reinforce the self-silencing of the silencer. Mutations affecting nuclear proteins DRD1 and Pol V (NRPE1 or NRPD2) relieved exo-Pdsi self-silencing, resulting in higher levels of Pdsi transcripts, which increased the non-cell autonomous silencing of endo-PDS. Our results suggest that in an experimental silencing pathway, methylation spreading on a silencer transgene may not have a direct endogenous plant counterpart when the protein-encoding gene is the target. DRD1-Pol V-dependent de novo methylation, by acting in cis to reinforce self-silencing of exo-IR, may play a role in restraining the inappropriate silencing of active protein-coding genes in plants.
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Affiliation(s)
- Li Dong
- State Key Laboratory of Plant Genomics and National Center for Plant gene research (Beijing), Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Meng Liu
- State Key Laboratory of Plant Genomics and National Center for Plant gene research (Beijing), Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yuan-Yuan Fang
- State Key Laboratory of Plant Genomics and National Center for Plant gene research (Beijing), Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jian-Hua Zhao
- State Key Laboratory of Plant Genomics and National Center for Plant gene research (Beijing), Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiang-Feng He
- State Key Laboratory of Plant Genomics and National Center for Plant gene research (Beijing), Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiao-Bao Ying
- State Key Laboratory of Plant Genomics and National Center for Plant gene research (Beijing), Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yi-Yue Zhang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qi Xie
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Nam-Hai Chua
- Laboratory of Plant Molecular Biology, The Rockefeller University, New York, New York 10021
| | - Hui-Shan Guo
- State Key Laboratory of Plant Genomics and National Center for Plant gene research (Beijing), Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- Corresponding author: Hui-Shan Guo, , Tel: 010-64847989, Fax: 010-64847989
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38
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Haag JR, Pikaard CS. Multisubunit RNA polymerases IV and V: purveyors of non-coding RNA for plant gene silencing. Nat Rev Mol Cell Biol 2011; 12:483-92. [PMID: 21779025 DOI: 10.1038/nrm3152] [Citation(s) in RCA: 285] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In all eukaryotes, nuclear DNA-dependent RNA polymerases I, II and III synthesize the myriad RNAs that are essential for life. Remarkably, plants have evolved two additional multisubunit RNA polymerases, RNA polymerases IV and V, which orchestrate non-coding RNA-mediated gene silencing processes affecting development, transposon taming, antiviral defence and allelic crosstalk. Biochemical details concerning the templates and products of RNA polymerases IV and V are lacking. However, their subunit compositions reveal that they evolved as specialized forms of RNA polymerase II, which provides the unique opportunity to study the functional diversification of a eukaryotic RNA polymerase family.
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Affiliation(s)
- Jeremy R Haag
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
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39
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SHH1, a homeodomain protein required for DNA methylation, as well as RDR2, RDM4, and chromatin remodeling factors, associate with RNA polymerase IV. PLoS Genet 2011; 7:e1002195. [PMID: 21811420 PMCID: PMC3141008 DOI: 10.1371/journal.pgen.1002195] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Accepted: 06/05/2011] [Indexed: 01/16/2023] Open
Abstract
DNA methylation is an evolutionarily conserved epigenetic modification that is critical for gene silencing and the maintenance of genome integrity. In Arabidopsis thaliana, the de novo DNA methyltransferase, domains rearranged methyltransferase 2 (DRM2), is targeted to specific genomic loci by 24 nt small interfering RNAs (siRNAs) through a pathway termed RNA-directed DNA methylation (RdDM). Biogenesis of the targeting siRNAs is thought to be initiated by the activity of the plant-specific RNA polymerase IV (Pol-IV). However, the mechanism through which Pol-IV is targeted to specific genomic loci and whether factors other than the core Pol-IV machinery are required for Pol-IV activity remain unknown. Through the affinity purification of nuclear RNA polymerase D1 (NRPD1), the largest subunit of the Pol-IV polymerase, we found that several previously identified RdDM components co-purify with Pol-IV, namely RNA-dependent RNA polymerase 2 (RDR2), CLASSY1 (CLSY1), and RNA-directed DNA methylation 4 (RDM4), suggesting that the upstream siRNA generating portion of the RdDM pathway may be more physically coupled than previously envisioned. A homeodomain protein, SAWADEE homeodomain homolog 1 (SHH1), was also found to co-purify with NRPD1; and we demonstrate that SHH1 is required for de novo and maintenance DNA methylation, as well as for the accumulation of siRNAs at specific loci, confirming it is a bonafide component of the RdDM pathway.
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40
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Lelandais-Brière C, Sorin C, Declerck M, Benslimane A, Crespi M, Hartmann C. Small RNA diversity in plants and its impact in development. Curr Genomics 2011; 11:14-23. [PMID: 20808519 PMCID: PMC2851111 DOI: 10.2174/138920210790217918] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2009] [Revised: 07/13/2009] [Accepted: 07/13/2009] [Indexed: 12/26/2022] Open
Abstract
MicroRNAs are a class of non-coding RNAs involved in post-transcriptional control of gene expression, either via degradation or translational inhibition of target mRNAs. Both experimental and computational approaches have been used to identify miRNAs and their target genes. In plants, deep sequencing methods have recently allowed the analysis of small RNA diversity in different species and/or mutants. Most sequencing efforts have been concentrated on the identification of miRNAs and their mRNA targets have been predicted based on complementarity criteria. The recent demonstration that certain plant miRNAs could act partly via inhibition of protein translation certainly opens new fields of analysis for plant miRNA function on a broader group of targets. The roles of conserved miRNAs on target mRNA stability have been analysed in different species and defined common mechanisms in development and stress responses. In contrast, much less is known about expression patterns or functions of non-conserved miRNAs. In this review, we focus on the comparative analyses of plant small RNA diversity and the action of si/miRNAs in post-transcriptional regulation of some key genes involved in root development.
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Affiliation(s)
- Christine Lelandais-Brière
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique (C.N.R.S.), F-91198 Gif-sur-Yvette Cedex, France
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41
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Law JA, Jacobsen SE. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet 2011; 11:204-20. [PMID: 20142834 DOI: 10.1038/nrg2719] [Citation(s) in RCA: 2486] [Impact Index Per Article: 191.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cytosine DNA methylation is a stable epigenetic mark that is crucial for diverse biological processes, including gene and transposon silencing, imprinting and X chromosome inactivation. Recent findings in plants and animals have greatly increased our understanding of the pathways used to accurately target, maintain and modify patterns of DNA methylation and have revealed unanticipated mechanistic similarities between these organisms. Key roles have emerged for small RNAs, proteins with domains that bind methylated DNA and DNA glycosylases in these processes. Drawing on insights from both plants and animals should deepen our understanding of the regulation and biological significance of DNA methylation.
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Affiliation(s)
- Julie A Law
- Department of Molecular, Cell and Developmental Biology, University of California-Los Angeles, 90095-1606, USA
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42
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Abstract
Mediator, a conserved multiprotein complex in animals, plants, and fungi, is a cofactor of RNA Polymerase II (Pol II). It is known to promote basal Pol II-mediated transcription as well as bridge sequence-specific transcriptional regulators and Pol II to integrate regulatory information. Pol II transcribes not only protein-coding genes but also intergenic regions to generate noncoding RNAs such as small RNAs (microRNAs and small interfering RNAs) and long noncoding RNAs. Intriguingly, two plant-specific polymerases, Pol IV and Pol V, have evolved from Pol II and play a role in the production of small interfering RNAs and long noncoding RNAs at heterochromatic regions to maintain genome stability through transcriptional gene silencing (TGS). Recent studies have defined the composition of the plant Mediator and evaluated its role in noncoding RNA production in relationship to Pol II, Pol IV and Pol V. Here, we review the functions of Mediator and that of noncoding RNAs generated by Pol II, Pol IV and Pol V in plants, and discuss a role of Mediator in epigenetic regulation via noncoding RNA production.
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Affiliation(s)
- Yun Ju Kim
- Department of Botany and Plant Sciences and Institute of Integrative Genome Biology, University of California, Riverside, CA 92521
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Greenberg MVC, Ausin I, Chan SWL, Cokus SJ, Cuperus JT, Feng S, Law JA, Chu C, Pellegrini M, Carrington JC, Jacobsen SE. Identification of genes required for de novo DNA methylation in Arabidopsis. Epigenetics 2011; 6:344-54. [PMID: 21150311 DOI: 10.4161/epi.6.3.14242] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
De novo DNA methylation in Arabidopsis thaliana is catalyzed by the methyltransferase DRM2, a homolog of the mammalian de novo methyltransferase DNMT3. DRM2 is targeted to DNA by small interfering RNAs (siRNAs) in a process known as RNA-directed DNA Methylation (RdDM). While several components of the RdDM pathway are known, a functional understanding of the underlying mechanism is far from complete. We employed both forward and reverse genetic approaches to identify factors involved in de novo methylation. We utilized the FWA transgene, which is methylated and silenced when transformed into wild-type plants, but unmethylated and expressed when transformed into de novo methylation mutants. Expression of FWA is marked by a late flowering phenotype, which is easily scored in mutant versus wild-type plants. By reverse genetics we discovered the requirement for known RdDM effectors AGO6 and NRPE5a for efficient de novo methylation. A forward genetic approach uncovered alleles of several components of the RdDM pathway, including alleles of clsy1, ktf1, and nrpd/e2, which have not been previously shown to be required for the initial establishment of DNA methylation. Mutations were mapped and genes cloned by both traditional and whole genome sequencing approaches. The methodologies and the mutant alleles discovered will be instrumental in further studies of de novo DNA methylation.
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Affiliation(s)
- Maxim V C Greenberg
- Department of Molecular, Cell and Developmental Biology, University of California Davis, USA
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He XJ, Chen T, Zhu JK. Regulation and function of DNA methylation in plants and animals. Cell Res 2011; 21:442-65. [PMID: 21321601 DOI: 10.1038/cr.2011.23] [Citation(s) in RCA: 326] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
DNA methylation is an important epigenetic mark involved in diverse biological processes. In plants, DNA methylation can be established through the RNA-directed DNA methylation pathway, an RNA interference pathway for transcriptional gene silencing (TGS), which requires 24-nt small interfering RNAs. In mammals, de novo DNA methylation occurs primarily at two developmental stages: during early embryogenesis and during gametogenesis. While it is not clear whether establishment of DNA methylation patterns in mammals involves RNA interference in general, de novo DNA methylation and suppression of transposons in germ cells require 24-32-nt piwi-interacting small RNAs. DNA methylation status is dynamically regulated by DNA methylation and demethylation reactions. In plants, active DNA demethylation relies on the repressor of silencing 1 family of bifunctional DNA glycosylases, which remove the 5-methylcytosine base and then cleave the DNA backbone at the abasic site, initiating a base excision repair (BER) pathway. In animals, multiple mechanisms of active DNA demethylation have been proposed, including a deaminase- and DNA glycosylase-initiated BER pathway. New information concerning the effects of various histone modifications on the establishment and maintenance of DNA methylation has broadened our understanding of the regulation of DNA methylation. The function of DNA methylation in plants and animals is also discussed in this review.
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Affiliation(s)
- Xin-Jian He
- National Institute of Biological Sciences, Beijing 102206, China.
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Abstract
The flowering plant germline is produced during the haploid gametophytic stage. Defining the germline is complicated by the extreme reduction of the male and female gametophytes, also referred to as pollen and embryo sac, respectively. Both male and female gamete progenitors are segregated by an asymmetric cell division, as is the case for the germline in animals. Genetic studies and access to the transcriptome of isolated gametes have provided a regulatory framework for the mechanisms that define the male germline. What specifies female germline identity remains unknown. Recent evidence indicates that an auxin gradient provides positional information and plays a role in defining the identity of the female gamete lineage. The animal germline is also marked by production of small RNAs, and recent evidence indicates that this trait might be shared with the plant gamete lineage.
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Affiliation(s)
- Frédéric Berger
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604
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The de novo cytosine methyltransferase DRM2 requires intact UBA domains and a catalytically mutated paralog DRM3 during RNA-directed DNA methylation in Arabidopsis thaliana. PLoS Genet 2010; 6:e1001182. [PMID: 21060858 PMCID: PMC2965745 DOI: 10.1371/journal.pgen.1001182] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2010] [Accepted: 09/28/2010] [Indexed: 11/19/2022] Open
Abstract
Eukaryotic DNA cytosine methylation can be used to transcriptionally silence repetitive sequences, including transposons and retroviruses. This silencing is stable between cell generations as cytosine methylation is maintained epigenetically through DNA replication. The Arabidopsis thaliana Dnmt3 cytosine methyltransferase ortholog DOMAINS rearranged methyltransferase2 (DRM2) is required for establishment of small interfering RNA (siRNA) directed DNA methylation. In mammals PIWI proteins and piRNA act in a convergently evolved RNA-directed DNA methylation system that is required to repress transposon expression in the germ line. De novo methylation may also be independent of RNA interference and small RNAs, as in Neurospora crassa. Here we identify a clade of catalytically mutated DRM2 paralogs in flowering plant genomes, which in A.thaliana we term domains rearranged methyltransferase3 (DRM3). Despite being catalytically mutated, DRM3 is required for normal maintenance of non-CG DNA methylation, establishment of RNA-directed DNA methylation triggered by repeat sequences and accumulation of repeat-associated small RNAs. Although the mammalian catalytically inactive Dnmt3L paralogs act in an analogous manner, phylogenetic analysis indicates that the DRM and Dnmt3 protein families diverged independently in plants and animals. We also show by site-directed mutagenesis that both the DRM2 N-terminal UBA domains and C-terminal methyltransferase domain are required for normal RNA-directed DNA methylation, supporting an essential targeting function for the UBA domains. These results suggest that plant and mammalian RNA-directed DNA methylation systems consist of a combination of ancestral and convergent features.
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Law JA, Ausin I, Johnson LM, Vashisht AA, Zhu JK, Wohlschlegel JA, Jacobsen SE. A protein complex required for polymerase V transcripts and RNA- directed DNA methylation in Arabidopsis. Curr Biol 2010; 20:951-6. [PMID: 20409711 PMCID: PMC2972704 DOI: 10.1016/j.cub.2010.03.062] [Citation(s) in RCA: 163] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2009] [Revised: 03/19/2010] [Accepted: 03/27/2010] [Indexed: 12/23/2022]
Abstract
DNA methylation is an epigenetic modification associated with gene silencing. In Arabidopsis, DNA methylation is established by DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2), which is targeted by small interfering RNAs through a pathway termed RNA-directed DNA methylation (RdDM). Recently, RdDM was shown to require intergenic noncoding (IGN) transcripts that are dependent on the Pol V polymerase. These transcripts are proposed to function as scaffolds for the recruitment of downstream RdDM proteins, including DRM2, to loci that produce both siRNAs and IGN transcripts. However, the mechanism(s) through which Pol V is targeted to specific genomic loci remains largely unknown. Through affinity purification of two known RdDM components, DEFECTIVE IN RNA-DIRECTED DNA METHYLATION 1 (DRD1) and DEFECTIVE IN MERISTEM SILENCING 3 (DMS3), we found that they copurify with each other and with a novel protein, RNA-DIRECTED DNA METHYLATION 1 (RDM1), forming a complex we term DDR. We also found that DRD1 copurified with Pol V subunits and that RDM1, like DRD1 and DMS3, is required for the production of Pol V-dependent transcripts. These results suggest that the DDR complex acts in RdDM at a step upstream of the recruitment or activation of Pol V.
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Affiliation(s)
- Julie A. Law
- Department of Molecular Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Israel Ausin
- Department of Molecular Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Lianna M. Johnson
- Life Sciences Core Curriculum, University of California Los Angeles, Los Angeles, California, USA
| | - Ajay A. Vashisht
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Box 951737, BSRB-377A, 615 Charles E. Young Drive South, Los Angeles, CA 90095-1737
| | - Jian-Kang Zhu
- Center for Plant Stress Genomics Research, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia, and Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - James A. Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Box 951737, BSRB-377A, 615 Charles E. Young Drive South, Los Angeles, CA 90095-1737
| | - Steven E. Jacobsen
- Department of Molecular Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, California 90095, USA
- Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, California 90095, USA
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49
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Searle IR, Pontes O, Melnyk CW, Smith LM, Baulcombe DC. JMJ14, a JmjC domain protein, is required for RNA silencing and cell-to-cell movement of an RNA silencing signal in Arabidopsis. Genes Dev 2010; 24:986-91. [PMID: 20478993 PMCID: PMC2867213 DOI: 10.1101/gad.579910] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2010] [Accepted: 03/26/2010] [Indexed: 11/24/2022]
Abstract
JMJ14 is a histone H3 Lys4 (H3K4) trimethyl demethylase that affects mobile RNA silencing in an Arabidopsis transgene system. It also influences CHH DNA methylation, abundance of endogenous transposon transcripts, and flowering time. JMJ14 acts at a point in RNA silencing pathways that is downstream from RNA-dependent RNA polymerase 2 (RDR2) and Argonaute 4 (AGO4). Our results illustrate a link between RNA silencing and demethylation of histone H3 trimethylysine. We propose that JMJ14 acts downstream from the Argonaute effector complex to demethylate histone H3K4 at the target of RNA silencing.
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Affiliation(s)
- Iain R. Searle
- Plant Sciences Department, Cambridge University, Cambridge CB2 3EA, United Kingdom
- The Sainsbury Laboratory, Norwich NR4 7UH, United Kingdom
| | - Olga Pontes
- Biology Department, Washington University, St. Louis, Missouri 63130, USA
| | - Charles W. Melnyk
- Plant Sciences Department, Cambridge University, Cambridge CB2 3EA, United Kingdom
- The Sainsbury Laboratory, Norwich NR4 7UH, United Kingdom
| | - Lisa M. Smith
- The Sainsbury Laboratory, Norwich NR4 7UH, United Kingdom
| | - David C. Baulcombe
- Plant Sciences Department, Cambridge University, Cambridge CB2 3EA, United Kingdom
- The Sainsbury Laboratory, Norwich NR4 7UH, United Kingdom
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50
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Karlowski WM, Zielezinski A, Carrère J, Pontier D, Lagrange T, Cooke R. Genome-wide computational identification of WG/GW Argonaute-binding proteins in Arabidopsis. Nucleic Acids Res 2010; 38:4231-45. [PMID: 20338883 PMCID: PMC2910046 DOI: 10.1093/nar/gkq162] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Domains in Arabidopsis proteins NRPE1 and SPT5-like, composed almost exclusively of repeated motifs in which only WG or GW sequences and an overall amino-acid preference are conserved, have been experimentally shown to bind multiple molecules of Argonaute (AGO) protein(s). Domain swapping between the WG/GW domains of NRPE1 and the human protein GW182 showed a conserved function. As classical sequence alignment methods are poorly-adapted to detect such weakly-conserved motifs, we have developed a tool to carry out a systematic analysis to identify genes potentially encoding AGO-binding GW/WG proteins. Here, we describe exhaustive analysis of the Arabidopsis genome for all regions potentially encoding proteins bearing WG/GW motifs and consider the possible role of some of them in AGO-dependent mechanisms. We identified 20 different candidate WG/GW genes, encoding proteins in which the predicted domains range from 92aa to 654aa. These mostly correspond to a limited number of families: RNA-binding proteins, transcription factors, glycine-rich proteins, translation initiation factors and known silencing-associated proteins such as SDE3. Recent studies have argued that the interaction between WG/GW-rich domains and AGO proteins is evolutionarily conserved. Here, we demonstrate by an in silico domain-swapping simulation between plant and mammalian WG/GW proteins that the biased amino-acid composition of the AGO-binding sites is conserved.
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Affiliation(s)
- Wojciech M Karlowski
- Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, 61-614 Poznan, Poland.
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