1
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Schröder JA, Bonnet DMV, Jullien PE. Non-cell-autonomous small RNA silencing in Arabidopsis female gametes. Curr Biol 2023; 33:183-188.e3. [PMID: 36516850 DOI: 10.1016/j.cub.2022.11.044] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 10/13/2022] [Accepted: 11/18/2022] [Indexed: 12/15/2022]
Abstract
In recent years, small RNA movement has been both hypothesized and shown to be an integral part of the epigenetic DNA methylation reprogramming occurring during plant reproduction.1It was suggested that the release of epigenetic silencing in accessory cell types or tissues is necessary to reinforce epigenetic silencing in the gametes (egg cell and sperm cells), which would in turn ensure the genomic stability of the next generation plant.2,3 In Arabidopsis thaliana, small RNA (sRNA) movement was indeed shown to occur during male gametogenesis.4,5,6 However, the situation within the female gametophyte and in early seed development is mostly unknown. Here, we show that small RNAs can induce non-cell-autonomous silencing from the central cell toward the egg cell but also from the synergids to the egg cell and central cell. Our data show that in addition to the movement of sRNAs during pollen development, hairpin RNAs can have non-cell-autonomous effects in the female gametes.
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Affiliation(s)
- Jens A Schröder
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Diane M V Bonnet
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Pauline E Jullien
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland.
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2
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Tirot L, Jullien PE. Epigenetic dynamics during sexual reproduction: At the nexus of developmental control and genomic integrity. Curr Opin Plant Biol 2022; 69:102278. [PMID: 35970063 DOI: 10.1016/j.pbi.2022.102278] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/20/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
Epigenetic marks influence gene regulation and genomic stability via the repression of transposable elements. During sexual reproduction, tight regulation of the epigenome must take place to maintain the repression of transposable elements while still allowing changes in cell-specific transcriptional programs. In plants, epigenetic marks are reorganized during reproduction and a reinforcing mechanism takes place to ensure transposable elements silencing. In this review, we describe the latest advances in characterizing the cell-specific epigenetic changes occurring from sporogenesis to seed development, with a focus on DNA methylation. We highlight the epigenetic co-regulation between transposable elements and developmental genes at different stages of plant reproduction.
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Affiliation(s)
- Louis Tirot
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
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3
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Tirot L, Bonnet DMV, Jullien PE. DNA Methyltransferase 3 (MET3) is regulated by Polycomb group complex during Arabidopsis endosperm development. Plant Reprod 2022; 35:141-151. [PMID: 35088155 PMCID: PMC9110472 DOI: 10.1007/s00497-021-00436-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
Complex epigenetic changes occur during plant reproduction. These regulations ensure the proper transmission of epigenetic information as well as allowing for zygotic totipotency. In Arabidopsis, the main DNA methyltransferase is called MET1 and is responsible for methylating cytosine in the CG context. The Arabidopsis genome encodes for three additional reproduction-specific homologs of MET1, namely MET2a, MET2b and MET3. In this paper, we show that the DNA methyltransferase MET3 is expressed in the seed endosperm and its expression is later restricted to the chalazal endosperm. MET3 is biallelically expressed in the endosperm but displays a paternal expression bias. We found that MET3 expression is regulated by the Polycomb complex proteins FIE and MSI1. Seed development is not impaired in met3 mutant, and we could not observe significant transcriptional changes in met3 mutant. MET3 might regulates gene expression in a Polycomb mutant background suggesting a further complexification of the interplay between H3K27me3 and DNA methylation in the seed endosperm. KEY MESSAGE: The DNA METHYLTRANSFERASE MET3 is controlled by Polycomb group complex during endosperm development.
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Affiliation(s)
- Louis Tirot
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Diane M V Bonnet
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
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4
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Oliver C, Annacondia ML, Wang Z, Jullien PE, Slotkin RK, Köhler C, Martinez G. The miRNome function transitions from regulating developmental genes to transposable elements during pollen maturation. Plant Cell 2022; 34:784-801. [PMID: 34755870 PMCID: PMC8824631 DOI: 10.1093/plcell/koab280] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 11/04/2021] [Indexed: 06/13/2023]
Abstract
Animal and plant microRNAs (miRNAs) are essential for the spatio-temporal regulation of development. Together with this role, plant miRNAs have been proposed to target transposable elements (TEs) and stimulate the production of epigenetically active small interfering RNAs. This activity is evident in the plant male gamete containing structure, the male gametophyte or pollen grain. How the dual role of plant miRNAs, regulating both genes and TEs, is integrated during pollen development and which mRNAs are regulated by miRNAs in this cell type at a genome-wide scale are unknown. Here, we provide a detailed analysis of miRNA dynamics and activity during pollen development in Arabidopsis thaliana using small RNA and degradome parallel analysis of RNA end high-throughput sequencing. Furthermore, we uncover miRNAs loaded into the two main active Argonaute (AGO) proteins in the uninuclear and mature pollen grain, AGO1 and AGO5. Our results indicate that the developmental progression from microspore to mature pollen grain is characterized by a transition from miRNAs targeting developmental genes to miRNAs regulating TE activity.
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Affiliation(s)
- Cecilia Oliver
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden
| | - Maria Luz Annacondia
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden
| | - Zhenxing Wang
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden
- College of Horticulture and State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs and Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, Nanjing Agricultural University, Nanjing 210095, China
| | - Pauline E Jullien
- Institute of Plant Sciences, University of Bern, Bern 3013, Switzerland
| | - R Keith Slotkin
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
- Division of Biological Sciences, University of Missouri Columbia, Columbia, Missouri 65201, USA
| | - Claudia Köhler
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
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5
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Jullien PE, Schröder JA, Bonnet DMV, Pumplin N, Voinnet O. Asymmetric expression of Argonautes in reproductive tissues. Plant Physiol 2022; 188:38-43. [PMID: 34687292 PMCID: PMC8774725 DOI: 10.1093/plphys/kiab474] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 09/13/2021] [Indexed: 06/01/2023]
Abstract
The Arabidopsis genome encodes ten Argonautes proteins showing distinct expression pattern as well as intracellular localisation during sexual reproduction.
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Affiliation(s)
- P E Jullien
- Institute of Plant Sciences, University of Bern, 3012 Bern, Switzerland
- Institute of Molecular Plant Biology—Swiss Federal Institute of Technology Zurich (ETH‐Zurich), 8092 Zurich, Switzerland
| | - J A Schröder
- Institute of Plant Sciences, University of Bern, 3012 Bern, Switzerland
| | - D M V Bonnet
- Institute of Plant Sciences, University of Bern, 3012 Bern, Switzerland
| | - N Pumplin
- Institute of Molecular Plant Biology—Swiss Federal Institute of Technology Zurich (ETH‐Zurich), 8092 Zurich, Switzerland
| | - O Voinnet
- Institute of Molecular Plant Biology—Swiss Federal Institute of Technology Zurich (ETH‐Zurich), 8092 Zurich, Switzerland
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6
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Jullien PE, Grob S, Marchais A, Pumplin N, Chevalier C, Bonnet DMV, Otto C, Schott G, Voinnet O. Functional characterization of Arabidopsis ARGONAUTE 3 in reproductive tissues. Plant J 2020; 103:1796-1809. [PMID: 32506562 DOI: 10.1111/tpj.14868] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 04/08/2020] [Accepted: 05/20/2020] [Indexed: 05/03/2023]
Abstract
Arabidopsis encodes 10 ARGONAUTE (AGO) effectors of RNA silencing, canonically loaded with either 21-22 nucleotide (nt) long small RNAs (sRNAs) to mediate post-transcriptional gene silencing (PTGS) or 24 nt sRNAs to promote RNA-directed DNA methylation. Using full-locus constructs, we characterized the expression, biochemical properties and possible modes of action of AGO3. Although AGO3 arose from a recent duplication at the AGO2 locus, their expression patterns differ drastically, with AGO2 being expressed in both male and female gametes whereas AGO3 accumulates in aerial vascular terminations and specifically in chalazal seed integuments. Accordingly, AGO3 downregulation alters gene expression in siliques. Similar to AGO2, AGO3 binds sRNAs with a strong 5' adenosine bias, but unlike Arabidopsis AGO2, it binds 24 nt sRNAs most efficiently. AGO3 immunoprecipitation experiments in siliques revealed that these sRNAs mostly correspond to genes and intergenic regions in a manner reflecting their respective accumulation from their loci of origin. AGO3 localizes to the cytoplasm and co-fractionates with polysomes to possibly mediate PTGS via translation inhibition.
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Affiliation(s)
- Pauline E Jullien
- Institute of Molecular Plant Biology, Swiss Federal Institute of Technology Zurich (ETH Zurich), Universitätstrasse 2, Zurich, 8092, Switzerland
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, 3013, Switzerland
| | - Stefan Grob
- Department of Plant and Microbial Biology, University of Zurich and Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, Zurich, 8008, Switzerland
| | - Antonin Marchais
- Institute of Molecular Plant Biology, Swiss Federal Institute of Technology Zurich (ETH Zurich), Universitätstrasse 2, Zurich, 8092, Switzerland
| | - Nathan Pumplin
- Institute of Molecular Plant Biology, Swiss Federal Institute of Technology Zurich (ETH Zurich), Universitätstrasse 2, Zurich, 8092, Switzerland
| | - Clement Chevalier
- Institute of Molecular Plant Biology, Swiss Federal Institute of Technology Zurich (ETH Zurich), Universitätstrasse 2, Zurich, 8092, Switzerland
| | - Diane M V Bonnet
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, 3013, Switzerland
| | - Caroline Otto
- Institute of Molecular Plant Biology, Swiss Federal Institute of Technology Zurich (ETH Zurich), Universitätstrasse 2, Zurich, 8092, Switzerland
| | - Gregory Schott
- Institute of Molecular Plant Biology, Swiss Federal Institute of Technology Zurich (ETH Zurich), Universitätstrasse 2, Zurich, 8092, Switzerland
| | - Olivier Voinnet
- Institute of Molecular Plant Biology, Swiss Federal Institute of Technology Zurich (ETH Zurich), Universitätstrasse 2, Zurich, 8092, Switzerland
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7
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Devers EA, Brosnan CA, Sarazin A, Albertini D, Amsler AC, Brioudes F, Jullien PE, Lim P, Schott G, Voinnet O. Movement and differential consumption of short interfering RNA duplexes underlie mobile RNA interference. Nat Plants 2020; 6:789-799. [PMID: 32632272 DOI: 10.1038/s41477-020-0687-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 05/06/2020] [Indexed: 05/19/2023]
Abstract
In RNA interference (RNAi), the RNase III Dicer processes long double-stranded RNA (dsRNA) into short interfering RNA (siRNA), which, when loaded into ARGONAUTE (AGO) family proteins, execute gene silencing1. Remarkably, RNAi can act non-cell autonomously2,3: it is graft transmissible4-7, and plasmodesmata-associated proteins modulate its cell-to-cell spread8,9. Nonetheless, the molecular mechanisms involved remain ill defined, probably reflecting a disparity of experimental settings. Among other caveats, these almost invariably cause artificially enhanced movement via transitivity, whereby primary RNAi-target transcripts are converted into further dsRNA sources of secondary siRNA5,10,11. Whether siRNA mobility naturally requires transitivity and whether it entails the same or distinct signals for cell-to-cell versus long-distance movement remains unclear, as does the identity of the mobile signalling molecules themselves. Movement of long single-stranded RNA, dsRNA, free/AGO-bound secondary siRNA or primary siRNA have all been advocated12-15; however, an entity necessary and sufficient for all known manifestations of plant mobile RNAi remains to be ascertained. Here, we show that the same primary RNAi signal endows both vasculature-to-epidermis and long-distance silencing movement from three distinct RNAi sources. The mobile entities are AGO-free primary siRNA duplexes spreading length and sequence independently. However, their movement is accompanied by selective siRNA depletion reflecting the AGO repertoires of traversed cell types. Coupling movement with this AGO-mediated consumption process creates qualitatively distinct silencing territories, potentially enabling unlimited spatial gene regulation patterns well beyond those granted by mere gradients.
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Affiliation(s)
| | - Christopher A Brosnan
- Department of Biology, ETH Zürich, Zurich, Switzerland
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia
| | | | | | | | | | - Pauline E Jullien
- Department of Biology, ETH Zürich, Zurich, Switzerland
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Peiqi Lim
- Department of Biology, ETH Zürich, Zurich, Switzerland
- QIAGEN Singapore, Singapore, Singapore
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8
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Abstract
Small RNAs gene regulation was first discovered about 20 years ago. It represents a conserve gene regulation mechanism across eukaryotes and is associated to key regulatory processes. In plants, small RNAs tightly regulate development, but also maintain genome stability and protect the plant against pathogens. Small RNA gene regulation in plants can be divided in two canonical pathways: Post-transcriptional Gene Silencing (PTGS) that results in transcript degradation and/or translational inhibition or Transcriptional Gene Silencing (TGS) that results in DNA methylation. In this review, we will focus on the model plant Arabidopsis thaliana. We will provide a brief overview of the molecular mechanisms involved in canonical small RNA pathways as well as introducing more atypical pathways recently discovered.
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9
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Tschopp MA, Iki T, Brosnan CA, Jullien PE, Pumplin N. A complex of Arabidopsis DRB proteins can impair dsRNA processing. RNA 2017; 23:782-797. [PMID: 28232389 PMCID: PMC5393186 DOI: 10.1261/rna.059519.116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 02/13/2017] [Indexed: 05/17/2023]
Abstract
Small RNAs play an important role in regulating gene expression through transcriptional and post-transcriptional gene silencing. Biogenesis of small RNAs from longer double-stranded (ds) RNA requires the activity of dicer-like ribonucleases (DCLs), which in plants are aided by dsRNA binding proteins (DRBs). To gain insight into this pathway in the model plant Arabidopsis, we searched for interactors of DRB4 by immunoprecipitation followed by mass spectrometry-based fingerprinting and discovered DRB7.1. This interaction, verified by reciprocal coimmunoprecipitation and bimolecular fluorescence complementation, colocalizes with markers of cytoplasmic siRNA bodies and nuclear dicing bodies. In vitro experiments using tobacco BY-2 cell lysate (BYL) revealed that the complex of DRB7.1/DRB4 impairs cleavage of diverse dsRNA substrates into 24-nucleotide (nt) small interfering (si) RNAs, an action performed by DCL3. DRB7.1 also negates the action of DRB4 in enhancing accumulation of 21-nt siRNAs produced by DCL4. Overexpression of DRB7.1 in Arabidopsis altered accumulation of siRNAs in a manner reminiscent of drb4 mutant plants, suggesting that DRB7.1 can antagonize the function of DRB4 in siRNA accumulation in vivo as well as in vitro. Specifically, enhanced accumulation of siRNAs from an endogenous inverted repeat correlated with enhanced DNA methylation, suggesting a biological impact for DRB7.1 in regulating epigenetic marks. We further demonstrate that RNase three-like (RTL) proteins RTL1 and RTL2 cleave dsRNA when expressed in BYL, and that this activity is impaired by DRB7.1/DRB4. Investigating the DRB7.1-DRB4 interaction thus revealed that a complex of DRB proteins can antagonize, rather than promote, RNase III activity and production of siRNAs in plants.
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Affiliation(s)
| | - Taichiro Iki
- Department of Biology, ETH Zürich, 8092 Zürich, Switzerland
- Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan
| | | | - Pauline E Jullien
- Department of Biology, ETH Zürich, 8092 Zürich, Switzerland
- IRD, 34394 Montpellier, France
| | - Nathan Pumplin
- Department of Biology, ETH Zürich, 8092 Zürich, Switzerland
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10
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Pumplin N, Sarazin A, Jullien PE, Bologna NG, Oberlin S, Voinnet O. DNA Methylation Influences the Expression of DICER-LIKE4 Isoforms, Which Encode Proteins of Alternative Localization and Function. Plant Cell 2016; 28:2786-2804. [PMID: 27956586 PMCID: PMC5155348 DOI: 10.1105/tpc.16.00554] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 10/21/2016] [Accepted: 11/12/2016] [Indexed: 05/08/2023]
Abstract
Plant RNA silencing operates via RNA-directed DNA-methylation (RdDM) to repress transcription or by targeting mRNAs via posttranscriptional gene silencing (PTGS). These pathways rely on distinct Dicer-like (DCL) proteins that process double-stranded RNA (dsRNA) into small-interfering RNAs (siRNAs). Here, we explored the expression and subcellular localization of Arabidopsis thaliana DCL4. DCL4 expression predominates as a transcription start site isoform encoding a cytoplasmic protein, which also represents the ancestral form in plants. A longer DCL4 transcript isoform encoding a nuclear localization signal, DCL4NLS, is present in Arabidopsis, but DNA methylation normally suppresses its expression. Hypomethylation caused by mutation, developmental reprogramming, and biotic stress correlates with enhanced DCL4NLS expression, while hypermethylation of a DCL4 transgene causes a reduction in DCL4NLS expression. DCL4NLS functions in a noncanonical siRNA pathway, producing a unique set of 21-nucleotide-long "disiRNAs," for DCL4NLS isoform-dependent siRNAs, through the nuclear RdDM dsRNA synthesis pathway. disiRNAs originate mostly from transposable elements (TEs) and TE-overlapping/proximal genes, load into the PTGS effector ARGONAUTE1 (AGO1), and display a subtle effect on transcript accumulation together with overlapping 24-nucleotide siRNAs. We propose that, via PTGS, disiRNAs could help to tighten the expression of epigenetically activated TEs and genes using the methylation-state-responsive DCL4NLS.
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Affiliation(s)
- Nathan Pumplin
- Department of Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - Alexis Sarazin
- Department of Biology, ETH Zurich, 8092 Zurich, Switzerland
| | | | | | - Stefan Oberlin
- Department of Biology, ETH Zurich, 8092 Zurich, Switzerland
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11
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Calarco JP, Borges F, Donoghue MT, Van Ex F, Jullien PE, Lopes T, Gardner R, Berger F, Feijó JA, Becker JD, Martienssen RA. Reprogramming of DNA methylation in pollen guides epigenetic inheritance via small RNA. Cell 2012; 151:194-205. [PMID: 23000270 PMCID: PMC3697483 DOI: 10.1016/j.cell.2012.09.001] [Citation(s) in RCA: 386] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 08/14/2012] [Accepted: 08/30/2012] [Indexed: 11/20/2022]
Abstract
Epigenetic inheritance is more widespread in plants than in mammals, in part because mammals erase epigenetic information by germline reprogramming. We sequenced the methylome of three haploid cell types from developing pollen: the sperm cell, the vegetative cell, and their precursor, the postmeiotic microspore, and found that unlike in mammals the plant germline retains CG and CHG DNA methylation. However, CHH methylation is lost from retrotransposons in microspores and sperm cells and restored by de novo DNA methyltransferase guided by 24 nt small interfering RNA, both in the vegetative nucleus and in the embryo after fertilization. In the vegetative nucleus, CG methylation is lost from targets of DEMETER (DME), REPRESSOR OF SILENCING 1 (ROS1), and their homologs, which include imprinted loci and recurrent epialleles that accumulate corresponding small RNA and are premethylated in sperm. Thus genome reprogramming in pollen contributes to epigenetic inheritance, transposon silencing, and imprinting, guided by small RNA.
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Affiliation(s)
- Joseph P. Calarco
- Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Filipe Borges
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal
| | - Mark T.A. Donoghue
- Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Frédéric Van Ex
- Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Pauline E. Jullien
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore
| | - Telma Lopes
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal
| | - Rui Gardner
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal
| | - Frédéric Berger
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore
| | - José A. Feijó
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal
- Universidade de Lisboa, Faculdade de Ciências, Departamento de Biologia Vegetal, Campo Grande C2, 1749-016 Lisboa, Portugal
| | - Jörg D. Becker
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal
| | - Robert A. Martienssen
- Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
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12
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Jullien PE, Susaki D, Yelagandula R, Higashiyama T, Berger F. DNA methylation dynamics during sexual reproduction in Arabidopsis thaliana. Curr Biol 2012; 22:1825-30. [PMID: 22940470 DOI: 10.1016/j.cub.2012.07.061] [Citation(s) in RCA: 145] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Revised: 06/26/2012] [Accepted: 07/27/2012] [Indexed: 11/30/2022]
Abstract
DNA methylation maintains genome stability and regulates gene expression [1]. In mammals, DNA methylation is reprogrammed in the germline from one generation to the next [2]. In plants, it was considered that patterns of DNA methylation are stably maintained through sexual reproduction [3-6]. However, a recent report showed discrete variations of DNA methylation profiles from mother to daughter plants [7]. The mechanisms that explain these variations have remained unknown. Here, we report that maintenance DNA methyltransferases are barely expressed during Arabidopsis female gametogenesis. In contrast, after fertilization both maintenance and de novo DNA methyltransferases are expressed strongly in the embryo. Embryogenesis is marked by increased de novo DNA methylation, reaching levels that are further maintained in the adult plant. The accumulation of these epigenetic marks after fertilization silences a methylation-sensitive fluorescent reporter. De novo DNA methylation in the embryo provides a mechanism that could account for the gradual remethylation of experimentally demethylated genomes [8, 9]. In conclusion, we uncover that DNA methylation activity fluctuates during sexual reproduction. This cycle likely explains variations of genome-wide patterns of DNA methylation across generations in Arabidopsis [7, 10] and enables a limited degree of reprogramming of the epigenome.
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Affiliation(s)
- Pauline E Jullien
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore.
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13
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Jullien PE, Berger F. DNA methylation reprogramming during plant sexual reproduction? Trends Genet 2010; 26:394-9. [DOI: 10.1016/j.tig.2010.06.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Revised: 06/02/2010] [Accepted: 06/04/2010] [Indexed: 02/02/2023]
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14
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Abstract
In mammals and in plants, parental genome dosage imbalance deregulates embryo growth and might be involved in reproductive isolation between emerging new species. Increased dosage of maternal genomes represses growth while an increased dosage of paternal genomes has the opposite effect. These observations led to the discovery of imprinted genes, which are expressed by a single parental allele. It was further proposed in the frame of the parental conflict theory that parental genome imbalances are directly mirrored by antagonistic regulations of imprinted genes encoding maternal growth inhibitors and paternal growth enhancers. However these hypotheses were never tested directly. Here, we investigated the effect of parental genome imbalance on the expression of Arabidopsis imprinted genes FERTILIZATION INDEPENDENT SEED2 (FIS2) and FLOWERING WAGENINGEN (FWA) controlled by DNA methylation, and MEDEA (MEA) and PHERES1 (PHE1) controlled by histone methylation. Genome dosage imbalance deregulated the expression of FIS2 and PHE1 in an antagonistic manner. In addition increased dosage of inactive alleles caused a loss of imprinting of FIS2 and MEA. Although FIS2 controls histone methylation, which represses MEA and PHE1 expression, the changes of PHE1 and MEA expression could not be fully accounted for by the corresponding fluctuations of FIS2 expression. Our results show that parental genome dosage imbalance deregulates imprinting using mechanisms, which are independent from known regulators of imprinting. The complexity of the network of regulations between expressed and silenced alleles of imprinted genes activated in response to parental dosage imbalance does not support simple models derived from the parental conflict hypothesis.
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Affiliation(s)
- Pauline E. Jullien
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore
- Zentrum für Molekularbiologie der Pflanzen, Entwicklungsgenetik, Universität Tübingen, Tübingen, Germany
| | - Frédéric Berger
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
- * E-mail:
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15
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Jullien PE, Mosquna A, Ingouff M, Sakata T, Ohad N, Berger F. Retinoblastoma and its binding partner MSI1 control imprinting in Arabidopsis. PLoS Biol 2008; 6:e194. [PMID: 18700816 PMCID: PMC2504488 DOI: 10.1371/journal.pbio.0060194] [Citation(s) in RCA: 191] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2007] [Accepted: 06/25/2008] [Indexed: 11/18/2022] Open
Abstract
Parental genomic imprinting causes preferential expression of one of the two parental alleles. In mammals, differential sex-dependent deposition of silencing DNA methylation marks during gametogenesis initiates a new cycle of imprinting. Parental genomic imprinting has been detected in plants and relies on DNA methylation by the methyltransferase MET1. However, in contrast to mammals, plant imprints are created by differential removal of silencing marks during gametogenesis. In Arabidopsis, DNA demethylation is mediated by the DNA glycosylase DEMETER (DME) causing activation of imprinted genes at the end of female gametogenesis. On the basis of genetic interactions, we show that in addition to DME, the plant homologs of the human Retinoblastoma (Rb) and its binding partner RbAp48 are required for the activation of the imprinted genes FIS2 and FWA. This Rb-dependent activation is mediated by direct transcriptional repression of MET1 during female gametogenesis. We have thus identified a new mechanism required for imprinting establishment, outlining a new role for the Retinoblastoma pathway, which may be conserved in mammals. Imprinting in plants and mammals involves a process whereby one of the two inherited gene variants (alleles) is inactivated. During imprinting, the transcriptional silencing of one allele is mediated by histone modifications or DNA methylation. The expressed parental allele is activated during gametogenesis by poorly understood mechanisms that remove silencing marks. In Arabidopsis, we studied genes expressed only from the maternal allele because the paternal allele is silenced by DNA methylation. We report that the expression of the maternal allele requires the repression of transcription of the major DNA methyltransferase by the sustained activity of the Arabidopsis homologs of the Retinoblastoma pathway. Repression is confined to the female gamete and is essential for the expression of imprinted genes in plants. The conserved transcriptional repression of DNA methyltransferases by the Retinoblastoma pathway suggests that this new regulation of imprinting might be also active in mammals. A new regulation of imprinting discovered in Arabidopsis involves the Retinoblastoma gene.
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Affiliation(s)
- Pauline E Jullien
- Chromatin and Reproduction Group, Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Republic of Singapore
- Zentrum für Molekularbiologie der Pflanzen (ZMBP), Entwicklungsgenetik, Universität Tübingen, Tübingen, Germany
| | - Assaf Mosquna
- Department of Plant Sciences, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Mathieu Ingouff
- Chromatin and Reproduction Group, Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Republic of Singapore
| | - Tadashi Sakata
- Chromatin and Reproduction Group, Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Republic of Singapore
| | - Nir Ohad
- Department of Plant Sciences, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Frédéric Berger
- Chromatin and Reproduction Group, Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Republic of Singapore
- * To whom correspondence should be addressed. E-mail:
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Abstract
Parental genomic imprinting is an epigenetic phenomenon causing the expression of a gene from one of the two parental alleles. Imprinting has been identified in plants and mammals. Recent evidence shows that DNA methylation and histone modifications are responsible for this parent-of-origin dependent expression of imprinted genes. We review the mechanisms and functions of imprinting in plants. We further describe the significance of imprinting for reproduction and discuss potential models for its evolution.
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Affiliation(s)
- Pauline E Jullien
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore, République de Singapour
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Aubourg S, Martin-Magniette ML, Brunaud V, Taconnat L, Bitton F, Balzergue S, Jullien PE, Ingouff M, Thareau V, Schiex T, Lecharny A, Renou JP. Analysis of CATMA transcriptome data identifies hundreds of novel functional genes and improves gene models in the Arabidopsis genome. BMC Genomics 2007; 8:401. [PMID: 17980019 PMCID: PMC2174955 DOI: 10.1186/1471-2164-8-401] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2007] [Accepted: 11/02/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Since the finishing of the sequencing of the Arabidopsis thaliana genome, the Arabidopsis community and the annotator centers have been working on the improvement of gene annotation at the structural and functional levels. In this context, we have used the large CATMA resource on the Arabidopsis transcriptome to search for genes missed by different annotation processes. Probes on the CATMA microarrays are specific gene sequence tags (GSTs) based on the CDS models predicted by the Eugene software. Among the 24 576 CATMA v2 GSTs, 677 are in regions considered as intergenic by the TAIR annotation. We analyzed the cognate transcriptome data in the CATMA resource and carried out data-mining to characterize novel genes and improve gene models. RESULTS The statistical analysis of the results of more than 500 hybridized samples distributed among 12 organs provides an experimental validation for 465 novel genes. The hybridization evidence was confirmed by RT-PCR approaches for 88% of the 465 novel genes. Comparisons with the current annotation show that these novel genes often encode small proteins, with an average size of 137 aa. Our approach has also led to the improvement of pre-existing gene models through both the extension of 16 CDS and the identification of 13 gene models erroneously constituted of two merged CDS. CONCLUSION This work is a noticeable step forward in the improvement of the Arabidopsis genome annotation. We increased the number of Arabidopsis validated genes by 465 novel transcribed genes to which we associated several functional annotations such as expression profiles, sequence conservation in plants, cognate transcripts and protein motifs.
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Affiliation(s)
- Sébastien Aubourg
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165-CNRS 8114-UEVE, 2 Rue Gaston Crémieux, 91057 Evry Cedex, France.
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Ingouff M, Jullien PE, Berger F. The female gametophyte and the endosperm control cell proliferation and differentiation of the seed coat in Arabidopsis. Plant Cell 2006; 18:3491-501. [PMID: 17172356 PMCID: PMC1785409 DOI: 10.1105/tpc.106.047266] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Double fertilization of the female gametophyte produces the endosperm and the embryo enclosed in the maternal seed coat. Proper seed communication necessitates exchanges of signals between the zygotic and maternal components of the seed. However, the nature of these interactions remains largely unknown. We show that double fertilization of the Arabidopsis thaliana female gametophyte rapidly triggers sustained cell proliferation in the seed coat. Cell proliferation and differentiation of the seed coat occur in autonomous seeds produced in the absence of fertilization of the multicopy suppressor of ira1 (msi1) mutant. As msi1 autonomous seeds mostly contain autonomous endosperm, our results indicate that the developing endosperm is sufficient to enhance cell proliferation and differentiation in the seed coat. We analyze the effect of autonomous proliferation in the retinoblastoma-related1 (rbr1) female gametophyte on seed coat development. In contrast with msi1, supernumerary nuclei in rbr1 female gametophytes originate mainly from the endosperm precursor lineage but do not express an endosperm fate marker. In addition, defects of the rbr1 female gametophyte also reduce cell proliferation in the ovule integuments before fertilization and prevent further differentiation of the seed coat. Our data suggest that coordinated development of the seed components relies on interactions before fertilization between the female gametophyte and the surrounding maternal ovule integuments and after fertilization between the endosperm and the seed coat.
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Affiliation(s)
- Mathieu Ingouff
- Chromatin and Reproduction Group, Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Republic of Singapore
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Jullien PE, Kinoshita T, Ohad N, Berger F. Maintenance of DNA methylation during the Arabidopsis life cycle is essential for parental imprinting. Plant Cell 2006; 18:1360-72. [PMID: 16648367 PMCID: PMC1475502 DOI: 10.1105/tpc.106.041178] [Citation(s) in RCA: 161] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2006] [Revised: 03/24/2006] [Accepted: 04/11/2006] [Indexed: 05/08/2023]
Abstract
Imprinted genes are expressed predominantly from either their paternal or their maternal allele. To date, all imprinted genes identified in plants are expressed in the endosperm. In Arabidopsis thaliana, maternal imprinting has been clearly demonstrated for the Polycomb group gene MEDEA (MEA) and for FWA. Direct repeats upstream of FWA are subject to DNA methylation. However, it is still not clear to what extent similar cis-acting elements may be part of a conserved molecular mechanism controlling maternally imprinted genes. In this work, we show that the Polycomb group gene FERTILIZATION-INDEPENDENT SEED2 (FIS2) is imprinted. Maintenance of FIS2 imprinting depends on DNA methylation, whereas loss of DNA methylation does not affect MEA imprinting. DNA methylation targets a small region upstream of FIS2 distinct from the target of DNA methylation associated with FWA. We show that FWA and FIS2 imprinting requires the maintenance of DNA methylation throughout the plant life cycle, including male gametogenesis and endosperm development. Our data thus demonstrate that parental genomic imprinting in plants depends on diverse cis-elements and mechanisms dependent or independent of DNA methylation. We propose that imprinting has evolved under constraints linked to the evolution of plant reproduction and not by the selection of a specific molecular mechanism.
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Affiliation(s)
- Pauline E Jullien
- Chromatin and Reproduction Group, Temasek Lifesciences Laboratory, National University of Singapore, Singapore 117604, Republic of Singapore
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Jullien PE, Katz A, Oliva M, Ohad N, Berger F. Polycomb group complexes self-regulate imprinting of the Polycomb group gene MEDEA in Arabidopsis. Curr Biol 2006; 16:486-92. [PMID: 16527743 DOI: 10.1016/j.cub.2006.01.020] [Citation(s) in RCA: 175] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2005] [Revised: 01/11/2006] [Accepted: 01/11/2006] [Indexed: 11/18/2022]
Abstract
Fertilization in flowering plants initiates the development of the embryo and endosperm, which nurtures the embryo. A few genes subjected to imprinting are expressed in endosperm from their maternal allele, while their paternal allele remains silenced. Imprinting of the FWA gene involves DNA methylation. Mechanisms controlling imprinting of the Polycomb group (Pc-G) gene MEDEA (MEA) are not yet fully understood. Here we report that MEA imprinting is regulated by histone methylation. This epigenetic chromatin modification is mediated by several Pc-G activities during the entire plant life cycle. We show that Pc-G complexes maintain MEA transcription silenced throughout vegetative life and male gametogenesis. In endosperm, the maternal allele of MEA encodes an essential component of a Pc-G complex, which maintains silencing of the paternal MEA allele. Hence, we conclude that a feedback loop controls MEA imprinting. This feedback loop ensures a complete maternal control of MEA expression from both parental alleles and might have provided a template for evolution of imprinting in plants.
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Affiliation(s)
- Pauline E Jullien
- Chromatin and Reproduction Group, Temasek LifeSciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore
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