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Hövel I, Bader R, Louwers M, Haring M, Peek K, Gent JI, Stam M. RNA-directed DNA methylation mutants reduce histone methylation at the paramutated maize booster1 enhancer. PLANT PHYSIOLOGY 2024; 195:1161-1179. [PMID: 38366582 PMCID: PMC11142347 DOI: 10.1093/plphys/kiae072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 12/19/2023] [Accepted: 12/25/2023] [Indexed: 02/18/2024]
Abstract
Paramutation is the transfer of mitotically and meiotically heritable silencing information between two alleles. With paramutation at the maize (Zea mays) booster1 (b1) locus, the low-expressed B' epiallele heritably changes the high-expressed B-I epiallele into B' with 100% frequency. This requires specific tandem repeats and multiple components of the RNA-directed DNA methylation pathway, including the RNA-dependent RNA polymerase (encoded by mediator of paramutation1, mop1), the second-largest subunit of RNA polymerase IV and V (NRP(D/E)2a, encoded by mop2), and the largest subunit of RNA Polymerase IV (NRPD1, encoded by mop3). Mutations in mop genes prevent paramutation and release silencing at the B' epiallele. In this study, we investigated the effect of mutations in mop1, mop2, and mop3 on chromatin structure and DNA methylation at the B' epiallele, and especially the regulatory hepta-repeat 100 kb upstream of the b1 gene. Mutations in mop1 and mop3 resulted in decreased repressive histone modifications H3K9me2 and H3K27me2 at the hepta-repeat. Associated with this decrease were partial activation of the hepta-repeat enhancer function, formation of a multi-loop structure, and elevated b1 expression. In mop2 mutants, which do not show elevated b1 expression, H3K9me2, H3K27me2 and a single-loop structure like in wild-type B' were retained. Surprisingly, high CG and CHG methylation levels at the B' hepta-repeat remained in all three mutants, and CHH methylation was low in both wild type and mutants. Our results raise the possibility of MOP factors mediating RNA-directed histone methylation rather than RNA-directed DNA methylation at the b1 locus.
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Affiliation(s)
- Iris Hövel
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, P.O. Box 1210, 1090 GE Amsterdam, The Netherlands
| | - Rechien Bader
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, P.O. Box 1210, 1090 GE Amsterdam, The Netherlands
| | - Marieke Louwers
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, P.O. Box 1210, 1090 GE Amsterdam, The Netherlands
- argenx BV, Industriepark Zwijnaarde 7, 9052 Zwijnaarde (Ghent), Belgium
| | - Max Haring
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, P.O. Box 1210, 1090 GE Amsterdam, The Netherlands
- University Library, Universiteit van Amsterdam, P.O. Box 19185, 1000 GD Amsterdam, The Netherlands
| | - Kevin Peek
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, P.O. Box 1210, 1090 GE Amsterdam, The Netherlands
| | - Jonathan I Gent
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Maike Stam
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, P.O. Box 1210, 1090 GE Amsterdam, The Netherlands
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Grypioti E, Richard H, Kryovrysanaki N, Jaubert M, Falciatore A, Verret F, Kalantidis K. Dicer-dependent heterochromatic small RNAs in the model diatom species Phaeodactylum tricornutum. THE NEW PHYTOLOGIST 2024; 241:811-826. [PMID: 38044751 DOI: 10.1111/nph.19429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 10/17/2023] [Indexed: 12/05/2023]
Abstract
Diatoms are eukaryotic microalgae responsible for nearly half of the marine productivity. RNA interference (RNAi) is a mechanism of regulation of gene expression mediated by small RNAs (sRNAs) processed by the endoribonuclease Dicer (DCR). To date, the mechanism and physiological role of RNAi in diatoms are unknown. We mined diatom genomes and transcriptomes for key RNAi effectors and retraced their phylogenetic history. We generated DCR knockout lines in the model diatom species Phaeodactylum tricornutum and analyzed their mRNA and sRNA populations, repression-associated histone marks, and acclimatory response to nitrogen starvation. Diatoms presented a diversification of key RNAi effectors whose distribution across species suggests the presence of distinct RNAi pathways. P. tricornutum DCR was found to process 26-31-nt-long double-stranded sRNAs originating mostly from transposons covered by repression-associated epigenetic marks. In parallel, P. tricornutum DCR was necessary for the maintenance of the repression-associated histone marks H3K9me2/3 and H3K27me3. Finally, PtDCR-KO lines presented a compromised recovery post nitrogen starvation suggesting a role for P. tricornutum DCR in the acclimation to nutrient stress. Our study characterized the molecular function of the single DCR homolog of P. tricornutum suggesting an association between RNAi and heterochromatin maintenance in this model diatom species.
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Affiliation(s)
- Emilia Grypioti
- Department of Biology, University of Crete, PO Box 2208, 70013, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 70013, Heraklion, Crete, Greece
- Institute of Marine Biology and Aquaculture, Hellenic Center for Marine Research, 71500, Gournes, Crete, Greece
- Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, UMR 7238 Sorbonne Université, 75005, Paris, France
| | - Hugues Richard
- Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, UMR 7238 Sorbonne Université, 75005, Paris, France
- Bioinformatics Unit, Genome Competence Center (MF1), Robert Koch Institute, 13353, Berlin, Germany
| | - Nikoleta Kryovrysanaki
- Department of Biology, University of Crete, PO Box 2208, 70013, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 70013, Heraklion, Crete, Greece
| | - Marianne Jaubert
- Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, UMR 7238 Sorbonne Université, 75005, Paris, France
- Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light Sensing in Microalgae, UMR7141 Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, 75005, Paris, France
| | - Angela Falciatore
- Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, UMR 7238 Sorbonne Université, 75005, Paris, France
- Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light Sensing in Microalgae, UMR7141 Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, 75005, Paris, France
| | - Frédéric Verret
- Department of Biology, University of Crete, PO Box 2208, 70013, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 70013, Heraklion, Crete, Greece
- Institute of Marine Biology and Aquaculture, Hellenic Center for Marine Research, 71500, Gournes, Crete, Greece
| | - Kriton Kalantidis
- Department of Biology, University of Crete, PO Box 2208, 70013, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 70013, Heraklion, Crete, Greece
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Fukudome A, Singh J, Mishra V, Reddem E, Martinez-Marquez F, Wenzel S, Yan R, Shiozaki M, Yu Z, Wang JCY, Takagi Y, Pikaard CS. Structure and RNA template requirements of Arabidopsis RNA-DEPENDENT RNA POLYMERASE 2. Proc Natl Acad Sci U S A 2021; 118:e2115899118. [PMID: 34903670 PMCID: PMC8713982 DOI: 10.1073/pnas.2115899118] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2021] [Indexed: 01/18/2023] Open
Abstract
RNA-dependent RNA polymerases play essential roles in RNA-mediated gene silencing in eukaryotes. In Arabidopsis, RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) physically interacts with DNA-dependent NUCLEAR RNA POLYMERASE IV (Pol IV) and their activities are tightly coupled, with Pol IV transcriptional arrest, induced by the nontemplate DNA strand, somehow enabling RDR2 to engage Pol IV transcripts and generate double-stranded RNAs. The double-stranded RNAs are then released from the Pol IV-RDR2 complex and diced into short-interfering RNAs that guide RNA-directed DNA methylation and silencing. Here we report the structure of full-length RDR2, at an overall resolution of 3.1 Å, determined by cryoelectron microscopy. The N-terminal region contains an RNA-recognition motif adjacent to a positively charged channel that leads to a catalytic center with striking structural homology to the catalytic centers of multisubunit DNA-dependent RNA polymerases. We show that RDR2 initiates 1 to 2 nt internal to the 3' ends of its templates and can transcribe the RNA of an RNA/DNA hybrid, provided that 9 or more nucleotides are unpaired at the RNA's 3' end. Using a nucleic acid configuration that mimics the arrangement of RNA and DNA strands upon Pol IV transcriptional arrest, we show that displacement of the RNA 3' end occurs as the DNA template and nontemplate strands reanneal, enabling RDR2 transcription. These results suggest a model in which Pol IV arrest and backtracking displaces the RNA 3' end as the DNA strands reanneal, allowing RDR2 to engage the RNA and synthesize the complementary strand.
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Affiliation(s)
- Akihito Fukudome
- HHMI, Indiana University, Bloomington, IN 47405
- Department of Biology, Indiana University, Bloomington, IN 47405
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405
| | - Jasleen Singh
- Department of Biology, Indiana University, Bloomington, IN 47405
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405
| | - Vibhor Mishra
- HHMI, Indiana University, Bloomington, IN 47405
- Department of Biology, Indiana University, Bloomington, IN 47405
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405
| | - Eswar Reddem
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 47405
| | - Francisco Martinez-Marquez
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 47405
| | - Sabine Wenzel
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 47405
| | - Rui Yan
- CryoEM Facility, Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147
| | - Momoko Shiozaki
- CryoEM Facility, Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147
| | - Zhiheng Yu
- CryoEM Facility, Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147
| | - Joseph Che-Yen Wang
- Indiana University Electron Microscopy Center, Indiana University, Bloomington, IN 47405
| | - Yuichiro Takagi
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 47405;
| | - Craig S Pikaard
- HHMI, Indiana University, Bloomington, IN 47405;
- Department of Biology, Indiana University, Bloomington, IN 47405
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405
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Abstract
Meiotic recombination is a fundamental process that generates genetic diversity and ensures the accurate segregation of homologous chromosomes. While a great deal is known about genetic factors that regulate recombination, relatively little is known about epigenetic factors, such as DNA methylation. In maize, we examined the effects on meiotic recombination of a mutation in a component of the RNA-directed DNA methylation pathway, Mop1 (Mediator of paramutation1), as well as a mutation in a component of the trans-acting small interference RNA biogenesis pathway, Lbl1 (Leafbladeless1). MOP1 is of particular interest with respect to recombination because it is responsible for methylation of transposable elements that are immediately adjacent to transcriptionally active genes. In the mop1 mutant, we found that meiotic recombination is uniformly decreased in pericentromeric regions but is generally increased in gene rich chromosomal arms. This observation was further confirmed by cytogenetic analysis showing that although overall crossover numbers are unchanged, they occur more frequently in chromosomal arms in mop1 mutants. Using whole genome bisulfite sequencing, our data show that crossover redistribution is driven by loss of CHH (where H = A, T, or C) methylation within regions near genes. In contrast to what we observed in mop1 mutants, no significant changes were observed in the frequency of meiotic recombination in lbl1 mutants. Our data demonstrate that CHH methylation has a significant impact on the overall recombination landscape in maize despite its low frequency relative to CG and CHG methylation.
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RNA-directed DNA methylation prevents rapid and heritable reversal of transposon silencing under heat stress in Zea mays. PLoS Genet 2021; 17:e1009326. [PMID: 34125827 PMCID: PMC8224964 DOI: 10.1371/journal.pgen.1009326] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 06/24/2021] [Accepted: 05/28/2021] [Indexed: 12/12/2022] Open
Abstract
In large complex plant genomes, RNA-directed DNA methylation (RdDM) ensures that epigenetic silencing is maintained at the boundary between genes and flanking transposable elements. In maize, RdDM is dependent on Mediator of Paramutation1 (Mop1), a gene encoding a putative RNA dependent RNA polymerase. Here we show that although RdDM is essential for the maintenance of DNA methylation of a silenced MuDR transposon in maize, a loss of that methylation does not result in a restoration of activity. Instead, heritable maintenance of silencing is maintained by histone modifications. At one terminal inverted repeat (TIR) of this element, heritable silencing is mediated via histone H3 lysine 9 dimethylation (H3K9me2), and histone H3 lysine 27 dimethylation (H3K27me2), even in the absence of DNA methylation. At the second TIR, heritable silencing is mediated by histone H3 lysine 27 trimethylation (H3K27me3), a mark normally associated with somatically inherited gene silencing. We find that a brief exposure of high temperature in a mop1 mutant rapidly reverses both of these modifications in conjunction with a loss of transcriptional silencing. These reversals are heritable, even in mop1 wild-type progeny in which methylation is restored at both TIRs. These observations suggest that DNA methylation is neither necessary to maintain silencing, nor is it sufficient to initiate silencing once has been reversed. However, given that heritable reactivation only occurs in a mop1 mutant background, these observations suggest that DNA methylation is required to buffer the effects of environmental stress on transposable elements. Most plant genomes are mostly transposable elements (TEs), most of which are held in check by modifications of both DNA and histones. The bulk of silenced TEs are associated with methylated DNA and histone H3 lysine 9 dimethylation (H3K9me2). In contrast, epigenetically silenced genes are often associated with histone lysine 27 trimethylation (H3K27me3). Although stress can affect each of these modifications, plants are generally competent to rapidly reset them following that stress. Here we demonstrate that although DNA methylation is not required to maintain silencing of the MuDR element, it is essential for preventing heat-induced, stable and heritable changes in both H3K9me2 and H3K27me3 at this element, and for concomitant changes in transcriptional activity. These finding suggest that RdDM acts to buffer the effects of heat on silenced transposable elements, and that a loss of DNA methylation under conditions of stress can have profound and long-lasting effects on epigenetic silencing in maize.
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Burgess D, Li H, Zhao M, Kim SY, Lisch D. Silencing of Mutator Elements in Maize Involves Distinct Populations of Small RNAs and Distinct Patterns of DNA Methylation. Genetics 2020; 215:379-391. [PMID: 32229532 PMCID: PMC7268996 DOI: 10.1534/genetics.120.303033] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 03/24/2020] [Indexed: 12/12/2022] Open
Abstract
Transposable elements (TEs) are a ubiquitous feature of plant genomes. Because of the threat they post to genome integrity, most TEs are epigenetically silenced. However, even closely related plant species often have dramatically different populations of TEs, suggesting periodic rounds of activity and silencing. Here, we show that the process of de novo methylation of an active element in maize involves two distinct pathways, one of which is directly implicated in causing epigenetic silencing and one of which is the result of that silencing. Epigenetic changes involve changes in gene expression that can be heritably transmitted to daughter cells in the absence of changes in DNA sequence. Epigenetics has been implicated in phenomena as diverse as development, stress response, and carcinogenesis. A significant challenge facing those interested in investigating epigenetic phenomena is determining causal relationships between DNA methylation, specific classes of small RNAs, and associated changes in gene expression. Because they are the primary targets of epigenetic silencing in plants and, when active, are often targeted for de novo silencing, TEs represent a valuable source of information about these relationships. We use a naturally occurring system in which a single TE can be heritably silenced by a single derivative of that TE. By using this system it is possible to unravel causal relationships between different size classes of small RNAs, patterns of DNA methylation, and heritable silencing. Here, we show that the long terminal inverted repeats within Zea mays MuDR transposons are targeted by distinct classes of small RNAs during epigenetic silencing that are dependent on distinct silencing pathways, only one of which is associated with transcriptional silencing of the transposon. Further, these small RNAs target distinct regions of the terminal inverted repeats, resulting in different patterns of cytosine methylation with different functional consequences with respect to epigenetic silencing and the heritability of that silencing.
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Affiliation(s)
- Diane Burgess
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
| | - Hong Li
- Bayer US, Crop Science, Chesterfield, Missouri 63017
| | - Meixia Zhao
- Department of Biology, Miami University, Oxford, Ohio 45056
| | - Sang Yeol Kim
- US Department of Agriculture, Agricultural Research Service, Urbana, Illinois 61801
| | - Damon Lisch
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
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Yildirim O, Izgu EC, Damle M, Chalei V, Ji F, Sadreyev RI, Szostak JW, Kingston RE. S-phase Enriched Non-coding RNAs Regulate Gene Expression and Cell Cycle Progression. Cell Rep 2020; 31:107629. [PMID: 32402276 PMCID: PMC7954657 DOI: 10.1016/j.celrep.2020.107629] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 02/20/2020] [Accepted: 04/20/2020] [Indexed: 12/13/2022] Open
Abstract
Many proteins that are needed for progression through S-phase are produced from transcripts that peak in the S-phase, linking temporal expression of those proteins to the time that they are required in cell cycle. Here, we explore the potential roles of long non-coding RNAs in cell cycle progression. We use a sensitive click-chemistry approach to isolate nascent RNAs in a human cell line, and we identify more than 900 long non-coding RNAs (lncRNAs) whose synthesis peaks during the S-phase. More than 200 of these are long intergenic non-coding RNAs (lincRNAs) with S-phase-specific expression. We characterize three of these lincRNAs by knockdown and find that all three lincRNAs are required for appropriate S-phase progression. We infer that non-coding RNAs are key regulatory effectors during the cell cycle, acting on distinct regulatory networks, and herein, we provide a large catalog of candidate cell-cycle regulatory RNAs.
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Affiliation(s)
- Ozlem Yildirim
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Enver C Izgu
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Manashree Damle
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Vladislava Chalei
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Fei Ji
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Ruslan I Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Jack W Szostak
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Robert E Kingston
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
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Abstract
Plants are subjected to extreme environmental conditions and must adapt rapidly. The phytohormone abscisic acid (ABA) accumulates during abiotic stress, signaling transcriptional changes that trigger physiological responses. Epigenetic modifications often facilitate transcription, particularly at genes exhibiting temporal, tissue-specific and environmentally-induced expression. In maize (Zea mays), MEDIATOR OF PARAMUTATION 1 (MOP1) is required for progression of an RNA-dependent epigenetic pathway that regulates transcriptional silencing of loci genomewide. MOP1 function has been previously correlated with genomic regions adjoining particular types of transposable elements and genic regions, suggesting that this regulatory pathway functions to maintain distinct transcriptional activities within genomic spaces, and that loss of MOP1 may modify the responsiveness of some loci to other regulatory pathways. As critical regulators of gene expression, MOP1 and ABA pathways each regulate specific genes. To determine whether loss of MOP1 impacts ABA-responsive gene expression in maize, mop1-1 and Mop1 homozygous seedlings were subjected to exogenous ABA and RNA-sequencing. A total of 3,242 differentially expressed genes (DEGs) were identified in four pairwise comparisons. Overall, ABA-induced changes in gene expression were enhanced in mop1-1 homozygous plants. The highest number of DEGs were identified in ABA-induced mop1-1 mutants, including many transcription factors; this suggests combinatorial regulatory scenarios including direct and indirect transcriptional responses to genetic disruption (mop1-1) and/or stimulus-induction of a hierarchical, cascading network of responsive genes. Additionally, a modest increase in CHH methylation at putative MOP1-RdDM loci in response to ABA was observed in some genotypes, suggesting that epigenetic variation might influence environmentally-induced transcriptional responses in maize.
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Serrato-Capuchina A, Matute DR. The Role of Transposable Elements in Speciation. Genes (Basel) 2018; 9:E254. [PMID: 29762547 PMCID: PMC5977194 DOI: 10.3390/genes9050254] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 04/26/2018] [Accepted: 04/26/2018] [Indexed: 01/20/2023] Open
Abstract
Understanding the phenotypic and molecular mechanisms that contribute to genetic diversity between and within species is fundamental in studying the evolution of species. In particular, identifying the interspecific differences that lead to the reduction or even cessation of gene flow between nascent species is one of the main goals of speciation genetic research. Transposable elements (TEs) are DNA sequences with the ability to move within genomes. TEs are ubiquitous throughout eukaryotic genomes and have been shown to alter regulatory networks, gene expression, and to rearrange genomes as a result of their transposition. However, no systematic effort has evaluated the role of TEs in speciation. We compiled the evidence for TEs as potential causes of reproductive isolation across a diversity of taxa. We find that TEs are often associated with hybrid defects that might preclude the fusion between species, but that the involvement of TEs in other barriers to gene flow different from postzygotic isolation is still relatively unknown. Finally, we list a series of guides and research avenues to disentangle the effects of TEs on the origin of new species.
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Affiliation(s)
- Antonio Serrato-Capuchina
- Biology Department, Genome Sciences Building, University of North Carolina, Chapel Hill, NC 27514, USA.
| | - Daniel R Matute
- Biology Department, Genome Sciences Building, University of North Carolina, Chapel Hill, NC 27514, USA.
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10
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Wang PH, Wittmeyer KT, Lee TF, Meyers BC, Chopra S. Overlapping RdDM and non-RdDM mechanisms work together to maintain somatic repression of a paramutagenic epiallele of maize pericarp color1. PLoS One 2017; 12:e0187157. [PMID: 29112965 PMCID: PMC5675401 DOI: 10.1371/journal.pone.0187157] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 10/14/2017] [Indexed: 11/18/2022] Open
Abstract
Allelic variation at the Zea mays (maize) pericarp color1 (p1) gene has been attributed to epigenetic gene regulation. A p1 distal enhancer, 5.2 kb upstream of the transcriptional start site, has demonstrated variation in DNA methylation in different p1 alleles/epialleles. In addition, DNA methylation of sequences within the 3’ end of intron 2 also plays a role in tissue-specific expression of p1 alleles. We show here a direct evidence for small RNAs’ involvement in regulating p1 that has not been demonstrated previously. The role of mediator of paramutation1 (mop1) was tested in the maintenance of somatic silencing at distinct p1 alleles: the non-paramutagenic P1-wr allele and paramutagenic P1-rr’ epiallele. The mop1-1 mutation gradually relieves the silenced phenotype after multiple generations of exposure; P1-wr;mop1-1 plants display a loss of 24-nt small RNAs and DNA methylation in the 3’ end of the intron 2, a region close to a Stowaway transposon. In addition, a MULE sequence within the proximal promoter of P1-wr shows depletion of 24nt siRNAs in mop1-1 plants. Release of silencing was not correlated with small RNAs at the distal enhancer region of the P1-wr allele. We found that the somatic silencing of the paramutagenic P1-rr’ is correlated with significantly reduced H3K9me2 in the distal enhancer of P1-rr’; mop1-1 plants, while symmetric DNA methylation is not significantly different. This study highlights that the epigenetic regulation of p1 alleles is controlled both via RdDM as well as non-RdDM mechanisms.
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Affiliation(s)
- Po-Hao Wang
- Department of Plant Science, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Kameron T. Wittmeyer
- Department of Plant Science, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Plant Biology Program, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Tzuu-fen Lee
- Department of Plant & Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, United States of America
| | - Blake C. Meyers
- Department of Plant & Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, United States of America
| | - Surinder Chopra
- Department of Plant Science, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Plant Biology Program, Pennsylvania State University, University Park, Pennsylvania, United States of America
- * E-mail:
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11
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Rodriguez JD, Myrick DA, Falciatori I, Christopher MA, Lee TW, Hannon GJ, Katz DJ. A Model for Epigenetic Inhibition via Transvection in the Mouse. Genetics 2017; 207:129-138. [PMID: 28696215 PMCID: PMC5586367 DOI: 10.1534/genetics.117.201913] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 06/21/2017] [Indexed: 01/21/2023] Open
Abstract
Transvection is broadly defined as the ability of one locus to affect its homologous locus in trans Although it was first discovered in the 1950s, there are only two known cases in mammals. Here, we report another instance of mammalian transvection induced by the Cre/LoxP system, which is widely used for conditional gene targeting in the mouse. We attempted to use the germline-expressed Vasa-Cre transgene to engineer a mouse mutation, but observe a dramatic reduction of LoxP recombination in mice that inherit an already deleted LoxP allele in trans A similar phenomenon has previously been observed with another Cre that is expressed during meiosis: Sycp-1-Cre This second example of LoxP inhibition in trans reinforces the conclusion that certain meiotically expressed Cre alleles can initiate transvection in mammals. However, unlike the previous example, we find that the inhibition of LoxP recombination is not due to DNA methylation. In addition, we demonstrate that LoxP inhibition is easily alleviated by adding an extra generation to our crossing scheme. This finding confirms that the LoxP sites are inhibited via an epigenetic mechanism, and provides a method for the use of other Cre transgenes associated with a similar LoxP inhibition event. Furthermore, the abrogation of LoxP inhibition by the simple addition of an extra generation in our crosses establishes a unique mouse system for future studies to uncover the mechanism of transvection in mammals.
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Affiliation(s)
- Juan D Rodriguez
- Cell Biology Department, Emory University, Atlanta, Georgia 30322
| | - Dexter A Myrick
- Cell Biology Department, Emory University, Atlanta, Georgia 30322
| | - Ilaria Falciatori
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE, United Kingdom
| | | | - Teresa W Lee
- Cell Biology Department, Emory University, Atlanta, Georgia 30322
| | - Gregory J Hannon
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE, United Kingdom
| | - David J Katz
- Cell Biology Department, Emory University, Atlanta, Georgia 30322
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12
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Epigenetic Control of Gene Expression in Maize. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2017; 328:25-48. [DOI: 10.1016/bs.ircmb.2016.08.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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13
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Abstract
The Mutator system of transposable elements (TEs) is a highly mutagenic family of transposons in maize. Because they transpose at high rates and target genic regions, these transposons can rapidly generate large numbers of new mutants, which has made the Mutator system a favored tool for both forward and reverse mutagenesis in maize. Low copy number versions of this system have also proved to be excellent models for understanding the regulation and behavior of Class II transposons in plants. Notably, the availability of a naturally occurring locus that can heritably silence autonomous Mutator elements has provided insights into the means by which otherwise active transposons are recognized and silenced. This chapter will provide a review of the biology, regulation, evolution and uses of this remarkable transposon system, with an emphasis on recent developments in our understanding of the ways in which this TE system is recognized and epigenetically silenced as well as recent evidence that Mu-like elements (MULEs) have had a significant impact on the evolution of plant genomes.
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14
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Ma L, Hatlen A, Kelly LJ, Becher H, Wang W, Kovarik A, Leitch IJ, Leitch AR. Angiosperms Are Unique among Land Plant Lineages in the Occurrence of Key Genes in the RNA-Directed DNA Methylation (RdDM) Pathway. Genome Biol Evol 2015; 7:2648-62. [PMID: 26338185 PMCID: PMC4607528 DOI: 10.1093/gbe/evv171] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The RNA-directed DNA methylation (RdDM) pathway can be divided into three phases: 1) small interfering RNA biogenesis, 2) de novo methylation, and 3) chromatin modification. To determine the degree of conservation of this pathway we searched for key genes among land plants. We used OrthoMCL and the OrthoMCL Viridiplantae database to analyze proteomes of species in bryophytes, lycophytes, monilophytes, gymnosperms, and angiosperms. We also analyzed small RNA size categories and, in two gymnosperms, cytosine methylation in ribosomal DNA. Six proteins were restricted to angiosperms, these being NRPD4/NRPE4, RDM1, DMS3 (defective in meristem silencing 3), SHH1 (SAWADEE homeodomain homolog 1), KTF1, and SUVR2, although we failed to find the latter three proteins in Fritillaria persica, a species with a giant genome. Small RNAs of 24 nt in length were abundant only in angiosperms. Phylogenetic analyses of Dicer-like (DCL) proteins showed that DCL2 was restricted to seed plants, although it was absent in Gnetum gnemon and Welwitschia mirabilis. The data suggest that phases (1) and (2) of the RdDM pathway, described for model angiosperms, evolved with angiosperms. The absence of some features of RdDM in F. persica may be associated with its large genome. Phase (3) is probably the most conserved part of the pathway across land plants. DCL2, involved in virus defense and interaction with the canonical RdDM pathway to facilitate methylation of CHH, is absent outside seed plants. Its absence in G. gnemon, and W. mirabilis coupled with distinctive patterns of CHH methylation, suggest a secondary loss of DCL2 following the divergence of Gnetales.
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Affiliation(s)
- Lu Ma
- School of Biological and Chemical Sciences, Queen Mary University of London, United Kingdom
| | - Andrea Hatlen
- School of Biological and Chemical Sciences, Queen Mary University of London, United Kingdom
| | - Laura J Kelly
- School of Biological and Chemical Sciences, Queen Mary University of London, United Kingdom
| | - Hannes Becher
- School of Biological and Chemical Sciences, Queen Mary University of London, United Kingdom
| | - Wencai Wang
- School of Biological and Chemical Sciences, Queen Mary University of London, United Kingdom
| | - Ales Kovarik
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Ilia J Leitch
- Department of Comparative Plant and Fungal Biology Royal Botanic Gardens, Kew, Richmond, Surrey, United Kingdom
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, United Kingdom
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15
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Klein-Cosson C, Chambrier P, Rogowsky PM, Vernoud V. Regulation of a maize HD-ZIP IV transcription factor by a non-conventional RDR2-dependent small RNA. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 81:747-758. [PMID: 25619590 DOI: 10.1111/tpj.12771] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 12/22/2014] [Accepted: 01/07/2015] [Indexed: 06/04/2023]
Abstract
Small non-coding RNAs are versatile riboregulators that control gene expression at the transcriptional or post-transcriptional level, governing many facets of plant development. Here we present evidence for the existence of a 24 nt small RNA (named small1) that is complementary to the 3' UTR of OCL1 (Outer Cell Layer1), the founding member of the maize HD-ZIP IV gene family encoding plant-specific transcription factors that are mainly involved in epidermis differentiation and specialization. The biogenesis of small1 depends on DICER-like 3 (DCL3), RNA-dependent RNA polymerase 2 (RDR2) and RNA polymerase IV, components that are usually required for RNA-dependent DNA-methylation. Unexpectedly, GFP sensor experiments in transient and stable transformation systems revealed that small1 may regulate its target at the post-transcriptional level, mainly through translational repression. This translational repression is attenuated in an rdr2 mutant background in which small1 does not accumulate. Our experiments further showed the possible involvement of a secondary stem-loop structure present in the 3' UTR of OCL1 for efficient target repression, suggesting the existence of several regulatory mechanisms affecting OCL1 mRNA stability and translation.
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Affiliation(s)
- Catherine Klein-Cosson
- Unité Reproduction et Développement des Plantes, Université de Lyon, Ecole Normale Supérieure de Lyon, Université Lyon 1, F-69364, Lyon, France; Institut National de la Recherche Agronomique, UMR879 Reproduction et Développement des Plantes, F-69364, Lyon, France; Centre National de la Recherche Scientifique, UMR5667 Reproduction et Développement des Plantes, F-69364, Lyon, France
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16
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Nascent transcription affected by RNA polymerase IV in Zea mays. Genetics 2015; 199:1107-25. [PMID: 25653306 DOI: 10.1534/genetics.115.174714] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 02/02/2015] [Indexed: 01/23/2023] Open
Abstract
All eukaryotes use three DNA-dependent RNA polymerases (RNAPs) to create cellular RNAs from DNA templates. Plants have additional RNAPs related to Pol II, but their evolutionary role(s) remain largely unknown. Zea mays (maize) RNA polymerase D1 (RPD1), the largest subunit of RNA polymerase IV (Pol IV), is required for normal plant development, paramutation, transcriptional repression of certain transposable elements (TEs), and transcriptional regulation of specific alleles. Here, we define the nascent transcriptomes of rpd1 mutant and wild-type (WT) seedlings using global run-on sequencing (GRO-seq) to identify the broader targets of RPD1-based regulation. Comparisons of WT and rpd1 mutant GRO-seq profiles indicate that Pol IV globally affects transcription at both transcriptional start sites and immediately downstream of polyadenylation addition sites. We found no evidence of divergent transcription from gene promoters as seen in mammalian GRO-seq profiles. Statistical comparisons identify genes and TEs whose transcription is affected by RPD1. Most examples of significant increases in genic antisense transcription appear to be initiated by 3'-proximal long terminal repeat retrotransposons. These results indicate that maize Pol IV specifies Pol II-based transcriptional regulation for specific regions of the maize genome including genes having developmental significance.
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17
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Gent JI, Madzima TF, Bader R, Kent MR, Zhang X, Stam M, McGinnis KM, Dawe RK. Accessible DNA and relative depletion of H3K9me2 at maize loci undergoing RNA-directed DNA methylation. THE PLANT CELL 2014; 26:4903-17. [PMID: 25465407 PMCID: PMC4311197 DOI: 10.1105/tpc.114.130427] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Revised: 11/03/2014] [Accepted: 11/18/2014] [Indexed: 05/18/2023]
Abstract
RNA-directed DNA methylation (RdDM) in plants is a well-characterized example of RNA interference-related transcriptional gene silencing. To determine the relationships between RdDM and heterochromatin in the repeat-rich maize (Zea mays) genome, we performed whole-genome analyses of several heterochromatic features: dimethylation of lysine 9 and lysine 27 (H3K9me2 and H3K27me2), chromatin accessibility, DNA methylation, and small RNAs; we also analyzed two mutants that affect these processes, mediator of paramutation1 and zea methyltransferase2. The data revealed that the majority of the genome exists in a heterochromatic state defined by inaccessible chromatin that is marked by H3K9me2 and H3K27me2 but that lacks RdDM. The minority of the genome marked by RdDM was predominantly near genes, and its overall chromatin structure appeared more similar to euchromatin than to heterochromatin. These and other data indicate that the densely staining chromatin defined as heterochromatin differs fundamentally from RdDM-targeted chromatin. We propose that small interfering RNAs perform a specialized role in repressing transposons in accessible chromatin environments and that the bulk of heterochromatin is incompatible with small RNA production.
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Affiliation(s)
- Jonathan I. Gent
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602
| | - Thelma F. Madzima
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306
| | - Rechien Bader
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Matthew R. Kent
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602
| | - Xiaoyu Zhang
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602
| | - Maike Stam
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Karen M. McGinnis
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306
| | - R. Kelly Dawe
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602
- Department of Genetics, University of Georgia, Athens, Georgia 30602
- Address correspondence to
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18
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Babenko O, Kovalchuk I, Metz GAS. Stress-induced perinatal and transgenerational epigenetic programming of brain development and mental health. Neurosci Biobehav Rev 2014; 48:70-91. [PMID: 25464029 DOI: 10.1016/j.neubiorev.2014.11.013] [Citation(s) in RCA: 323] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 09/19/2014] [Accepted: 11/17/2014] [Indexed: 12/20/2022]
Abstract
Research efforts during the past decades have provided intriguing evidence suggesting that stressful experiences during pregnancy exert long-term consequences on the future mental wellbeing of both the mother and her baby. Recent human epidemiological and animal studies indicate that stressful experiences in utero or during early life may increase the risk of neurological and psychiatric disorders, arguably via altered epigenetic regulation. Epigenetic mechanisms, such as miRNA expression, DNA methylation, and histone modifications are prone to changes in response to stressful experiences and hostile environmental factors. Altered epigenetic regulation may potentially influence fetal endocrine programming and brain development across several generations. Only recently, however, more attention has been paid to possible transgenerational effects of stress. In this review we discuss the evidence of transgenerational epigenetic inheritance of stress exposure in human studies and animal models. We highlight the complex interplay between prenatal stress exposure, associated changes in miRNA expression and DNA methylation in placenta and brain and possible links to greater risks of schizophrenia, attention deficit hyperactivity disorder, autism, anxiety- or depression-related disorders later in life. Based on existing evidence, we propose that prenatal stress, through the generation of epigenetic alterations, becomes one of the most powerful influences on mental health in later life. The consideration of ancestral and prenatal stress effects on lifetime health trajectories is critical for improving strategies that support healthy development and successful aging.
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Affiliation(s)
- Olena Babenko
- Canadian Centre for Behavioural Neuroscience, Department of Neuroscience, University of Lethbridge, 4401 University Drive, Lethbridge, AB, Canada T1K 3M4; Department of Biological Sciences, University of Lethbridge, 4401 University Drive, Lethbridge, AB, Canada T1K 3M4
| | - Igor Kovalchuk
- Department of Biological Sciences, University of Lethbridge, 4401 University Drive, Lethbridge, AB, Canada T1K 3M4
| | - Gerlinde A S Metz
- Canadian Centre for Behavioural Neuroscience, Department of Neuroscience, University of Lethbridge, 4401 University Drive, Lethbridge, AB, Canada T1K 3M4
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19
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Madzima TF, Huang J, McGinnis KM. Chromatin structure and gene expression changes associated with loss of MOP1 activity in Zea mays. Epigenetics 2014; 9:1047-59. [PMID: 24786611 PMCID: PMC4143406 DOI: 10.4161/epi.29022] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Though the mechanisms governing nuclear organization are not well understood, it is apparent that epigenetic modifications coordinately modulate chromatin organization as well as transcription. In maize, MEDIATOR OF PARAMUTATION1 (MOP1) is required for 24 nt siRNA-mediated epigenetic regulation and transcriptional gene silencing via a putative Pol IV- RdDM pathway. To elucidate the mechanisms of nuclear chromatin organization, we investigated the relationship between chromatin structure and transcription in response to loss of MOP1 function. We used a microarray based micrococcal nuclease sensitivity assay to identify genome-wide changes in chromatin structure in mop1-1 immature ears and observed an increase in chromatin accessibility at chromosome arms associated with loss of MOP1 function. Within the many genes misregulated in mop1 mutants, we identified one subset likely to be direct targets of epigenetic transcriptional silencing via Pol-IV RdDM. We found that target specificity for MOP1-mediated RdDM activity is governed by multiple signals that include accumulation of 24 nt siRNAs and the presence of specific classes of gene-proximal transposons, but neither of these attributes alone is sufficient to predict transcriptional misregulation in mop1-1 homozygous mutants. Our results suggest a role for MOP1 in regulation of higher-order chromatin organization where loss of MOP1 activity at a subset of loci triggers a broader cascade of transcriptional consequences and genome-wide changes in chromatin structure.
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Affiliation(s)
- Thelma F Madzima
- Department of Biological Science; Florida State University; Tallahassee, FL USA
| | - Ji Huang
- Department of Biological Science; Florida State University; Tallahassee, FL USA
| | - Karen M McGinnis
- Department of Biological Science; Florida State University; Tallahassee, FL USA
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20
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Diez CM, Meca E, Tenaillon MI, Gaut BS. Three groups of transposable elements with contrasting copy number dynamics and host responses in the maize (Zea mays ssp. mays) genome. PLoS Genet 2014; 10:e1004298. [PMID: 24743518 PMCID: PMC3990487 DOI: 10.1371/journal.pgen.1004298] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 02/21/2014] [Indexed: 12/19/2022] Open
Abstract
Most angiosperm nuclear DNA is repetitive and derived from silenced transposable elements (TEs). TE silencing requires substantial resources from the plant host, including the production of small interfering RNAs (siRNAs). Thus, the interaction between TEs and siRNAs is a critical aspect of both the function and the evolution of plant genomes. Yet the co-evolutionary dynamics between these two entities remain poorly characterized. Here we studied the organization of TEs within the maize (Zea mays ssp mays) genome, documenting that TEs fall within three groups based on the class and copy numbers. These groups included DNA elements, low copy RNA elements and higher copy RNA elements. The three groups varied statistically in characteristics that included length, location, age, siRNA expression and 24∶22 nucleotide (nt) siRNA targeting ratios. In addition, the low copy retroelements encompassed a set of TEs that had previously been shown to decrease expression within a 24 nt siRNA biogenesis mutant (mop1). To investigate the evolutionary dynamics of the three groups, we estimated their abundance in two landraces, one with a genome similar in size to that of the maize reference and the other with a 30% larger genome. For all three accessions, we assessed TE abundance as well as 22 nt and 24 nt siRNA content within leaves. The high copy number retroelements are under targeted similarly by siRNAs among accessions, appear to be born of a rapid bust of activity, and may be currently transpositionally dead or limited. In contrast, the lower copy number group of retrolements are targeted more dynamically and have had a long and ongoing history of transposition in the maize genome. Because transposable elements (TEs) constitute most angiosperm nuclear DNA, the interaction between TEs and their host genome is a key component for understanding the function and evolution of plant genomes. The diversity of the host response has been studied a great deal, including the biogenesis of small interfering RNAs (siRNAs) that target TEs for epigenetic modifications. However, little is known about variation in TE content among closely related genomes and whether siRNA expression tracks this variation. To that end, we surveyed both the copy number and the siRNA targeting of more than 1500 distinct TE subfamilies in the B73 maize reference genome. These surveys indicated that TE subfamilies fall naturally into three distinctive groups based on their class and copy number, but these groups also differ with respect to their location in the genome, their age, their expression and their siRNA regulation. The presence and consistency of these TE groups was also assessed in two genetically distant maize landraces with contrasting genome sizes. The variation in siRNA targeting across different TE groups and families, as well as the lack of correlation between TE and siRNA abundances, argues for the existence of multiple mechanisms and strategies for TE silencing.
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Affiliation(s)
- Concepcion M. Diez
- Dept. of Ecology and Evolutionary Biology, UC Irvine, Irvine, California, United States of America
- Departamento de Agronomía, Universidad de Córdoba, Campus de Excelencia Internacional Agroalimentario, ceiA3, Cordoba, Spain
| | - Esteban Meca
- Department of Mathematics, UC Irvine, Irvine, California, United States of America
| | - Maud I. Tenaillon
- CNRS, UMR de Génétique Végétale, INRA/CNRS/Univ Paris-Sud/AgroParisTech, Ferme du Moulon, Gif-sur-Yvette, France
| | - Brandon S. Gaut
- Dept. of Ecology and Evolutionary Biology, UC Irvine, Irvine, California, United States of America
- * E-mail:
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21
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Kubo T, Fujita M, Takahashi H, Nakazono M, Tsutsumi N, Kurata N. Transcriptome analysis of developing ovules in rice isolated by laser microdissection. PLANT & CELL PHYSIOLOGY 2013; 54:750-65. [PMID: 23411663 DOI: 10.1093/pcp/pct029] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Comprehensive genome-wide gene expression profiles during plant male gametogenesis have been thoroughly analyzed over the last decade. In contrast, gene expression profiles during female gametogenesis have been studied relatively little, and our knowledge concerning plant female gametogenesis is limited. We determined the genome-wide gene expression profiles of developing ovules containing female gametophytes from the megaspore mother cell at the pre-meiotic stage to the mature embryo sac in rice (Oryza sativa) using microarrays. In order to separate ovules from scutellum, we used a laser microdissection (LM) technique. Dynamic gene expression was revealed in developing ovules, and a major transition of the transcriptome was observed between middle and late meiotic stages, where many genes were down-regulated >10-fold. Many potential players in female gametogenesis, that showed dynamic or enriched expression, were highlighted. We identified the temporal and dramatic up-regulation of a subset of transposable elements during female meiotic stages that were not observed in males. Transcription factor genes enriched in developing ovules were also uncovered, which may play crucial roles during female gametogenesis. This is the first report of comprehensive genome-wide gene expression profiles during female gametogenesis useful for plant reproductive studies. Combined with additional experiments, our data may provide important clues to understand female gametogenesis in plants.
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Affiliation(s)
- Takahiko Kubo
- Plant Genetics Laboratory, National Institute of Genetics, Mishima, 411-8540 Japan
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22
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Gent JI, Ellis NA, Guo L, Harkess AE, Yao Y, Zhang X, Dawe RK. CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize. Genome Res 2013. [PMID: 23269663 DOI: 10.1101/gr.146985.112.as] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Small RNA-mediated regulation of chromatin structure is an important means of suppressing unwanted genetic activity in diverse plants, fungi, and animals. In plants specifically, 24-nt siRNAs direct de novo methylation to repetitive DNA, both foreign and endogenous, in a process known as RNA-directed DNA methylation (RdDM). Many components of the de novo methylation machinery have been identified recently, including multiple RNA polymerases, but specific genetic features that trigger methylation remain poorly understood. By applying whole-genome bisulfite sequencing to maize, we found that transposons close to cellular genes (particularly within 1 kb of either a gene start or end) are strongly associated with de novo methylation, as evidenced both by 24-nt siRNAs and by methylation specifically in the CHH sequence context. In addition, we found that the major classes of transposons exhibited a gradient of CHH methylation determined by proximity to genes. Our results further indicate that intergenic chromatin in maize exists in two major forms that are distinguished based on proximity to genes-one form marked by dense CG and CHG methylation and lack of transcription, and one marked by CHH methylation and activity of multiple forms of RNA polymerase. The existence of the latter, which we call CHH islands, may have implications for how cellular gene expression could be coordinated with immediately adjacent transposon repression in a large genome with a complex organization of genes interspersed in a landscape of transposons.
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Affiliation(s)
- Jonathan I Gent
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
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23
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Gent JI, Ellis NA, Guo L, Harkess AE, Yao Y, Zhang X, Dawe RK. CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize. Genome Res 2013; 23:628-37. [PMID: 23269663 PMCID: PMC3613580 DOI: 10.1101/gr.146985.112] [Citation(s) in RCA: 228] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 12/18/2012] [Indexed: 11/24/2022]
Abstract
Small RNA-mediated regulation of chromatin structure is an important means of suppressing unwanted genetic activity in diverse plants, fungi, and animals. In plants specifically, 24-nt siRNAs direct de novo methylation to repetitive DNA, both foreign and endogenous, in a process known as RNA-directed DNA methylation (RdDM). Many components of the de novo methylation machinery have been identified recently, including multiple RNA polymerases, but specific genetic features that trigger methylation remain poorly understood. By applying whole-genome bisulfite sequencing to maize, we found that transposons close to cellular genes (particularly within 1 kb of either a gene start or end) are strongly associated with de novo methylation, as evidenced both by 24-nt siRNAs and by methylation specifically in the CHH sequence context. In addition, we found that the major classes of transposons exhibited a gradient of CHH methylation determined by proximity to genes. Our results further indicate that intergenic chromatin in maize exists in two major forms that are distinguished based on proximity to genes-one form marked by dense CG and CHG methylation and lack of transcription, and one marked by CHH methylation and activity of multiple forms of RNA polymerase. The existence of the latter, which we call CHH islands, may have implications for how cellular gene expression could be coordinated with immediately adjacent transposon repression in a large genome with a complex organization of genes interspersed in a landscape of transposons.
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Affiliation(s)
| | | | | | | | | | | | - R. Kelly Dawe
- Department of Plant Biology
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
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24
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Erhard KF, Parkinson SE, Gross SM, Barbour JER, Lim JP, Hollick JB. Maize RNA polymerase IV defines trans-generational epigenetic variation. THE PLANT CELL 2013; 25:808-19. [PMID: 23512852 PMCID: PMC3634690 DOI: 10.1105/tpc.112.107680] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 02/20/2013] [Accepted: 02/26/2013] [Indexed: 05/19/2023]
Abstract
The maize (Zea mays) RNA Polymerase IV (Pol IV) largest subunit, RNA Polymerase D1 (RPD1 or NRPD1), is required for facilitating paramutations, restricting expression patterns of genes required for normal development, and generating small interfering RNA (siRNAs). Despite this expanded role for maize Pol IV relative to Arabidopsis thaliana, neither the general characteristics of Pol IV-regulated haplotypes, nor their prevalence, are known. Here, we show that specific haplotypes of the purple plant1 locus, encoding an anthocyanin pigment regulator, acquire and retain an expanded expression domain following transmission from siRNA biogenesis mutants. This conditioned expression pattern is progressively enhanced over generations in Pol IV mutants and then remains heritable after restoration of Pol IV function. This unusual genetic behavior is associated with promoter-proximal transposon fragments but is independent of sequences required for paramutation. These results indicate that trans-generational Pol IV action defines the expression patterns of haplotypes using co-opted transposon-derived sequences as regulatory elements. Our results provide a molecular framework for the concept that induced changes to the heterochromatic component of the genome are coincident with heritable changes in gene regulation. Alterations of this Pol IV-based regulatory system can generate potentially desirable and adaptive traits for selection to act upon.
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Affiliation(s)
- Karl F. Erhard
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102
| | - Susan E. Parkinson
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102
| | - Stephen M. Gross
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102
| | - Joy-El R. Barbour
- Department of Molecular Cell Biology, University of California, Berkeley, California 94720-3200
| | - Jana P. Lim
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102
| | - Jay B. Hollick
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102
- Address correspondence to
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25
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Abstract
The Mutator system has proved to be an invaluable tool for elucidating gene function via insertional mutagenesis. Its high copy number, high transposition frequency, relative lack of insertion specificity, and ease of use has made it the preferred method for gene tagging in maize. Recent advances in high throughput sequencing of insertion sites, combined with the availability of large numbers of pre-mutagenized and sequence-indexed stocks, ensure that this resource will only be more useful in the years ahead. Muk is a locus that can silence Mu-active lines, making it possible to ameliorate the phenotypic effects of high numbers of active Mu transposons and reduce the copy number of these elements during introgressions.
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Affiliation(s)
- Damon Lisch
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
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26
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Lisch D. Regulation of transposable elements in maize. CURRENT OPINION IN PLANT BIOLOGY 2012; 15:511-516. [PMID: 22824142 DOI: 10.1016/j.pbi.2012.07.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 07/04/2012] [Indexed: 06/01/2023]
Abstract
Maize is a typical plant with respect to the proportion of its genome that is composed of transposable elements (TEs), but it is unusual in the number of well-characterized active TEs that it hosts. This has made it possible to examine in some detail the factors responsible for regulating the activity of these elements, particularly the means by which they are recognized and epigenetically silenced. That analysis has revealed that TE silencing is a complex process that involves careful distinctions of different developmental times and tissue types. The available evidence from maize and other species suggests that these distinctions are made in order to generate information in somatic tissues that can be used to induce or reinforce silencing in germinal tissues.
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Affiliation(s)
- Damon Lisch
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, United States.
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27
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Fujimoto R, Sasaki T, Ishikawa R, Osabe K, Kawanabe T, Dennis ES. Molecular mechanisms of epigenetic variation in plants. Int J Mol Sci 2012; 13:9900-9922. [PMID: 22949838 PMCID: PMC3431836 DOI: 10.3390/ijms13089900] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/27/2012] [Accepted: 07/30/2012] [Indexed: 12/11/2022] Open
Abstract
Natural variation is defined as the phenotypic variation caused by spontaneous mutations. In general, mutations are associated with changes of nucleotide sequence, and many mutations in genes that can cause changes in plant development have been identified. Epigenetic change, which does not involve alteration to the nucleotide sequence, can also cause changes in gene activity by changing the structure of chromatin through DNA methylation or histone modifications. Now there is evidence based on induced or spontaneous mutants that epigenetic changes can cause altering plant phenotypes. Epigenetic changes have occurred frequently in plants, and some are heritable or metastable causing variation in epigenetic status within or between species. Therefore, heritable epigenetic variation as well as genetic variation has the potential to drive natural variation.
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Affiliation(s)
- Ryo Fujimoto
- Graduate School of Science and Technology, Niigata University, Nishi-ku, Niigata 950-2181, Japan
| | - Taku Sasaki
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Dr. Bohrgasse 3, Vienna 1030, Austria; E-Mail:
| | - Ryo Ishikawa
- Laboratory of Plant Breeding, Graduate School of Agricultural Science, Kobe University, Nada, Kobe 657-8510, Japan; E-Mail:
- Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
| | - Kenji Osabe
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Plant Industry, Canberra ACT 2601, Australia; E-Mails: (K.O.); (E.S.D.)
| | - Takahiro Kawanabe
- Watanabe Seed Co., Ltd, Machiyashiki, Misato-cho, Miyagi 987-8607, Japan; E-Mail:
| | - Elizabeth S. Dennis
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Plant Industry, Canberra ACT 2601, Australia; E-Mails: (K.O.); (E.S.D.)
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28
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Barbour JER, Liao IT, Stonaker JL, Lim JP, Lee CC, Parkinson SE, Kermicle J, Simon SA, Meyers BC, Williams-Carrier R, Barkan A, Hollick JB. required to maintain repression2 is a novel protein that facilitates locus-specific paramutation in maize. THE PLANT CELL 2012; 24:1761-1775. [PMID: 22562610 PMCID: PMC3442568 DOI: 10.1105/tpc.112.097618] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 03/29/2012] [Accepted: 04/11/2012] [Indexed: 05/27/2023]
Abstract
Meiotically heritable epigenetic changes in gene regulation known as paramutations are facilitated by poorly understood trans-homolog interactions. Mutations affecting paramutations in maize (Zea mays) identify components required for the accumulation of 24-nucleotide RNAs. Some of these components have Arabidopsis thaliana orthologs that are part of an RNA-directed DNA methylation (RdDM) pathway. It remains unclear if small RNAs actually mediate paramutations and whether the maize-specific molecules identified to date define a mechanism distinct from RdDM. Here, we identify a novel protein required for paramutation at the maize purple plant1 locus. This required to maintain repression2 (RMR2) protein represents the founding member of a plant-specific clade of predicted proteins. We show that RMR2 is required for transcriptional repression at the Pl1-Rhoades haplotype, for accumulation of 24-nucleotide RNA species, and for maintenance of a 5-methylcytosine pattern distinct from that maintained by RNA polymerase IV. Genetic tests indicate that RMR2 is not required for paramutation occurring at the red1 locus. These results distinguish the paramutation-type mechanisms operating at specific haplotypes. The RMR2 clade of proteins provides a new entry point for understanding the diversity of epigenomic control operating in higher plants.
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Affiliation(s)
- Joy-El R. Barbour
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3200
| | - Irene T. Liao
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102
| | - Jennifer L. Stonaker
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102
| | - Jana P. Lim
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102
| | - Clarissa C. Lee
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102
| | - Susan E. Parkinson
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102
| | - Jerry Kermicle
- Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Stacey A. Simon
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711
| | - Blake C. Meyers
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711
| | | | - Alice Barkan
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - Jay B. Hollick
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102
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29
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Skibbe DS, Fernandes JF, Walbot V. Mu killer-Mediated and Spontaneous Silencing of Zea mays Mutator Family Transposable Elements Define Distinctive Paths of Epigenetic Inactivation. FRONTIERS IN PLANT SCIENCE 2012; 3:212. [PMID: 22993515 PMCID: PMC3440606 DOI: 10.3389/fpls.2012.00212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 08/23/2012] [Indexed: 05/03/2023]
Abstract
Mu killer contains a partial inverted duplication of the mudrA transposase gene and two copies of the terminal inverted repeat A (TIRA) region of the master MuDR element of maize. Mu killer can effectively silence single copy MuDR/Mu lines, and it is proposed that a ∼4 kb hairpin RNA is generated by read through transcription from a flanking gene and that this transcript serves as a substrate for siRNA production. Mu killer was sequenced, except for a recalcitrant portion in the center of the locus, and shown to be co-linear with mudrA as originally proposed. The ability of the dominant Mu killer locus to silence a standard high copy number MuDR/Mu transposon line was evaluated. After two generations of exposure, about three quarters of individuals were silenced indicating reasonable effectiveness as measured by the absence of mudrA transposase transcripts. Mu killer individuals that effectively silenced MuDR expressed two short antisense transcripts. In contrast, Mu killer individuals that failed to silence MuDR expressed multiple sense transcripts, derived from read through transcription initiating in a flanking gene, but no antisense transcripts were detected.
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Affiliation(s)
| | - J. F. Fernandes
- Department of Biology, Stanford UniversityStanford, CA, USA
- *Correspondence: J. F. Fernandes and Virginia Walbot, Department of Biology, 385 Serra Mall, Stanford University, Stanford, CA 94305-5020, USA. e-mail: ;
| | - Virginia Walbot
- Department of Biology, Stanford UniversityStanford, CA, USA
- *Correspondence: J. F. Fernandes and Virginia Walbot, Department of Biology, 385 Serra Mall, Stanford University, Stanford, CA 94305-5020, USA. e-mail: ;
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30
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Greer EL, Maures TJ, Ucar D, Hauswirth AG, Mancini E, Lim JP, Benayoun BA, Shi Y, Brunet A. Transgenerational epigenetic inheritance of longevity in Caenorhabditis elegans. Nature 2011; 479:365-71. [PMID: 22012258 PMCID: PMC3368121 DOI: 10.1038/nature10572] [Citation(s) in RCA: 493] [Impact Index Per Article: 37.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2010] [Accepted: 09/26/2011] [Indexed: 11/21/2022]
Abstract
Chromatin modifiers regulate lifespan in several organisms, raising the question of whether changes in chromatin states in the parental generation could be incompletely reprogrammed in the next generation and thereby affect the lifespan of descendents. The histone H3 lysine 4 trimethylation (H3K4me3) complex composed of ASH-2, WDR-5, and the histone methyltransferase SET-2 regulates C. elegans lifespan. Here we show that deficiencies in the H3K4me3 chromatin modifiers ASH-2, WDR-5, or SET-2 in the parental generation extend the lifespan of descendents up until the third generation. The transgenerational inheritance of lifespan extension by members of the ASH-2 complex is dependent on the H3K4me3 demethylase RBR-2, and requires the presence of a functioning germline in the descendents. Transgenerational inheritance of lifespan is specific for the H3K4me3 methylation complex and is associated with epigenetic changes in gene expression. Thus, manipulation of specific chromatin modifiers only in parents can induce an epigenetic memory of longevity in descendents.
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Affiliation(s)
- Eric L Greer
- Department of Genetics, Stanford University, 300 Pasteur Drive, Stanford, California 94305, USA
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31
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Brzeski J, Brzeska K. The maze of paramutation: a rough guide to the puzzling epigenetics of paramutation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 2:863-74. [PMID: 21976288 DOI: 10.1002/wrna.97] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Epigenetic mechanisms maintain gene expression states through mitotic and sometimes meiotic cell divisions. Paramutation is an extreme example of epigenetic processes. Not only an established expression state is transmitted through meiosis to the following generations but also an information transfer occurs between alleles and leads to heritable changes in expression state. As a consequence the expression states can rapidly propagate in population, violating Mendelian genetics. Recent findings unraveled an essential role for siRNA-dependent processes in paramutation. Despite significant progress, the overall picture is still puzzling and many important questions remain to be answered.
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Affiliation(s)
- Jan Brzeski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
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32
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Lisch D, Bennetzen JL. Transposable element origins of epigenetic gene regulation. CURRENT OPINION IN PLANT BIOLOGY 2011; 14:156-61. [PMID: 21444239 DOI: 10.1016/j.pbi.2011.01.003] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Accepted: 01/22/2011] [Indexed: 05/07/2023]
Abstract
Transposable elements (TEs) are massively abundant and unstable in all plant genomes, but are mostly silent because of epigenetic suppression. Because all known epigenetic pathways act on all TEs, it is likely that the specialized epigenetic regulation of regular host genes (RHGs) was co-opted from this ubiquitous need for the silencing of TEs and viruses. With their internally repetitive and rearranging structures, and the acquisition of fragments of RHGs, the expression of TEs commonly makes antisense RNAs for both TE genes and RHGs. These antisense RNAs, particularly from heterochromatic reservoirs of 'zombie' TEs that are rearranged to form variously internally repetitive structures, may be advantageous because their induction will help rapidly suppress active TEs of the same family. RHG fragments within rapidly rearranging TEs may also provide the raw material for the ongoing generation of miRNA genes. TE gene expression is regulated by both environmental and developmental signals, and insertions can place nearby RHGs under the regulation (both standard and epigenetic) of the TE. The ubiquity of TEs, their frequent preferential association with RHGs, and their ability to be programmed by epigenetic signals all indicate that RGHs have nearly unlimited access to novel regulatory cassettes to assist plant adaptation.
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Affiliation(s)
- Damon Lisch
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.
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33
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Abstract
It is widely accepted that ncRNAs (non-coding RNAs), as opposed to protein-coding RNAs, represent the majority of human transcripts; and the regulatory roles of many of these ncRNAs have been elucidated over the past decade. One important role so far recognized for ncRNAs is their participation in the epigenetic regulation of genes. Indeed, it is becoming increasingly apparent that most epigenetic mechanisms of gene expression are controlled by ncRNAs. In this review, the different types of ncRNA that are strongly linked to epigenetic regulation are characterized and their possible mechanisms discussed.
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34
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Lisch D, Slotkin RK. Strategies for silencing and escape: the ancient struggle between transposable elements and their hosts. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2011; 292:119-52. [PMID: 22078960 DOI: 10.1016/b978-0-12-386033-0.00003-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Over the past several years, there has been an explosion in our understanding of the mechanisms by which plant transposable elements (TEs) are epigenetically silenced and maintained in an inactive state over long periods of time. This highly efficient process results in vast numbers of inactive TEs; indeed, the majority of many plant genomes are composed of these quiescent elements. This observation has led to the rather static view that TEs represent an essentially inert portion of plant genomes. However, recent work has demonstrated that TE silencing is a highly dynamic process that often involves transcription of TEs at particular times and places during plant development. Plants appear to use transcripts from silenced TEs as an ongoing source of information concerning the mobile portion of the genome. In contrast to our understanding of silencing pathways, we know relatively little about the ways in which TEs evade silencing. However, vast differences in TE content between even closely related plant species suggest that they are often wildly successful at doing so. Here, we discuss TE activity in plants as the result of a constantly shifting balance between host strategies for TE silencing and TE strategies for escape and amplification.
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Affiliation(s)
- Damon Lisch
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
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35
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Abstract
An important step during plant development is the transition from juvenile to adult growth. It is only after this transition that plants are reproductively competent. Given the great danger that transposon activity represents to the germ line, this may also be an important period during development with respect to transposon regulation and silencing. We demonstrate that a change in expression of a key component of the RNA silencing pathway is associated with both vegetative phase change and shifts in epigenetic regulation of a maize transposon.
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36
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Abstract
Paramutation describes a heritable change of gene expression that is brought about through interactions between homologous chromosomes. Genetic analyses in plants and, more recently, in mouse indicate that genomic sequences related to transcriptional control and molecules related to small RNA biology are necessary for specific examples of paramutation. Some of the molecules identified in maize are also required for normal plant development. These observations indicate a functional relationship between the nuclear mechanisms responsible for paramutation and modes of developmental gene control.
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Affiliation(s)
- Jay B Hollick
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102, USA.
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37
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Haring M, Bader R, Louwers M, Schwabe A, van Driel R, Stam M. The role of DNA methylation, nucleosome occupancy and histone modifications in paramutation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 63:366-78. [PMID: 20444233 DOI: 10.1111/j.1365-313x.2010.04245.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Paramutation is the transfer of epigenetic information between alleles that leads to a heritable change in expression of one of these alleles. Paramutation at the tissue-specifically expressed maize (Zea mays) b1 locus involves the low-expressing B' and high-expressing B-I allele. Combined in the same nucleus, B' heritably changes B-I into B'. A hepta-repeat located 100-kb upstream of the b1 coding region is required for paramutation and for high b1 expression. The role of epigenetic modifications in paramutation is currently not well understood. In this study, we show that the B' hepta-repeat is DNA-hypermethylated in all tissues analyzed. Importantly, combining B' and B-I in one nucleus results in de novo methylation of the B-I repeats early in plant development. These findings indicate a role for hepta-repeat DNA methylation in the establishment and maintenance of the silenced B' state. In contrast, nucleosome occupancy, H3 acetylation, and H3K9 and H3K27 methylation are mainly involved in tissue-specific regulation of the hepta-repeat. Nucleosome depletion and H3 acetylation are tissue-specifically regulated at the B-I hepta-repeat and associated with enhancement of b1 expression. H3K9 and H3K27 methylation are tissue-specifically localized at the B' hepta-repeat and reinforce the silenced B' chromatin state. The B' coding region is H3K27 dimethylated in all tissues analyzed, indicating a role in the maintenance of the silenced B' state. Taken together, these findings provide insight into the mechanisms underlying paramutation and tissue-specific regulation of b1 at the level of chromatin structure.
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Affiliation(s)
- Max Haring
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH Amsterdam, the NetherlandsNetherlands Institute for Systems Biology (NISB), Centre for Mathematics and Computer Science (CWI), Science Park 123, 1098 XG Amsterdam, the Netherlands
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38
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RNA-mediated trans-communication can establish paramutation at the b1 locus in maize. Proc Natl Acad Sci U S A 2010; 107:12986-91. [PMID: 20616013 DOI: 10.1073/pnas.1007972107] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Paramutation is the epigenetic transfer of information between alleles that leads to the heritable change of expression of one allele. Paramutation at the b1 locus in maize requires seven noncoding tandem repeat (b1TR) sequences located approximately 100 kb upstream of the transcription start site of b1, and mutations in several genes required for paramutation implicate an RNA-mediated mechanism. The mediator of paramutation (mop1) gene, which encodes a protein closely related to RNA-dependent RNA polymerases, is absolutely required for paramutation. Herein, we investigate the potential function of mop1 and the siRNAs that are produced from the b1TR sequences. Production of siRNAs from the b1TR sequences depends on a functional mop1 gene, but transcription of the repeats is not dependent on mop1. Further nuclear transcription assays suggest that the b1TR sequences are likely transcribed predominantly by RNA polymerase II. To address whether production of b1TR-siRNAs correlated with paramutation, we examined siRNA production in alleles that cannot undergo paramutation. Alleles that cannot participate in paramutation also produce b1TR-siRNAs, suggesting that b1TR-siRNAs are not sufficient for paramutation in the tissues analyzed. However, when b1TR-siRNAs are produced from a transgene expressing a hairpin RNA, b1 paramutation can be recapitulated. We hypothesize that either the b1TR-siRNAs or the dsRNA template mediates the trans-communication between the alleles that establishes paramutation. In addition, we uncovered a role for mop1 in the biogenesis of a subset of microRNAs (miRNAs) and show that it functions at the level of production of the primary miRNA transcripts.
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39
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Qüesta JI, Walbot V, Casati P. Mutator transposon activation after UV-B involves chromatin remodeling. Epigenetics 2010; 5:352-63. [PMID: 20421734 DOI: 10.4161/epi.5.4.11751] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Spontaneous silencing of MuDR/Mu transposons occurs in approximately 10-100% of the progeny of an active plant, and once silenced reactivation is very rare. To date, only radiation treatments have reactivated silenced Mu; for example UV-B radiation reactivated Mutator activities. Here we have investigated possible mechanisms by which UV-B could reactivate Mu transposons by monitoring transcript abundance, epigenetic DNA marks, and chromatin factors associated with these elements. We demonstrate that both mudrA and B transcripts are expressed at higher levels after an 8 h-UV-B treatment, in both active Mutator and silencing plants, and that different chromatin remodeling events occur in the promoter regions of MuDR than in non-autonomous Mu1 elements. Increased transcript abundance is accompanied by an increase in histone H3 acetylation and by decreased DNA and H3K9me2 methylation. No changes in siRNA levels were detected. In contrast, the decrease in H3K9me2 present at Mu elements after UV-B is significant in silencing plants, suggesting that early changes in H3 methylation in K9, chromatin remodeling, and transcription factor binding contribute directly to transposon reactivation by UV-B in maize.
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Affiliation(s)
- Julia I Qüesta
- Centro de Estudios Fotosintéticos y Bioquímicos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
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40
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Mosher RA. Maternal control of Pol IV-dependent siRNAs in Arabidopsis endosperm. THE NEW PHYTOLOGIST 2010; 186:358-364. [PMID: 20074090 DOI: 10.1111/j.1469-8137.2009.03144.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Small RNAs recently emerged as ubiquitous regulators of gene expression. However, the most abundant class of small RNAs in flowering plants is poorly understood. Known as Pol IV-dependent (p4-)siRNAs, these small RNAs are associated with transcriptional gene silencing, transposable elements and heterochromatin formation. Recent research demonstrates that they are initially expressed in the maternal gametophyte and uniparentally expressed from maternal chromosomes in developing endosperm. This unique expression pattern links p4-siRNAs to double fertilization, parental genome interactions and imprinted gene expression.
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Affiliation(s)
- Rebecca A Mosher
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK.
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41
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Arteaga-Vazquez MA, Chandler VL. Paramutation in maize: RNA mediated trans-generational gene silencing. Curr Opin Genet Dev 2010; 20:156-63. [PMID: 20153628 DOI: 10.1016/j.gde.2010.01.008] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Revised: 01/18/2010] [Accepted: 01/22/2010] [Indexed: 11/29/2022]
Abstract
Paramutation involves trans-interactions between alleles or homologous sequences that establish distinct gene expression states that are heritable for generations. It was first described in maize by Alexander Brink in the 1950s, with his studies of the red1 (r1) locus. Since that time, paramutation-like phenomena have been reported in other maize genes, other plants, fungi, and animals. Paramutation can occur between endogenous genes, two transgenes or an endogenous gene, and transgene. Recent results indicate that paramutation involves RNA-mediated heritable chromatin changes and a number of genes implicated in RNAi pathways. However, not all aspects of paramutation can be explained by known mechanisms of RNAi-mediated transcriptional silencing.
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42
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Jia Y, Lisch DR, Ohtsu K, Scanlon MJ, Nettleton D, Schnable PS. Loss of RNA-dependent RNA polymerase 2 (RDR2) function causes widespread and unexpected changes in the expression of transposons, genes, and 24-nt small RNAs. PLoS Genet 2009; 5:e1000737. [PMID: 19936292 PMCID: PMC2774947 DOI: 10.1371/journal.pgen.1000737] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2009] [Accepted: 10/21/2009] [Indexed: 11/18/2022] Open
Abstract
Transposable elements (TEs) comprise a substantial portion of many eukaryotic genomes and are typically transcriptionally silenced. RNA–dependent RNA polymerase 2 (RDR2) is a component of the RNA–directed DNA methylation (RdDM) silencing pathway. In maize, loss of mediator of paramutation1 (mop1) encoded RDR2 function results in reactivation of transcriptionally silenced Mu transposons and a substantial reduction in the accumulation of 24 nt short-interfering RNAs (siRNAs) that recruit RNA silencing components. An RNA–seq experiment conducted on shoot apical meristems (SAMs) revealed that, as expected based on a model in which RDR2 generates 24 nt siRNAs that suppress expression, most differentially expressed DNA TEs (78%) were up-regulated in the mop1 mutant. In contrast, most differentially expressed retrotransposons (68%) were down-regulated. This striking difference suggests that distinct silencing mechanisms are applied to different silencing templates. In addition, >6,000 genes (24% of analyzed genes), including nearly 80% (286/361) of genes in chromatin modification pathways, were differentially expressed. Overall, two-thirds of differentially regulated genes were down-regulated in the mop1 mutant. This finding suggests that RDR2 plays a significant role in regulating the expression of not only transposons, but also of genes. A re-analysis of existing small RNA data identified both RDR2–sensitive and RDR2–resistant species of 24 nt siRNAs that we hypothesize may at least partially explain the complex changes in the expression of genes and transposons observed in the mop1 mutant. Shoot apical meristems (SAMs) are ultimately responsible for generating all above-ground plant tissues. Recent studies highlighted the effects of chromatin remodeling on the expression of various genes important to SAM development. The transposons that comprise a substantial portion of many eukaryotic genomes are typically transcriptionally silenced, presumably to promote genome stability. We demonstrate that a loss of a key component of the RNA–dependent DNA Methylation (RdDM) silencing pathway affects the expression of not only transposons but also thousands of genes, including nearly 80% of the chromatin-associated genes. Surprisingly, the expression of many transposons and genes is down-regulated via the loss of this component of the silencing pathway. In this study, we have shown that a maize mutation of RDR2 causes significant changes in SAM morphology. In combination, these observations indicate the complexity of transcriptome regulation and the crucial roles of RDR2 on transcriptome regulation, chromatin modification, and SAM development.
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Affiliation(s)
- Yi Jia
- Interdepartmental Plant Biology Program, Iowa State University, Ames, Iowa, United States of America
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa, United States of America
| | - Damon R. Lisch
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Kazuhiro Ohtsu
- Department of Agronomy, Iowa State University, Ames, Iowa, United States of America
| | - Michael J. Scanlon
- Department of Plant Biology, Cornell University, Ithaca, New York, United States of America
| | - Dan Nettleton
- Department of Statistics, Iowa State University, Ames, Iowa, United States of America
| | - Patrick S. Schnable
- Interdepartmental Plant Biology Program, Iowa State University, Ames, Iowa, United States of America
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa, United States of America
- Department of Agronomy, Iowa State University, Ames, Iowa, United States of America
- Center for Plant Genomics, Iowa State University, Ames, Iowa, United States of America
- * E-mail:
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43
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Stonaker JL, Lim JP, Erhard KF, Hollick JB. Diversity of Pol IV function is defined by mutations at the maize rmr7 locus. PLoS Genet 2009; 5:e1000706. [PMID: 19936246 PMCID: PMC2775721 DOI: 10.1371/journal.pgen.1000706] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2009] [Accepted: 10/15/2009] [Indexed: 12/03/2022] Open
Abstract
Mutations affecting the heritable maintenance of epigenetic states in maize identify multiple small RNA biogenesis factors including NRPD1, the largest subunit of the presumed maize Pol IV holoenzyme. Here we show that mutations defining the required to maintain repression7 locus identify a second RNA polymerase subunit related to Arabidopsis NRPD2a, the sole second largest subunit shared between Arabidopsis Pol IV and Pol V. A phylogenetic analysis shows that, in contrast to representative eudicots, grasses have retained duplicate loci capable of producing functional NRPD2-like proteins, which is indicative of increased RNA polymerase diversity in grasses relative to eudicots. Together with comparisons of rmr7 mutant plant phenotypes and their effects on the maintenance of epigenetic states with parallel analyses of NRPD1 defects, our results imply that maize utilizes multiple functional NRPD2-like proteins. Despite the observation that RMR7/NRPD2, like NRPD1, is required for the accumulation of most siRNAs, our data indicate that different Pol IV isoforms play distinct roles in the maintenance of meiotically-heritable epigenetic information in the grasses. Multicellular plants possess a unique set of DNA–dependent RNA polymerase complexes (RNAPs) that prevent certain repetitious regions of the genome from being copied into stable RNAs. Two distinct RNAPs, termed Pol IV and Pol V, are required for this type of genome-silencing behavior in the eudicot Arabidopsis thaliana, but the mechanism by which these RNAPs accomplish this function is still relatively unknown. Using genetic and molecular methodologies, we identified a Pol IV–type subunit protein as being involved in a process of meiotically-heritable gene silencing in the maize plant known as paramutation. Our analyses of the available plant genome sequences indicate that monocots have a greater potential for RNAP diversity due to having duplicate variants of this particular subunit. Consistent with this inferred diversity, comparative analyses with plants defective in a different core Pol IV subunit indicate that the Pol IV–type RNAP in maize has distinct functional isoforms. The mechanistic and biological role(s) of these specific RNAPs in mediating genome regulation and heritable gene silencing in large genome cereals should now be tractable by biochemical approaches.
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Affiliation(s)
- Jennifer L. Stonaker
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Jana P. Lim
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Karl F. Erhard
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Jay B. Hollick
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
- * E-mail:
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Wei F, Stein JC, Liang C, Zhang J, Fulton RS, Baucom RS, De Paoli E, Zhou S, Yang L, Han Y, Pasternak S, Narechania A, Zhang L, Yeh CT, Ying K, Nagel DH, Collura K, Kudrna D, Currie J, Lin J, Kim H, Angelova A, Scara G, Wissotski M, Golser W, Courtney L, Kruchowski S, Graves TA, Rock SM, Adams S, Fulton LA, Fronick C, Courtney W, Kramer M, Spiegel L, Nascimento L, Kalyanaraman A, Chaparro C, Deragon JM, Miguel PS, Jiang N, Wessler SR, Green PJ, Yu Y, Schwartz DC, Meyers BC, Bennetzen JL, Martienssen RA, McCombie WR, Aluru S, Clifton SW, Schnable PS, Ware D, Wilson RK, Wing RA. Detailed analysis of a contiguous 22-Mb region of the maize genome. PLoS Genet 2009; 5:e1000728. [PMID: 19936048 PMCID: PMC2773423 DOI: 10.1371/journal.pgen.1000728] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2009] [Accepted: 10/16/2009] [Indexed: 12/20/2022] Open
Abstract
Most of our understanding of plant genome structure and evolution has come from the careful annotation of small (e.g., 100 kb) sequenced genomic regions or from automated annotation of complete genome sequences. Here, we sequenced and carefully annotated a contiguous 22 Mb region of maize chromosome 4 using an improved pseudomolecule for annotation. The sequence segment was comprehensively ordered, oriented, and confirmed using the maize optical map. Nearly 84% of the sequence is composed of transposable elements (TEs) that are mostly nested within each other, of which most families are low-copy. We identified 544 gene models using multiple levels of evidence, as well as five miRNA genes. Gene fragments, many captured by TEs, are prevalent within this region. Elimination of gene redundancy from a tetraploid maize ancestor that originated a few million years ago is responsible in this region for most disruptions of synteny with sorghum and rice. Consistent with other sub-genomic analyses in maize, small RNA mapping showed that many small RNAs match TEs and that most TEs match small RNAs. These results, performed on approximately 1% of the maize genome, demonstrate the feasibility of refining the B73 RefGen_v1 genome assembly by incorporating optical map, high-resolution genetic map, and comparative genomic data sets. Such improvements, along with those of gene and repeat annotation, will serve to promote future functional genomic and phylogenomic research in maize and other grasses.
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Affiliation(s)
- Fusheng Wei
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
| | - Joshua C. Stein
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Chengzhi Liang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Jianwei Zhang
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
| | - Robert S. Fulton
- The Genome Center and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Regina S. Baucom
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Emanuele De Paoli
- Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, United States of America
| | - Shiguo Zhou
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, University of Wisconsin Madison, Madison, Wisconsin, United States of America
| | - Lixing Yang
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Yujun Han
- Department of Plant Biology, University of Georgia, Athens, Georgia, United States of America
| | - Shiran Pasternak
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Apurva Narechania
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Lifang Zhang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Cheng-Ting Yeh
- Department of Agronomy and Center for Plant Genomics, Iowa State University, Ames, Iowa, United States of America
| | - Kai Ying
- Department of Agronomy and Center for Plant Genomics, Iowa State University, Ames, Iowa, United States of America
| | - Dawn H. Nagel
- Department of Plant Biology, University of Georgia, Athens, Georgia, United States of America
| | - Kristi Collura
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
| | - David Kudrna
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
| | - Jennifer Currie
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
| | - Jinke Lin
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
| | - HyeRan Kim
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
| | - Angelina Angelova
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
| | - Gabriel Scara
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
| | - Marina Wissotski
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
| | - Wolfgang Golser
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
| | - Laura Courtney
- The Genome Center and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Scott Kruchowski
- The Genome Center and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Tina A. Graves
- The Genome Center and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Susan M. Rock
- The Genome Center and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Stephanie Adams
- The Genome Center and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Lucinda A. Fulton
- The Genome Center and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Catrina Fronick
- The Genome Center and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - William Courtney
- The Genome Center and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Melissa Kramer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Lori Spiegel
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Lydia Nascimento
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Ananth Kalyanaraman
- School of Electrical Engineering and Computer Science, Washington State University, Pullman, Washington, United States of America
| | - Cristian Chaparro
- Université de Perpignan Via Domitia, CNRS UMR 5096, Perpignan, France
| | - Jean-Marc Deragon
- Université de Perpignan Via Domitia, CNRS UMR 5096, Perpignan, France
| | - Phillip San Miguel
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, United States of America
| | - Ning Jiang
- Department of Horticulture, Michigan State University, East Lansing, Michigan, United States of America
| | - Susan R. Wessler
- Department of Plant Biology, University of Georgia, Athens, Georgia, United States of America
| | - Pamela J. Green
- Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, United States of America
| | - Yeisoo Yu
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
| | - David C. Schwartz
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, University of Wisconsin Madison, Madison, Wisconsin, United States of America
| | - Blake C. Meyers
- Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, United States of America
| | - Jeffrey L. Bennetzen
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Robert A. Martienssen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - W. Richard McCombie
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Srinivas Aluru
- Department of Electrical and Computer Engineering, Iowa State University, Ames, Iowa, United States of America
| | - Sandra W. Clifton
- The Genome Center and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Patrick S. Schnable
- Department of Agronomy and Center for Plant Genomics, Iowa State University, Ames, Iowa, United States of America
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Richard K. Wilson
- The Genome Center and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Rod A. Wing
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
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Sidorenko L, Dorweiler JE, Cigan AM, Arteaga-Vazquez M, Vyas M, Kermicle J, Jurcin D, Brzeski J, Cai Y, Chandler VL. A dominant mutation in mediator of paramutation2, one of three second-largest subunits of a plant-specific RNA polymerase, disrupts multiple siRNA silencing processes. PLoS Genet 2009; 5:e1000725. [PMID: 19936058 PMCID: PMC2774164 DOI: 10.1371/journal.pgen.1000725] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2009] [Accepted: 10/15/2009] [Indexed: 01/03/2023] Open
Abstract
Paramutation involves homologous sequence communication that leads to meiotically heritable transcriptional silencing. We demonstrate that mop2 (mediator of paramutation2), which alters paramutation at multiple loci, encodes a gene similar to Arabidopsis NRPD2/E2, the second-largest subunit of plant-specific RNA polymerases IV and V. In Arabidopsis, Pol-IV and Pol-V play major roles in RNA-mediated silencing and a single second-largest subunit is shared between Pol-IV and Pol-V. Maize encodes three second-largest subunit genes: all three genes potentially encode full length proteins with highly conserved polymerase domains, and each are expressed in multiple overlapping tissues. The isolation of a recessive paramutation mutation in mop2 from a forward genetic screen suggests limited or no functional redundancy of these three genes. Potential alternative Pol-IV/Pol-V-like complexes could provide maize with a greater diversification of RNA-mediated transcriptional silencing machinery relative to Arabidopsis. Mop2-1 disrupts paramutation at multiple loci when heterozygous, whereas previously silenced alleles are only up-regulated when Mop2-1 is homozygous. The dramatic reduction in b1 tandem repeat siRNAs, but no disruption of silencing in Mop2-1 heterozygotes, suggests the major role for tandem repeat siRNAs is not to maintain silencing. Instead, we hypothesize the tandem repeat siRNAs mediate the establishment of the heritable silent state-a process fully disrupted in Mop2-1 heterozygotes. The dominant Mop2-1 mutation, which has a single nucleotide change in a domain highly conserved among all polymerases (E. coli to eukaryotes), disrupts both siRNA biogenesis (Pol-IV-like) and potentially processes downstream (Pol-V-like). These results suggest either the wild-type protein is a subunit in both complexes or the dominant mutant protein disrupts both complexes. Dominant mutations in the same domain in E. coli RNA polymerase suggest a model for Mop2-1 dominance: complexes containing Mop2-1 subunits are non-functional and compete with wild-type complexes.
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Affiliation(s)
- Lyudmila Sidorenko
- Department of Plant Sciences, University of Arizona, Tucson, Arizona, United States of America
| | - Jane E. Dorweiler
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, United States of America
| | - A. Mark Cigan
- Pioneer Hi-Bred International, Johnston, Iowa, United States of America
| | - Mario Arteaga-Vazquez
- Department of Plant Sciences, University of Arizona, Tucson, Arizona, United States of America
| | - Meenal Vyas
- Department of Plant Sciences, University of Arizona, Tucson, Arizona, United States of America
| | - Jerry Kermicle
- Genetics Department, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Diane Jurcin
- Department of Plant Sciences, University of Arizona, Tucson, Arizona, United States of America
| | - Jan Brzeski
- Department of Plant Sciences, University of Arizona, Tucson, Arizona, United States of America
| | - Yu Cai
- Department of Plant Sciences, University of Arizona, Tucson, Arizona, United States of America
| | - Vicki L. Chandler
- Department of Plant Sciences, University of Arizona, Tucson, Arizona, United States of America
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46
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Hale CJ, Erhard KF, Lisch D, Hollick JB. Production and processing of siRNA precursor transcripts from the highly repetitive maize genome. PLoS Genet 2009; 5:e1000598. [PMID: 19680464 PMCID: PMC2725412 DOI: 10.1371/journal.pgen.1000598] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2009] [Accepted: 07/14/2009] [Indexed: 11/18/2022] Open
Abstract
Mutations affecting the maintenance of heritable epigenetic states in maize identify multiple RNA–directed DNA methylation (RdDM) factors including RMR1, a novel member of a plant-specific clade of Snf2-related proteins. Here we show that RMR1 is necessary for the accumulation of a majority of 24 nt small RNAs, including those derived from Long-Terminal Repeat (LTR) retrotransposons, the most common repetitive feature in the maize genome. A genetic analysis of DNA transposon repression indicates that RMR1 acts upstream of the RNA–dependent RNA polymerase, RDR2 (MOP1). Surprisingly, we show that non-polyadenylated transcripts from a sampling of LTR retrotransposons are lost in both rmr1 and rdr2 mutants. In contrast, plants deficient for RNA Polymerase IV (Pol IV) function show an increase in polyadenylated LTR RNA transcripts. These findings support a model in which Pol IV functions independently of the small RNA accumulation facilitated by RMR1 and RDR2 and support that a loss of Pol IV leads to RNA Polymerase II–based transcription. Additionally, the lack of changes in general genome homeostasis in rmr1 mutants, despite the global loss of 24 nt small RNAs, challenges the perceived roles of siRNAs in maintaining functional heterochromatin in the genomes of outcrossing grass species. Most eukaryotic genomes are divided into two functional classes of regulation: the euchromatic and the heterochromatic. Heterochromatic regions, often composed of potentially deleterious transposons and retrotransposons, are typically viewed as “silent” or not transcribed. Paradoxically, evidence from multiple organisms indicates that heterochromatic regions must be transcribed to maintain a heterochromatic character. In plants, specialized RNA polymerase complexes are thought to specifically process repetitive regions of the genome into small RNA molecules that facilitate maintenance of a heterochromatic environment. We investigated the role of this specialized polymerase pathway in maintaining maize genome homeostasis with particular focus on RMR1, a novel protein related to a family of DNA repair proteins, whose function in modifying repetitive regions of the genome is unknown. We find most small RNA generation is dependent on RMR1, which appears to function downstream of the specialized polymerase, RNA polymerase IV. However, we provide evidence that the function of RNA polymerase IV is not disrupted by the absence of small RNA generation. Our results suggest the division of the plant genome into euchromatin and heterochromatin is maintained by template competition between the specialized plant polymerases and canonical RNA polymerase II, and not by the subsequent generation of small RNA molecules.
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Affiliation(s)
- Christopher J. Hale
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Karl F. Erhard
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Damon Lisch
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Jay B. Hollick
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
- * E-mail:
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47
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Rensing L, Koch M, Becker A. A comparative approach to the principal mechanisms of different memory systems. Naturwissenschaften 2009; 96:1373-84. [PMID: 19680619 DOI: 10.1007/s00114-009-0591-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2009] [Revised: 07/07/2009] [Accepted: 07/12/2009] [Indexed: 02/07/2023]
Abstract
The term "memory" applies not only to the preservation of information in neuronal and immune systems but also to phenomena observed for example in plants, single cells, and RNA viruses. We here compare the different forms of information storage with respect to possible common features. The latter may be characterized by (1) selection of pre-existing information, (2) activation of memory systems often including transcriptional, and translational, as well as epigenetic and genetic mechanisms, (3) subsequent consolidation of the activated state in a latent form (standby mode), and (4) reactivation of the latent state of memory systems when the organism is exposed to the same (or conditioned) signal or to previous selective constraints. These features apparently also exist in the "evolutionary memory," i.e., in evolving populations which have highly variable mutant spectra.
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Affiliation(s)
- Ludger Rensing
- Department of Biology, University of Bremen, 28334, Bremen, Germany.
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48
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Elling AA, Deng XW. Next-generation sequencing reveals complex relationships between the epigenome and transcriptome in maize. PLANT SIGNALING & BEHAVIOR 2009; 4:760-762. [PMID: 19820310 PMCID: PMC2801393 DOI: 10.4161/psb.4.8.9174] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Accepted: 06/03/2009] [Indexed: 05/22/2023]
Abstract
Epigenetic modifications and small RNAs play an important role in gene regulation. Here, we discuss results of our Solexa/Illumina 1G sequencing-based survey of DNA methylation, activating and repressive histone modifications, small RNAs and mRNA in the maize genome. We analyze tissue-specific epigenetic patterns, discuss antagonistic relationships between repressive epigenetic marks and highlight synergistic relationships between activating histone modifications. We discuss our observation that small RNAs show a tissue-specific distribution in maize. Whereas 24-nucleotide long small interfering RNAs (siRNAs) accumulated preferentially in shoots, 21-nucleotide long micro RNAs (miRNAs) were the most abundant group in roots, which follows the transcript level of mop1. Furthermore, we discuss the possibility that a novel class of 22-nucleotide siRNAs might originate from long double-stranded RNAs in an RNA-dependent RNA polymerase (RdRP)-independent manner. This supports the intriguing possibility that maize possesses at least two distinct pathways to generate siRNAs, one of which relies on RdRP and a second one that might be RdRP-independent.
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Affiliation(s)
- Axel A Elling
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
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49
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Johnson C, Kasprzewska A, Tennessen K, Fernandes J, Nan GL, Walbot V, Sundaresan V, Vance V, Bowman LH. Clusters and superclusters of phased small RNAs in the developing inflorescence of rice. Genome Res 2009; 19:1429-40. [PMID: 19584097 DOI: 10.1101/gr.089854.108] [Citation(s) in RCA: 217] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
To address the role of small regulatory RNAs in rice development, we generated a large data set of small RNAs from mature leaves and developing roots, shoots, and inflorescences. Using a spatial clustering algorithm, we identified 36,780 genomic groups of small RNAs. Most consisted of 24-nt RNAs that are expressed in all four tissues and enriched in repeat regions of the genome; 1029 clusters were composed primarily of 21-nt small RNAs and, strikingly, 831 of these contained phased RNAs and were preferentially expressed in developing inflorescences. Thirty-eight of the 24-mer clusters were also phased and preferentially expressed in inflorescences. The phased 21-mer clusters derive from nonprotein coding, nonrepeat regions of the genome and are grouped together into superclusters containing 10-46 clusters. The majority of these 21-mer clusters (705/831) are flanked by a degenerate 22-nt motif that is offset by 12 nt from the main phase of the cluster. Small RNAs complementary to these flanking 22-nt motifs define a new miRNA family, which is conserved in maize and expressed in developing reproductive tissues in both plants. These results suggest that the biogenesis of phased inflorescence RNAs resembles that of tasiRNAs and raise the possibility that these novel small RNAs function in early reproductive development in rice and other monocots.
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Affiliation(s)
- Cameron Johnson
- Section of Plant Biology, College of Biological Sciences, University of California Davis, Davis, California 95616, USA
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50
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Stam M. Paramutation: a heritable change in gene expression by allelic interactions in trans. MOLECULAR PLANT 2009; 2:578-588. [PMID: 19825640 DOI: 10.1093/mp/ssp020] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Epigenetic gene regulation involves the stable propagation of gene activity states through mitotic, and sometimes even meiotic, cell divisions without changes in DNA sequence. Paramutation is an epigenetic phenomenon involving changes in gene expression that are stably transmitted through mitosis as well as meiosis. These heritable changes are mediated by in trans interactions between homologous DNA sequences on different chromosomes. During these in trans interactions, epigenetic information is transferred from one allele of a gene to another allele of the same gene, resulting in a change in gene expression. Although paramutation was initially discovered in plants, it has recently been observed in mammals as well, suggesting that the mechanisms underlying paramutation might be evolutionarily conserved. Recent findings point to a crucial role for small RNAs in the paramutation process. In mice, small RNAs appear sufficient to induce paramutation, whereas in maize, it seems not to be the only player in the process. In this review, potential mechanisms are discussed in relation to the various paramutation phenomena.
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Affiliation(s)
- Maike Stam
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
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