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Ando A, Kirkbride RC, Qiao H, Chen ZJ. Endosperm and Maternal-specific expression of EIN2 in the endosperm affects endosperm cellularization and seed size in Arabidopsis. Genetics 2023; 223:iyac161. [PMID: 36282525 PMCID: PMC9910398 DOI: 10.1093/genetics/iyac161] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 10/05/2022] [Indexed: 11/13/2022] Open
Abstract
Seed size is related to plant evolution and crop yield and is affected by genetic mutations, imprinting, and genome dosage. Imprinting is a widespread epigenetic phenomenon in mammals and flowering plants. ETHYLENE INSENSITIVE2 (EIN2) encodes a membrane protein that links the ethylene perception to transcriptional regulation. Interestingly, during seed development EIN2 is maternally expressed in Arabidopsis and maize, but the role of EIN2 in seed development is unknown. Here, we show that EIN2 is expressed specifically in the endosperm, and the maternal-specific EIN2 expression affects temporal regulation of endosperm cellularization. As a result, seed size increases in the genetic cross using the ein2 mutant as the maternal parent or in the ein2 mutant. The maternal-specific expression of EIN2 in the endosperm is controlled by DNA methylation but not by H3K27me3 or by ethylene and several ethylene pathway genes tested. RNA-seq analysis in the endosperm isolated by laser-capture microdissection show upregulation of many endosperm-expressed genes such as AGAMOUS-LIKEs (AGLs) in the ein2 mutant or when the maternal EIN2 allele is not expressed. EIN2 does not interact with DNA and may act through ETHYLENE INSENSITIVE3 (EIN3), a DNA-binding protein present in sporophytic tissues, to activate target genes like AGLs, which in turn mediate temporal regulation of endosperm cellularization and seed size. These results provide mechanistic insights into endosperm and maternal-specific expression of EIN2 on endosperm cellularization and seed development, which could help improve seed production in plants and crops.
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Affiliation(s)
- Atsumi Ando
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ryan C Kirkbride
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Hong Qiao
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Z Jeffrey Chen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
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2
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Duszynska D, Vilhjalmsson B, Castillo Bravo R, Swamidatta S, Juenger TE, Donoghue MTA, Comte A, Nordborg M, Sharbel TF, Brychkova G, McKeown PC, Spillane C. Transgenerational effects of inter-ploidy cross direction on reproduction and F2 seed development of Arabidopsis thaliana F1 hybrid triploids. PLANT REPRODUCTION 2019; 32:275-289. [PMID: 30903284 PMCID: PMC6675909 DOI: 10.1007/s00497-019-00369-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 03/05/2019] [Indexed: 05/15/2023]
Abstract
KEY MESSAGE Reproduction in triploid plants is important for understanding polyploid population dynamics. We show that genetically identical reciprocal F1 hybrid triploids can display transgenerational epigenetic effects on viable F2 seed development. The success or failure of reproductive outcomes from intra-species crosses between plants of different ploidy levels is an important factor in flowering plant evolution and crop breeding. However, the effects of inter-ploidy cross directions on F1 hybrid offspring fitness are poorly understood. In Arabidopsis thaliana, hybridization between diploid and tetraploid plants can produce viable F1 triploid plants. When selfed, such F1 triploid plants act as aneuploid gamete production "machines" where the vast majority of gametes generated are aneuploid which, following sexual reproduction, can generate aneuploid swarms of F2 progeny (Henry et al. 2009). There is potential for some aneuploids to cause gametophyte abortion and/or F2 seed abortion (Henry et al. 2009). In this study, we analyse the reproductive success of 178 self-fertilized inter-accession F1 hybrid triploids and demonstrate that the proportions of aborted or normally developed F2 seeds from the selfed F1 triploids depend upon a combination of natural variation and cross direction, with strong interaction between these factors. Single-seed ploidy analysis indicates that the embryonic DNA content of phenotypically normal F2 seeds is highly variable and that these DNA content distributions are also affected by genotype and cross direction. Notably, genetically identical reciprocal F1 hybrid triploids display grandparent-of-origin effects on F2 seed set, and hence on the ability to tolerate aneuploidy in F2 seed. There are differences between reciprocal F1 hybrid triploids regarding the proportions of normal and aborted F2 seeds generated, and also for the DNA content averages and distributions of the F2 seeds. To identify genetic variation for tolerance of aneuploidy in F2 seeds, we carried out a GWAS which identified two SNPs, termed MOT and POT, which represent candidate loci for genetic control of the proportion of normal F2 seeds obtained from selfed F1 triploids. Parental and grandparental effects on F2 seeds obtained from selfed F1 triploids can have transgenerational consequences for asymmetric gene flow, emergence of novel genotypes in polyploid populations, and for control of F2 seed set in triploid crops.
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Affiliation(s)
- Dorota Duszynska
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland, Galway, H91 REW4 Ireland
| | - Bjarni Vilhjalmsson
- Gregor Mendel Institute of Molecular Plant Biology, Vienna, Austria
- Present Address: Bioinformatics Research Centre, Aarhus University, Århus, Denmark
| | - Rosa Castillo Bravo
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland, Galway, H91 REW4 Ireland
| | - Sandesh Swamidatta
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland, Galway, H91 REW4 Ireland
- Present Address: Department of Biology, Centre for Novel Agricultural Products (CNAP), University of York, York, UK
| | - Thomas E. Juenger
- Section of Integrative Biology and Institute for Cellular and Molecular Biology, University of Texas, Austin, USA
| | - Mark T. A. Donoghue
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland, Galway, H91 REW4 Ireland
- Present Address: Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Aurélie Comte
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland, Galway, H91 REW4 Ireland
| | - Magnus Nordborg
- Gregor Mendel Institute of Molecular Plant Biology, Vienna, Austria
| | - Timothy F. Sharbel
- Apomixis Research Group, Department of Cytogenetics and Genome Analysis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- Seed and Developmental Biology Program, Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4J8 Canada
| | - Galina Brychkova
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland, Galway, H91 REW4 Ireland
| | - Peter C. McKeown
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland, Galway, H91 REW4 Ireland
| | - Charles Spillane
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland, Galway, H91 REW4 Ireland
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3
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Tuteja R, McKeown PC, Ryan P, Morgan CC, Donoghue MTA, Downing T, O'Connell MJ, Spillane C. Paternally Expressed Imprinted Genes under Positive Darwinian Selection in Arabidopsis thaliana. Mol Biol Evol 2019; 36:1239-1253. [PMID: 30913563 PMCID: PMC6526901 DOI: 10.1093/molbev/msz063] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Genomic imprinting is an epigenetic phenomenon where autosomal genes display uniparental expression depending on whether they are maternally or paternally inherited. Genomic imprinting can arise from parental conflicts over resource allocation to the offspring, which could drive imprinted loci to evolve by positive selection. We investigate whether positive selection is associated with genomic imprinting in the inbreeding species Arabidopsis thaliana. Our analysis of 140 genes regulated by genomic imprinting in the A. thaliana seed endosperm demonstrates they are evolving more rapidly than expected. To investigate whether positive selection drives this evolutionary acceleration, we identified orthologs of each imprinted gene across 34 plant species and elucidated their evolutionary trajectories. Increased positive selection was sought by comparing its incidence among imprinted genes with nonimprinted controls. Strikingly, we find a statistically significant enrichment of imprinted paternally expressed genes (iPEGs) evolving under positive selection, 50.6% of the total, but no such enrichment for positive selection among imprinted maternally expressed genes (iMEGs). This suggests that maternally- and paternally expressed imprinted genes are subject to different selective pressures. Almost all positively selected amino acids were fixed across 80 sequenced A. thaliana accessions, suggestive of selective sweeps in the A. thaliana lineage. The imprinted genes under positive selection are involved in processes important for seed development including auxin biosynthesis and epigenetic regulation. Our findings support a genomic imprinting model for plants where positive selection can affect paternally expressed genes due to continued conflict with maternal sporophyte tissues, even when parental conflict is reduced in predominantly inbreeding species.
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Affiliation(s)
- Reetu Tuteja
- Genetics & Biotechnology Lab, Plant & AgriBiosciences Research Centre (PABC), School of Natural Sciences, Ryan Institute, National University of Ireland Galway, Galway, Ireland.,Center for Genomics and Systems Biology, New York University, New York, NY
| | - Peter C McKeown
- Genetics & Biotechnology Lab, Plant & AgriBiosciences Research Centre (PABC), School of Natural Sciences, Ryan Institute, National University of Ireland Galway, Galway, Ireland
| | - Pat Ryan
- Genetics & Biotechnology Lab, Plant & AgriBiosciences Research Centre (PABC), School of Natural Sciences, Ryan Institute, National University of Ireland Galway, Galway, Ireland
| | - Claire C Morgan
- School of Biotechnology, Faculty of Biological Sciences, Dublin City University, Dublin, Ireland.,Division of Diabetes, Endocrinology and Metabolism, Imperial College London, London, United Kingdom
| | - Mark T A Donoghue
- Genetics & Biotechnology Lab, Plant & AgriBiosciences Research Centre (PABC), School of Natural Sciences, Ryan Institute, National University of Ireland Galway, Galway, Ireland.,Memorial Sloan Kettering Cancer Center, New York, NY
| | - Tim Downing
- School of Biotechnology, Faculty of Biological Sciences, Dublin City University, Dublin, Ireland
| | - Mary J O'Connell
- Computational and Molecular Evolutionary Biology Research Group, School of Biology, Faculty of Biological Sciences, The University of Leeds, Leeds, United Kingdom.,Computational and Molecular Evolutionary Biology Group, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Charles Spillane
- Genetics & Biotechnology Lab, Plant & AgriBiosciences Research Centre (PABC), School of Natural Sciences, Ryan Institute, National University of Ireland Galway, Galway, Ireland
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4
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Consistent Reanalysis of Genome-wide Imprinting Studies in Plants Using Generalized Linear Models Increases Concordance across Datasets. Sci Rep 2019; 9:1320. [PMID: 30718537 PMCID: PMC6362150 DOI: 10.1038/s41598-018-36768-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 11/27/2018] [Indexed: 11/30/2022] Open
Abstract
Genomic imprinting leads to different expression levels of maternally and paternally derived alleles. Over the last years, major progress has been made in identifying novel imprinted candidate genes in plants, owing to affordable next-generation sequencing technologies. However, reports on sequencing the transcriptome of hybrid F1 seed tissues strongly disagree about how many and which genes are imprinted. This raises questions about the relative impact of biological, environmental, technical, and analytic differences or biases. Here, we adopt a statistical approach, frequently used in RNA-seq data analysis, which properly models count overdispersion and considers replicate information of reciprocal crosses. We show that our statistical pipeline outperforms other methods in identifying imprinted genes in simulated and real data. Accordingly, reanalysis of genome-wide imprinting studies in Arabidopsis and maize shows that, at least for Arabidopsis, an increased agreement across datasets could be observed. For maize, however, consistent reanalysis did not yield a larger overlap between the datasets. This suggests that the discrepancy across publications might be partially due to different analysis pipelines but that technical, biological, and environmental factors underlie much of the discrepancy between datasets. Finally, we show that the set of genes that can be characterized regarding allelic bias by all studies with minimal confidence is small (~8,000/27,416 genes for Arabidopsis and ~12,000/39,469 for maize). In conclusion, we propose to use biologically replicated reciprocal crosses, high sequence coverage, and a generalized linear model approach to identify differentially expressed alleles in developing seeds.
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Blunk I, Mayer M, Hamann H, Reinsch N. Scanning the genomes of parents for imprinted loci acting in their un-genotyped progeny. Sci Rep 2019; 9:654. [PMID: 30679576 PMCID: PMC6345920 DOI: 10.1038/s41598-018-36939-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 11/23/2018] [Indexed: 11/09/2022] Open
Abstract
Depending on their parental origin, alleles at imprinted loci are fully or partially inactivated through epigenetic mechanisms. Their effects contribute to the broader class of parent-of-origin effects. Standard methodology for mapping imprinted quantitative trait loci in association studies requires phenotypes and parental origin of marker alleles (ordered genotypes) to be simultaneously known for each individual. As such, many phenotypes are known from un-genotyped offspring in ongoing breeding programmes (e.g. meat animals), while their parents have known genotypes but no phenotypes. By theoretical considerations and simulations, we showed that the limitations of standard methodology can be overcome in such situations. This is achieved by first estimating parent-of-origin effects, which then serve as dependent variables in association analyses, in which only imprinted loci give a signal. As a theoretical foundation, the regression of parent-of-origin effects on the number of B-alleles at a biallelic locus — representing the un-ordered genotype — equals the imprinting effect. The applicability to real data was demonstrated for about 1800 genotyped Brown Swiss bulls and their un-genotyped fattening progeny. Thus, this approach unlocks vast data resources in various species for imprinting analyses and offers valuable clues as to what extent imprinted loci contribute to genetic variability.
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Affiliation(s)
- Inga Blunk
- Faculty of Agricultural and Environmental Sciences, University of Rostock, Justus-von-Liebig-Weg 6, 18059, Rostock, Germany.,Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Manfred Mayer
- Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Henning Hamann
- State-Office for Geo-Information and Rural Development, Geodata-Center, Stuttgarter Straße 161, 70806, Kornwestheim, Germany
| | - Norbert Reinsch
- Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany.
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6
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DNA demethylase ROS1 negatively regulates the imprinting of DOGL4 and seed dormancy in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2018; 115:E9962-E9970. [PMID: 30266793 DOI: 10.1073/pnas.1812847115] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Genomic imprinting is a form of epigenetic regulation resulting in differential gene expression that reflects the parent of origin. In plants, imprinted gene expression predominantly occurs in the seed endosperm. Maternal-specific DNA demethylation by the DNA demethylase DME frequently underlies genomic imprinting in endosperm. Whether other more ubiquitously expressed DNA demethylases regulate imprinting is unknown. Here, we found that the DNA demethylase ROS1 regulates the imprinting of DOGL4 DOGL4 is expressed from the maternal allele in endosperm and displays preferential methylation and suppression of the paternal allele. We found that ROS1 negatively regulates imprinting by demethylating the paternal allele, preventing its hypermethylation and complete silencing. Furthermore, we found that DOGL4 negatively affects seed dormancy and response to the phytohormone abscisic acid and that ROS1 controls these processes by regulating DOGL4 Our results reveal roles for ROS1 in mitigating imprinted gene expression and regulating seed dormancy.
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7
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Roth M, Florez-Rueda AM, Paris M, Städler T. Wild tomato endosperm transcriptomes reveal common roles of genomic imprinting in both nuclear and cellular endosperm. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:1084-1101. [PMID: 29953688 DOI: 10.1111/tpj.14012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 06/01/2018] [Accepted: 06/20/2018] [Indexed: 05/06/2023]
Abstract
Genomic imprinting is a conspicuous feature of the endosperm, a triploid tissue nurturing the embryo and synchronizing angiosperm seed development. An unknown subset of imprinted genes (IGs) is critical for successful seed development and should have highly conserved functions. Recent genome-wide studies have found limited conservation of IGs among distantly related species, but there is a paucity of data from closely related lineages. Moreover, most studies focused on model plants with nuclear endosperm development, and comparisons with properties of IGs in cellular-type endosperm development are lacking. Using laser-assisted microdissection, we characterized parent-specific expression in the cellular endosperm of three wild tomato lineages (Solanum section Lycopersicon). We identified 1025 candidate IGs and 167 with putative homologs previously identified as imprinted in distantly related taxa with nuclear-type endosperm. Forty-two maternally expressed genes (MEGs) and 17 paternally expressed genes (PEGs) exhibited conserved imprinting status across all three lineages, but differences in power to assess imprinted expression imply that the actual degree of conservation might be higher than that directly estimated (20.7% for PEGs and 10.4% for MEGs). Regardless, the level of shared imprinting status was higher for PEGs than for MEGs, indicating dissimilar evolutionary trajectories. Expression-level data suggest distinct epigenetic modulation of MEGs and PEGs, and gene ontology analyses revealed MEGs and PEGs to be enriched for different functions. Importantly, our data provide evidence that MEGs and PEGs interact in modulating both gene expression and the endosperm cell cycle, and uncovered conserved cellular functions of IGs uniting taxa with cellular- and nuclear-type endosperm.
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Affiliation(s)
- Morgane Roth
- Plant Ecological Genetics, Institute of Integrative Biology & Zurich-Basel Plant Science Center, ETH Zurich, 8092, Zurich, Switzerland
| | - Ana M Florez-Rueda
- Plant Ecological Genetics, Institute of Integrative Biology & Zurich-Basel Plant Science Center, ETH Zurich, 8092, Zurich, Switzerland
| | - Margot Paris
- Plant Ecological Genetics, Institute of Integrative Biology & Zurich-Basel Plant Science Center, ETH Zurich, 8092, Zurich, Switzerland
| | - Thomas Städler
- Plant Ecological Genetics, Institute of Integrative Biology & Zurich-Basel Plant Science Center, ETH Zurich, 8092, Zurich, Switzerland
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8
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Corbin C, Drouet S, Markulin L, Auguin D, Lainé É, Davin LB, Cort JR, Lewis NG, Hano C. A genome-wide analysis of the flax (Linum usitatissimum L.) dirigent protein family: from gene identification and evolution to differential regulation. PLANT MOLECULAR BIOLOGY 2018; 97:73-101. [PMID: 29713868 DOI: 10.1007/s11103-018-0725-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 04/02/2018] [Indexed: 05/21/2023]
Abstract
Identification of DIR encoding genes in flax genome. Analysis of phylogeny, gene/protein structures and evolution. Identification of new conserved motifs linked to biochemical functions. Investigation of spatio-temporal gene expression and response to stress. Dirigent proteins (DIRs) were discovered during 8-8' lignan biosynthesis studies, through identification of stereoselective coupling to afford either (+)- or (-)-pinoresinols from E-coniferyl alcohol. DIRs are also involved or potentially involved in terpenoid, allyl/propenyl phenol lignan, pterocarpan and lignin biosynthesis. DIRs have very large multigene families in different vascular plants including flax, with most still of unknown function. DIR studies typically focus on a small subset of genes and identification of biochemical/physiological functions. Herein, a genome-wide analysis and characterization of the predicted flax DIR 44-membered multigene family was performed, this species being a rich natural grain source of 8-8' linked secoisolariciresinol-derived lignan oligomers. All predicted DIR sequences, including their promoters, were analyzed together with their public gene expression datasets. Expression patterns of selected DIRs were examined using qPCR, as well as through clustering analysis of DIR gene expression. These analyses further implicated roles for specific DIRs in (-)-pinoresinol formation in seed-coats, as well as (+)-pinoresinol in vegetative organs and/or specific responses to stress. Phylogeny and gene expression analysis segregated flax DIRs into six distinct clusters with new cluster-specific motifs identified. We propose that these findings can serve as a foundation to further systematically determine functions of DIRs, i.e. other than those already known in lignan biosynthesis in flax and other species. Given the differential expression profiles and inducibility of the flax DIR family, we provisionally propose that some DIR genes of unknown function could be involved in different aspects of secondary cell wall biosynthesis and plant defense.
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Affiliation(s)
- Cyrielle Corbin
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRA USC1328, Université d'Orléans, 28000, Chartres, France
- COSM'ACTIFS, CNRS GDR3711, 28000, Chartres, France
| | - Samantha Drouet
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRA USC1328, Université d'Orléans, 28000, Chartres, France
- COSM'ACTIFS, CNRS GDR3711, 28000, Chartres, France
| | - Lucija Markulin
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRA USC1328, Université d'Orléans, 28000, Chartres, France
- COSM'ACTIFS, CNRS GDR3711, 28000, Chartres, France
| | - Daniel Auguin
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRA USC1328, Université d'Orléans, 28000, Chartres, France
- COSM'ACTIFS, CNRS GDR3711, 28000, Chartres, France
| | - Éric Lainé
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRA USC1328, Université d'Orléans, 28000, Chartres, France
- COSM'ACTIFS, CNRS GDR3711, 28000, Chartres, France
| | - Laurence B Davin
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164-6340, USA
| | - John R Cort
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Norman G Lewis
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164-6340, USA.
| | - Christophe Hano
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRA USC1328, Université d'Orléans, 28000, Chartres, France.
- COSM'ACTIFS, CNRS GDR3711, 28000, Chartres, France.
- Pôle Universitaire d'Eure et Loir, 21 Rue de Loigny la Bataille, 28000, Chartres, France.
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Zuma B, Dana MB, Wang D. Prolonged Expression of a Putative Invertase Inhibitor in Micropylar Endosperm Suppressed Embryo Growth in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2018; 9:61. [PMID: 29441087 PMCID: PMC5797552 DOI: 10.3389/fpls.2018.00061] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 01/12/2018] [Indexed: 05/21/2023]
Abstract
Proper seed development requires coordinated growth among the three genetically distinct components, the embryo, the endosperm, and the seed coat. In Arabidopsis, embryo growth rate accelerates after endosperm cellularization, which requires a chromatin-remodeling complex, the FIS2-Polycomb Repressive Complex 2 (PRC2). After cellularization, the endosperm ceases to grow and is eventually absorbed by the embryo. This sequential growth pattern displayed by the endosperm and the embryo suggests a possibility that the supply of sugar might be shifted from the endosperm to the embryo upon endosperm cellularization. Since invertases and invertase inhibitors play an important role in sugar partition, we investigated their expression pattern during early stages of seed development in Arabidopsis. Two putative invertase inhibitors (InvINH1 and InvINH2) were identified as being preferentially expressed in the micropylar endosperm that surrounds the embryo. After endosperm cellularization, InvINH1 and InvINH2 were down-regulated in a FIS2-dependent manner. We hypothesized that FIS2-PRC2 complex either directly or indirectly represses InvINH1 and InvINH2 to increase invertase activity around the embryo, making more hexose available to support the accelerated embryo growth after endosperm cellularization. In support of our hypothesis, embryo growth was delayed in transgenic lines that ectopically expressed InvINH1 in the cellularized endosperm. Our data suggested a novel mechanism for the FIS2-PRC2 complex to control embryo growth rate via the regulation of invertase activity in the endosperm.
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10
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Fort A, Tuteja R, Braud M, McKeown PC, Spillane C. Parental-genome dosage effects on the transcriptome of F1 hybrid triploid embryos of Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:1044-1058. [PMID: 29024088 DOI: 10.1111/tpj.13740] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 09/07/2017] [Accepted: 09/29/2017] [Indexed: 05/27/2023]
Abstract
Genomic imprinting in the seed endosperm could be due to unequal parental-genome contribution effects in triploid endosperm tissue that trigger parent-of-origin specific activation and/or silencing of loci prone to genomic imprinting. To determine whether genomic imprinting is triggered by unequal parental-genome contribution effects, we generated a whole-genome transcriptome dataset of F1 hybrid triploid embryos (as mimics of F1 hybrid triploid endosperm). For the vast majority of genes, the parental contributions to their expression levels in the F1 triploid hybrid embryos follow a biallelic and linear expression pattern. While allele-specific expression (ASE) bias was detected, such effects were predominantly parent-of-origin independent. We demonstrate that genomic imprinting is largely absent from F1 triploid embryos, strongly suggesting that neither triploidy nor unequal parental-genome contribution are key triggers of genomic imprinting in plants. However, extensive parental-genome dosage effects on gene expression were observed between the reciprocal F1 hybrid embryos, particularly for genes involved in defence response and nutrient reservoir activity, potentially leading to the seed size differences between reciprocal triploids. We further determined that unequal parental-genome contribution in F1 triploids can lead to overexpression effects that are parent-of-origin dependent, and which are not observed in diploid or tetraploid embryos in which the parental-genome dosage is balanced. Overall, our study demonstrates that neither triploidy nor unequal parental-genome contribution is sufficient to trigger imprinting in plant tissues, suggesting that genomic imprinting is an intrinsic and unique feature of the triploid seed endosperm.
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Affiliation(s)
- Antoine Fort
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - Reetu Tuteja
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - Martin Braud
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - Peter C McKeown
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - Charles Spillane
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
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11
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Carlson CH, Choi Y, Chan AP, Serapiglia MJ, Town CD, Smart LB. Dominance and Sexual Dimorphism Pervade the Salix purpurea L. Transcriptome. Genome Biol Evol 2017; 9:2377-2394. [PMID: 28957462 PMCID: PMC5622329 DOI: 10.1093/gbe/evx174] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2017] [Indexed: 12/24/2022] Open
Abstract
The heritability of gene expression is critical in understanding heterosis and is dependent on allele-specific regulation by local and remote factors in the genome. We used RNA-Seq to test whether variation in gene expression among F1 and F2 intraspecific Salix purpurea progeny is attributable to cis- and trans-regulatory divergence. We assessed the mode of inheritance based on gene expression levels and allele-specific expression for F1 and F2 intraspecific progeny in two distinct tissue types: shoot tip and stem internode. In addition, we explored sexually dimorphic patterns of inheritance and regulatory divergence among F1 progeny individuals. We show that in S. purpurea intraspecific crosses, gene expression inheritance largely exhibits a maternal dominant pattern, regardless of tissue type or pedigree. A significantly greater number of cis- and trans-regulated genes coincided with upregulation of the maternal parent allele in the progeny, irrespective of the magnitude, whereas the paternal allele was higher expressed for genes showing cis × trans or compensatory regulation. Importantly, consistent with previous genetic mapping results for sex in shrub willow, we have delimited sex-biased gene expression to a 2 Mb pericentromeric region on S. purpurea chr15 and further refined the sex determination region. Altogether, our results offer insight into the inheritance of gene expression in S. purpurea as well as evidence of sexually dimorphic expression which may have contributed to the evolution of dioecy in Salix.
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Affiliation(s)
- Craig H. Carlson
- Horticulture Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, New York 14456 USA
| | - Yongwook Choi
- J. Craig Venter Institute, Rockville, Maryland 20850 USA
| | - Agnes P. Chan
- J. Craig Venter Institute, Rockville, Maryland 20850 USA
| | - Michelle J. Serapiglia
- Horticulture Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, New York 14456 USA
| | | | - Lawrence B. Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, New York 14456 USA
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12
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Święcicka M, Skowron W, Cieszyński P, Dąbrowska-Bronk J, Matuszkiewicz M, Filipecki M, Koter MD. The suppression of tomato defence response genes upon potato cyst nematode infection indicates a key regulatory role of miRNAs. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2017; 113:51-55. [PMID: 28182967 DOI: 10.1016/j.plaphy.2017.01.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 01/23/2017] [Accepted: 01/27/2017] [Indexed: 05/20/2023]
Abstract
Potato cyst nematode Globodera rostochiensis is an obligate parasite of solanaceous plants, triggering metabolic and morphological changes in roots which may result in substantial crop yield losses. Previously, we used the cDNA-AFLP to study the transcriptional dynamics in nematode infected tomato roots. Now, we present the rescreening of already published, upregulated transcript-derived fragment dataset using the most current tomato transcriptome sequences. Our reanalysis allowed to add 54 novel genes to 135, already found as upregulated in tomato roots upon G. rostochiensis infection (in total - 189). We also created completely new catalogue of downregulated sequences leading to the discovery of 76 novel genes. Functional classification of candidates showed that the 'wound, stress and defence response' category was enriched in the downregulated genes. We confirmed the transcriptional dynamics of six genes by qRT-PCR. To place our results in a broader context, we compared the tomato data with Arabidopsis thaliana, revealing similar proportions of upregulated and downregulated genes as well as similar enrichment of defence related transcripts in the downregulated group. Since transcript suppression is quite common in plant-nematode interactions, we assessed the possibility of miRNA-mediated inverse correlation on several tomato sequences belonging to NB-LRR and receptor-like kinase families. The qRT-PCR of miRNAs and putative target transcripts showed an opposite expression pattern in 9 cases. These results together with in silico analyses of potential miRNA targeting to the full repertoire of tomato R-genes show that miRNA mediated gene suppression may be a key regulatory mechanism during nematode parasitism.
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Affiliation(s)
- Magdalena Święcicka
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-787, Warsaw, Poland
| | - Waldemar Skowron
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-787, Warsaw, Poland
| | - Piotr Cieszyński
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-787, Warsaw, Poland
| | - Joanna Dąbrowska-Bronk
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-787, Warsaw, Poland
| | - Mateusz Matuszkiewicz
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-787, Warsaw, Poland
| | - Marcin Filipecki
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-787, Warsaw, Poland
| | - Marek Daniel Koter
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-787, Warsaw, Poland.
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13
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Luo A, Zhao P, Zhang LY, Sun MX. Initiation of programmed cell death in the suspensor is predominantly regulated maternally in a tobacco hybrid. Sci Rep 2016; 6:29467. [PMID: 27432530 PMCID: PMC4949469 DOI: 10.1038/srep29467] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 06/20/2016] [Indexed: 11/16/2022] Open
Abstract
Maternal gene products deposited in the egg regulate early embryogenesis before activation of the embryonic genome in animals. While in higher plants, it is believed that genes of parental origin contribute to early embryogenesis. However, little is known regarding the particular processes in which genes of parental origin are involved during early embryogenesis. Previously, we found that the initiation of programmed cell death (PCD) in the suspensor of the embryo is regulated by the cystatin, NtCYS. Here, we confirmed that both parental transcripts contribute to PCD, but the relative expression level of the maternal NtCYS allele was much higher than that of the paternal allele in early embryos of tobacco interspecific hybrids. The expression level of the maternal NtCYS allele was decreased markedly, which was necessary for the initiation of PCD, while the paternal allele didn't change. Interestingly, the pattern of PCD in the hybrid suspensor and the morphology of the hybrid suspensor were similar to those of the maternal parent. Our results suggest that NtCYS-mediated PCD initiation in the hybrid suspensor is likely controlled in a maternal dominant manner. This finding represents an example of the involvement of parental transcripts in a specific developmental event during early embryogenesis.
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Affiliation(s)
- An Luo
- College of Life Science, State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China
- College of Life Science, Yangtze University, Jingzhou, 434023, China
| | - Peng Zhao
- College of Life Science, State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China
| | - Li-Yao Zhang
- College of Life Science, State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China
| | - Meng-Xiang Sun
- College of Life Science, State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China
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14
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Homoeologue expression insights into the basis of growth heterosis at the intersection of ploidy and hybridity in Cyprinidae. Sci Rep 2016; 6:27040. [PMID: 27265401 PMCID: PMC4893626 DOI: 10.1038/srep27040] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 05/12/2016] [Indexed: 11/09/2022] Open
Abstract
Hybridization and polyploidization are considered important driving forces that form new epigenetic regulations. To study the changing patterns of expression accompanying hybridization and polyploidization, we used RNA-seq and qRT-PCR to investigate global expression and homoeologue expression in diploid and tetraploid hybrids of Carassius auratus red var. (♀) (R) and Cyprinus carpio (♂) (C). By comparing the relative expression levels between the hybrids and their parents, we defined the expression level dominance (ELD) and homoeologue expression bias (HEB) in liver tissue. The results showed that polyploidization contributed to the conversion of homoeologue ELD. In addition, hybridization had more effect on the change in HEB than polyploidization, while polyploidization had more effect on the change of global gene expression than hybridization. Meanwhile, similar expression patterns were found in growth-related genes. The results suggested that hybridization and polyploidization result in differential degrees of maternal HEB in three tissues (liver, muscle and ovary) tested. The results of this study will increase our understanding of the underlying regulation mechanism of rapid growth in diploid hybrids and allotetraploids. The differential degrees of global expression and homoeologue expression contribute to growth heterosis in newly formed hybrids, ensuring the on-going success of allotetraploid speciation.
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15
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Videvall E, Sletvold N, Hagenblad J, Ågren J, Hansson B. Strong Maternal Effects on Gene Expression inArabidopsis lyrataHybrids. Mol Biol Evol 2015; 33:984-94. [DOI: 10.1093/molbev/msv342] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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16
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García-Aguilar M, Gillmor CS. Zygotic genome activation and imprinting: parent-of-origin gene regulation in plant embryogenesis. CURRENT OPINION IN PLANT BIOLOGY 2015; 27:29-35. [PMID: 26051360 DOI: 10.1016/j.pbi.2015.05.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 05/15/2015] [Accepted: 05/18/2015] [Indexed: 05/05/2023]
Abstract
Parent-of-origin dependent gene expression refers to differential activity of alleles inherited from the egg and sperm. In plants, zygotic genome activation (ZGA) and gene imprinting are two examples of this phenomenon, both of which occur during seed development. As its name implies, ZGA is a genome-wide process that occurs in embryos during the first few days after fertilization. Evidence exists that maternal alleles initially predominate during ZGA, although most genes also show some paternal activity. By contrast, imprinting can be defined as a bias in gene expression that lasts beyond the first few days of seed development. Hundreds of imprinted genes have been discovered in the endosperm, and a few have been described in the embryo. This review discusses recent advances in our understanding of the phenomena and mechanisms of ZGA and imprinting in seeds, with an emphasis on embryo development. Important unanswered questions and areas for future research are highlighted.
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Affiliation(s)
- Marcelina García-Aguilar
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados (CINVESTAV), Irapuato, Guanajuato 36821, México
| | - C Stewart Gillmor
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados (CINVESTAV), Irapuato, Guanajuato 36821, México.
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17
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Jeong CW, Park GT, Yun H, Hsieh TF, Choi YD, Choi Y, Lee JS. Control of Paternally Expressed Imprinted UPWARD CURLY LEAF1, a Gene Encoding an F-Box Protein That Regulates CURLY LEAF Polycomb Protein, in the Arabidopsis Endosperm. PLoS One 2015; 10:e0117431. [PMID: 25689861 PMCID: PMC4331533 DOI: 10.1371/journal.pone.0117431] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 12/22/2014] [Indexed: 12/22/2022] Open
Abstract
Genomic imprinting, an epigenetic process in mammals and flowering plants, refers to the differential expression of alleles of the same genes in a parent-of-origin-specific manner. In Arabidopsis, imprinting occurs primarily in the endosperm, which nourishes the developing embryo. Recent high-throughput sequencing analyses revealed that more than 200 loci are imprinted in Arabidopsis; however, only a few of these imprinted genes and their imprinting mechanisms have been examined in detail. Whereas most imprinted loci characterized to date are maternally expressed imprinted genes (MEGs), PHERES1 (PHE1) and ADMETOS (ADM) are paternally expressed imprinted genes (PEGs). Here, we report that UPWARD CURLY LEAF1 (UCL1), a gene encoding an E3 ligase that degrades the CURLY LEAF (CLF) polycomb protein, is a PEG. After fertilization, paternally inherited UCL1 is expressed in the endosperm, but not in the embryo. The expression pattern of a β-glucuronidase (GUS) reporter gene driven by the UCL1 promoter suggests that the imprinting control region (ICR) of UCL1 is adjacent to a transposable element in the UCL1 5′-upstream region. Polycomb Repressive Complex 2 (PRC2) silences the maternal UCL1 allele in the central cell prior to fertilization and in the endosperm after fertilization. The UCL1 imprinting pattern was not affected in paternal PRC2 mutants. We found unexpectedly that the maternal UCL1 allele is reactivated in the endosperm of Arabidopsis lines with mutations in cytosine DNA METHYLTRANSFERASE 1 (MET1) or the DNA glycosylase DEMETER (DME), which antagonistically regulate CpG methylation of DNA. By contrast, maternal UCL1 silencing was not altered in mutants with defects in non-CpG methylation. Thus, silencing of the maternal UCL1 allele is regulated by both MET1 and DME as well as by PRC2, suggesting that divergent mechanisms for the regulation of PEGs evolved in Arabidopsis.
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Affiliation(s)
- Cheol Woong Jeong
- School of Biological Sciences, Seoul National University, Seoul, Korea
| | - Guen Tae Park
- School of Biological Sciences, Seoul National University, Seoul, Korea
| | - Hyein Yun
- School of Biological Sciences, Seoul National University, Seoul, Korea
| | - Tzung-Fu Hsieh
- Plants for Human Health Institute & Department of Plant and Microbial Biology, North Carolina State University, Kannapolis, North Carolina, United State of America
| | - Yang Do Choi
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Yeonhee Choi
- School of Biological Sciences, Seoul National University, Seoul, Korea
- * E-mail: (YC); (JSL)
| | - Jong Seob Lee
- School of Biological Sciences, Seoul National University, Seoul, Korea
- * E-mail: (YC); (JSL)
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18
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Chen L, Bernhardt A, Lee J, Hellmann H. Identification of Arabidopsis MYB56 as a novel substrate for CRL3(BPM) E3 ligases. MOLECULAR PLANT 2015; 8:242-50. [PMID: 25618823 DOI: 10.1016/j.molp.2014.10.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2014] [Revised: 10/15/2014] [Accepted: 10/16/2014] [Indexed: 05/18/2023]
Abstract
Controlled stability of proteins is a highly efficient mechanism to direct diverse processes in living cells. A key regulatory system for protein stability is given by the ubiquitin proteasome pathway, which uses E3 ligases to mark specific proteins for degradation. In this work, MYB56 is identified as a novel target of a CULLIN3 (CUL3)-based E3 ligase. Its stability depends on the presence of MATH-BTB/POZ (BPM) proteins, which function as substrate adaptors to the E3 ligase. Genetic studies have indicated that MYB56 is a negative regulator of flowering, while BPMs positively affect this developmental program. The interaction between BPMs and MYB56 occurs at the promoter of FLOWERING LOCUS T (FT), a key regulator in initiating flowering in Arabidopsis, and results in instability of MYB56. Overall the work establishes MYB transcription factors as substrates of BPM proteins, and provides novel information on components that participate in controlling flowering time in plants.
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Affiliation(s)
- Liyuan Chen
- School of Biological Sciences, Washington State University, Abelson 435, Pullman, WA 99164-4236, USA
| | - Anne Bernhardt
- School of Biological Sciences, Washington State University, Abelson 435, Pullman, WA 99164-4236, USA
| | - JooHyun Lee
- School of Biological Sciences, Washington State University, Abelson 435, Pullman, WA 99164-4236, USA
| | - Hanjo Hellmann
- School of Biological Sciences, Washington State University, Abelson 435, Pullman, WA 99164-4236, USA.
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19
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Screening for imprinted genes using high-resolution melting analysis of PCR amplicons. Methods Mol Biol 2014; 1112:71-83. [PMID: 24478008 DOI: 10.1007/978-1-62703-773-0_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
High-resolution melting (HRM) analysis is a technique that enables researchers to detect polymorphisms in DNA molecules based on different melting profiles and is becoming widely used as a method for detecting SNPs in genomic DNA. In this chapter, we describe how HRM analysis can be used to detect allelic imbalances typical of imprinted genes, where alleles are differentially expressed based on their parent of origin. This involves first producing hybrid seed using parental plants that have sufficient genetic differences to distinguish the parental origin of each allele of the candidate genes. RNA is then isolated from the hybrid seed and converted to cDNA. PCR amplicons are produced using primers designed to span a polymorphic sequence within the transcript of the candidate gene. By using a real-time PCR machine with HRM analysis capability, the PCR amplicons can be analyzed without further manipulations directly after amplification to detect instances of strong allelic imbalance and parent-of-origin-dependent expression.
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20
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Patten MM, Ross L, Curley JP, Queller DC, Bonduriansky R, Wolf JB. The evolution of genomic imprinting: theories, predictions and empirical tests. Heredity (Edinb) 2014; 113:119-28. [PMID: 24755983 PMCID: PMC4105453 DOI: 10.1038/hdy.2014.29] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 10/29/2013] [Indexed: 12/23/2022] Open
Abstract
The epigenetic phenomenon of genomic imprinting has motivated the development of numerous theories for its evolutionary origins and genomic distribution. In this review, we examine the three theories that have best withstood theoretical and empirical scrutiny. These are: Haig and colleagues' kinship theory; Day and Bonduriansky's sexual antagonism theory; and Wolf and Hager's maternal–offspring coadaptation theory. These theories have fundamentally different perspectives on the adaptive significance of imprinting. The kinship theory views imprinting as a mechanism to change gene dosage, with imprinting evolving because of the differential effect that gene dosage has on the fitness of matrilineal and patrilineal relatives. The sexual antagonism and maternal–offspring coadaptation theories view genomic imprinting as a mechanism to modify the resemblance of an individual to its two parents, with imprinting evolving to increase the probability of expressing the fitter of the two alleles at a locus. In an effort to stimulate further empirical work on the topic, we carefully detail the logic and assumptions of all three theories, clarify the specific predictions of each and suggest tests to discriminate between these alternative theories for why particular genes are imprinted.
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Affiliation(s)
- M M Patten
- Department of Biology, Georgetown University, Washington, DC, USA
| | - L Ross
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - J P Curley
- Psychology Department, Columbia University, New York, NY, USA
| | - D C Queller
- Department of Biology, Washington University, St Louis, MO, USA
| | - R Bonduriansky
- Evolution & Ecology Research Centre and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - J B Wolf
- Department of Biology and Biochemistry, University of Bath, Bath, UK
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McKeown PC, Spillane C. Landscaping plant epigenetics. Methods Mol Biol 2014; 1112:1-24. [PMID: 24478004 DOI: 10.1007/978-1-62703-773-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The understanding of epigenetic mechanisms is necessary for assessing the potential impacts of epigenetics on plant growth, development and reproduction, and ultimately for the response of these factors to evolutionary pressures and crop breeding programs. This volume highlights the latest in laboratory and bioinformatic techniques used for the investigation of epigenetic phenomena in plants. Such techniques now allow genome-wide analyses of epigenetic regulation and help to advance our understanding of how epigenetic regulatory mechanisms affect cellular and genome function. To set the scene, we begin with a short background of how the field of epigenetics has evolved, with a particular focus on plant epigenetics. We consider what has historically been understood by the term "epigenetics" before turning to the advances in biochemistry, molecular biology, and genetics which have led to current-day definitions of the term. Following this, we pay attention to key discoveries in the field of epigenetics that have emerged from the study of unusual and enigmatic phenomena in plants. Many of these phenomena have involved cases of non-Mendelian inheritance and have often been dismissed as mere curiosities prior to the elucidation of their molecular mechanisms. In the penultimate section, consideration is given to how advances in molecular techniques are opening the doors to a more comprehensive understanding of epigenetic phenomena in plants. We conclude by assessing some opportunities, challenges, and techniques for epigenetic research in both model and non-model plants, in particular for advancing understanding of the regulation of genome function by epigenetic mechanisms.
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Affiliation(s)
- Peter C McKeown
- Genetics & Biotechnology Lab, Plant & Agribiosciences Centre (PABC), School of Natural Sciences, National University of Ireland, Galway (NUI Galway), Ireland
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McKeown PC, Fort A, Spillane C. Analysis of genomic imprinting by quantitative allele-specific expression by Pyrosequencing(®). Methods Mol Biol 2014; 1112:85-104. [PMID: 24478009 DOI: 10.1007/978-1-62703-773-0_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Genomic imprinting is a parent-of-origin phenomenon whereby gene expression is restricted to the allele inherited from either the maternal or paternal parent. It has been described from flowering plants and eutherian mammals and may have evolved due to parental conflicts over resource allocation. In mammals, imprinted genes are responsible for ensuring correct rates of embryo development and for preventing parthenogenesis. The molecular basis of imprinting depends upon the presence of differential epigenetic marks on the alleles inherited from each parent, although in plants the exact mechanisms that control imprinting are still unclear in many cases. Recent studies have identified large numbers of candidate imprinted genes from Arabidopsis thaliana and other plants (see Chap. 7 by Köhler and colleagues elsewhere in this volume) providing the tools for more thorough investigation into how imprinted gene networks (IGNs) are regulated. Analysis of genomic imprinting in animals has revealed important information on how IGNs are regulated during development, which often involves intermediate levels of imprinting. In some instances, small but significant changes in the degree of parental bias in gene expression have been linked to developmental traits, livestock phenotypes, and human disease. As some of the imprinted genes recently reported from plants show differential rather than complete (binary) imprinting, there is a clear need for tools that can quantify the degree of allelic expression bias occurring at a transcribed locus. In this chapter, we describe the use of Quantification of Allele-Specific Expression by Pyrosequencing(®) (QUASEP) as a tool suitable for this challenge. We describe in detail the factors which ensure that a Pyrosequencing(®) assay will be suitable for giving robust QUASEP and the problems which may be encountered during the study of imprinted genes by Pyrosequencing(®), with particular reference to our work in A. thaliana and in cattle. We also discuss some considerations with respect to the statistical analysis of the resulting data. Finally, we provide a brief overview of the future possibility of adapting Pyrosequencing(®) for analyzing other aspects of imprinting including the analysis of methylated regions.
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Affiliation(s)
- Peter C McKeown
- Genetics & Biotechnology Lab, Plant & Agribiosciences Centre (PABC), School of Natural Sciences, National University of Ireland, Galway (NUI Galway), Ireland
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Genomic imprinting in the Arabidopsis embryo is partly regulated by PRC2. PLoS Genet 2013; 9:e1003862. [PMID: 24339783 PMCID: PMC3854695 DOI: 10.1371/journal.pgen.1003862] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 08/22/2013] [Indexed: 12/18/2022] Open
Abstract
Genomic imprinting results in monoallelic gene expression in a parent-of-origin-dependent manner and is regulated by the differential epigenetic marking of the parental alleles. In plants, genomic imprinting has been primarily described for genes expressed in the endosperm, a tissue nourishing the developing embryo that does not contribute to the next generation. In Arabidopsis, the genes MEDEA (MEA) and PHERES1 (PHE1), which are imprinted in the endosperm, are also expressed in the embryo; whether their embryonic expression is regulated by imprinting or not, however, remains controversial. In contrast, the maternally expressed in embryo 1 (mee1) gene of maize is clearly imprinted in the embryo. We identified several imprinted candidate genes in an allele-specific transcriptome of hybrid Arabidopsis embryos and confirmed parent-of-origin-dependent, monoallelic expression for eleven maternally expressed genes (MEGs) and one paternally expressed gene (PEG) in the embryo, using allele-specific expression analyses and reporter gene assays. Genetic studies indicate that the Polycomb Repressive Complex 2 (PRC2) but not the DNA METHYLTRANSFERASE1 (MET1) is involved in regulating imprinted expression in the embryo. In the seedling, all embryonic MEGs and the PEG are expressed from both parents, suggesting that the imprint is erased during late embryogenesis or early vegetative development. Our finding that several genes are regulated by genomic imprinting in the Arabidopsis embryo clearly demonstrates that this epigenetic phenomenon is not a unique feature of the endosperm in both monocots and dicots. In most cells nuclear genes are present in two copies, with one maternal and one paternal allele. Usually, the two alleles share the same fate regarding their activity, with both copies being active or both being silent. An exception to this rule are genes that are regulated by genomic imprinting, where only one allele is expressed and the other one remains silent depending on the parent it was inherited from. The two alleles are equal in terms of their DNA sequence but carry different epigenetic marks distinguishing them. Genomic imprinting evolved independently in mammals and flowering plants. In mammals, genes regulated by genomic imprinting are expressed in a wide range of tissues including the embryo and the placenta. In plants, genomic imprinting has been primarily described for genes expressed in the endosperm, a nutritive tissue in the seed with a function similar to that of the mammalian placenta. Here, we describe that some genes are also regulated by genomic imprinting in the embryo of the model plant Arabidopsis thaliana. An epigenetic silencing complex, the Polycomb Repressive Complex 2 (PRC2), partly regulates genomic imprinting in the embryo. Interestingly, embryonic imprints seem to be erased during late embryo or early seedling development.
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Corral JM, Vogel H, Aliyu OM, Hensel G, Thiel T, Kumlehn J, Sharbel TF. A conserved apomixis-specific polymorphism is correlated with exclusive exonuclease expression in premeiotic ovules of apomictic boechera species. PLANT PHYSIOLOGY 2013; 163:1660-72. [PMID: 24163323 PMCID: PMC3850208 DOI: 10.1104/pp.113.222430] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 10/23/2013] [Indexed: 05/19/2023]
Abstract
Apomixis (asexual seed production) is characterized by meiotically unreduced egg cell production (apomeiosis) followed by its parthenogenetic development into offspring that are genetic clones of the mother plant. Fertilization (i.e. pseudogamy) of the central cell is important for the production of a functional endosperm with a balanced 2:1 maternal:paternal genome ratio. Here, we present the APOLLO (for apomixis-linked locus) gene, an Aspartate Glutamate Aspartate Aspartate histidine exonuclease whose transcripts are down-regulated in sexual ovules entering meiosis while being up-regulated in apomeiotic ovules at the same stage of development in plants of the genus Boechera. APOLLO has both "apoalleles," which are characterized by a set of linked apomixis-specific polymorphisms, and "sexalleles." All apomictic Boechera spp. accessions proved to be heterozygous for the APOLLO gene (having at least one apoallele and one sexallele), while all sexual genotypes were homozygous for sexalleles. Apoalleles contained a 20-nucleotide polymorphism present in the 5' untranslated region that contains specific transcription factor-binding sites for ARABIDOPSIS THALIANA HOMEOBOX PROTEIN5, LIM1 (for LINEAGE ABNORMAL11, INSULIN1, MECHANOSENSORY PROTEIN3), SORLIP1AT (for SEQUENCES OVERREPRESENTED IN LIGHT-INDUCED PROMOTERS IN ARABIDOPSIS THALIANA1), SORLIP2AT, and POLYA SIGNAL1. In the same region, sexalleles contain transcription factor-binding sites for DNA BINDING WITH ONE FINGER2, DNA BINDING WITH ONE FINGER3, and PROLAMIN BOX-BINDING FACTOR. Our results suggest that the expression of a single deregulated allele could induce the cascade of events leading to asexual female gamete formation in an apomictic plant.
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25
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Donoghue MT, Fort A, Clifton R, Zhang X, McKeown PC, Voigt-Zielinksi M, Borevitz JO, Spillane C. C(m)CGG methylation-independent parent-of-origin effects on genome-wide transcript levels in isogenic reciprocal F1 triploid plants. DNA Res 2013; 21:141-51. [PMID: 24212467 PMCID: PMC3989486 DOI: 10.1093/dnares/dst046] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Triploid F1 hybrids generated via reciprocal interploidy crosses between genetically distinct parental plants can display parent-of-origin effects on gene expression or phenotypes. Reciprocal triploid F1 isogenic plants generated from interploidy crosses in the same genetic background allow investigation on parent-of-origin-specific (parental) genome-dosage effects without confounding effects of hybridity involving heterozygous mutations. Whole-genome transcriptome profiling was conducted on reciprocal F1 isogenic triploid (3x) seedlings of A. thaliana. The genetically identical reciprocal 3x genotypes had either an excess of maternally inherited 3x(m) or paternally inherited 3x(p) genomes. We identify a major parent-of-origin-dependent genome-dosage effect on transcript levels, whereby 602 genes exhibit differential expression between the reciprocal F1 triploids. In addition, using methylation-sensitive DNA tiling arrays, constitutive and polymorphic CG DNA methylation patterns at CCGG sites were analysed, which revealed that paternal-excess F1 triploid seedling C(m)CGG sites are overall hypermethylated. However, no correlation exists between C(m)CGG methylation polymorphisms and transcriptome dysregulation between the isogenic reciprocal F1 triploids. Overall, our study indicates that parental genome-dosage effects on the transcriptome levels occur in paternal-excess triploids, which are independent of C(m)CGG methylation polymorphisms. Such findings have implications for understanding parental effects and genome-dosage effects on gene expression and phenotypes in polyploid plants.
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Affiliation(s)
- Mark T.A. Donoghue
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, Aras de Brun, National University of Ireland, Galway (NUI Galway), Ireland
| | - Antoine Fort
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, Aras de Brun, National University of Ireland, Galway (NUI Galway), Ireland
| | - Rachel Clifton
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, Aras de Brun, National University of Ireland, Galway (NUI Galway), Ireland
| | - Xu Zhang
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Peter C. McKeown
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, Aras de Brun, National University of Ireland, Galway (NUI Galway), Ireland
| | - M.L. Voigt-Zielinksi
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, Aras de Brun, National University of Ireland, Galway (NUI Galway), Ireland
| | - Justin O. Borevitz
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Charles Spillane
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, Aras de Brun, National University of Ireland, Galway (NUI Galway), Ireland
- To whom correspondence should be addressed: E-mail:
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26
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Abstract
Imprinted gene expression--the biased expression of alleles dependent on their parent of origin--is an important type of epigenetic gene regulation in flowering plants and mammals. In plants, genes are imprinted primarily in the endosperm, the triploid placenta-like tissue that surrounds and nourishes the embryo during its development. Differential allelic expression is correlated with active DNA demethylation by DNA glycosylases and repressive targeting by the Polycomb group proteins. Imprinted gene expression is one consequence of a large-scale remodeling to the epigenome, primarily directed at transposable elements, that occurs in gametes and seeds. This remodeling could be important for maintaining the epigenome in the embryo as well as for establishing gene imprinting.
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Affiliation(s)
- Mary Gehring
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142;
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27
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Borges F, Calarco JP, Martienssen RA. Reprogramming the epigenome in Arabidopsis pollen. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2013; 77:1-5. [PMID: 23619015 DOI: 10.1101/sqb.2013.77.014969] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Epigenetic reprogramming in Arabidopsis thaliana occurs in developing pollen. The male gametophyte is derived from haploid microspores via two postmeiotic cell divisions to give rise to the gametes (sperm cells, SC) and the vegetative cell (VC). The purification of individual cell types during pollen development coupled with genome-wide DNA methylation analysis and small RNA sequencing has revealed a dynamic regulation of the epigenome during gametogenesis. Interestingly, imprinted loci and previously identified variable epialleles are hypermethylated in the germline; however, their stability after fertilization appears to require targeted demethylation in the neighboring vegetative cell nucleus, possibly by releasing mobile small RNAs that reinforce transcriptional gene silencing and DNA methylation in the gametes. These results have led to a new model for the establishment and transgenerational maintenance of epigenetic marks in flowering plants.
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Affiliation(s)
- F Borges
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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28
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Gaur U, Li K, Mei S, Liu G. Research progress in allele-specific expression and its regulatory mechanisms. J Appl Genet 2013; 54:271-83. [PMID: 23609142 DOI: 10.1007/s13353-013-0148-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 03/22/2013] [Accepted: 04/03/2013] [Indexed: 12/12/2022]
Abstract
Although the majority of genes are expressed equally from both alleles, some genes are differentially expressed. Organisms possess characteristics to preferentially express a particular allele under regulatory factors, which is termed allele-specific expression (ASE). It is one of the important genetic factors that lead to phenotypic variation and can be used to identify the variance of gene regulation factors. ASE indicates mechanisms such as DNA methylation, histone modifications, and non-coding RNAs function. Here, we review a broad survey of progress in ASE studies, and what this simple yet very effective approach can offer in functional genomics, and possible implications toward our better understanding of the underlying mechanisms of complex traits.
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Affiliation(s)
- Uma Gaur
- Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Yaoyuan No. 1, Nanhu, Hongshan District, Wuhan, 430064, People's Republic of China
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29
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Willi Y. The battle of the sexes over seed size: support for both kinship genomic imprinting and interlocus contest evolution. Am Nat 2013; 181:787-98. [PMID: 23669541 DOI: 10.1086/670196] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Outcrossing creates a venue for parental conflict. When one sex provides parental care to offspring fertilized by several partners, the nonproviding sex is under selection to maximally exploit the caring sex. The caring sex may counteradapt, and a coevolutionary arms race ensues. Genetic models of this conflict include the kinship theory of genomic imprinting (parent-of-origin-specific expression of maternal-care effectors) and interlocus conflict evolution (interaction between male selfish signals and female abatement). Predictions were tested by measuring the sizes of seeds produced by within-population crosses (diallel design) and between-population crosses in outcrossing and selfing populations of Arabidopsis lyrata. Within-population diallel crosses revealed substantial maternal variance in seed size in most populations. The comparison of between- and within-population crosses showed that seeds were larger when pollen came from another outcrossing population than when pollen came from a selfing or the same population, supporting interlocus contest evolution between male selfish genes and female recognition genes. Evidence for kinship genomic imprinting came from complementary trait means of seed size in reciprocal between-population crosses independent of whether populations were predominantly selfing or outcrossing. Hence, both kinship genomic imprinting and interlocus contest are supported in outcrossing Arabidopsis, whereas only kinship genomic imprinting is important in selfing populations.
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Affiliation(s)
- Yvonne Willi
- Institute of Biology, Evolutionary Botany, University of Neuchâtel, CH-2000 Neuchâtel, Switzerland.
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30
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Peng Q, Ecker JR. Detection of allele-specific methylation through a generalized heterogeneous epigenome model. Bioinformatics 2013; 28:i163-71. [PMID: 22689757 PMCID: PMC3371863 DOI: 10.1093/bioinformatics/bts231] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Motivations: High-throughput sequencing has made it possible to sequence DNA methylation of a whole genome at the single-base resolution. A sample, however, may contain a number of distinct methylation patterns. For instance, cells of different types and in different developmental stages may have different methylation patterns. Alleles may be differentially methylated, which may partially explain that the large portions of epigenomes from single cell types are partially methylated, and may have major effects on transcriptional output. Approaches relying on DNA sequence polymorphism to identify individual patterns from a mixture of heterogeneous epigenomes are insufficient as methylcytosines occur at a much higher density than SNPs. Results: We have developed a mixture model-based approach for resolving distinct epigenomes from a heterogeneous sample. In particular, the model is applied to the detection of allele-specific methylation (ASM). The methods are tested on a synthetic methylome and applied to an Arabidopsis single root cell methylome. Contact:qpeng@cs.ucsd.edu
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Affiliation(s)
- Qian Peng
- Department of Computer Science and Engineering, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
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31
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Gutierrez-Marcos JF, Constância M, Burton GJ. Maternal to offspring resource allocation in plants and mammals. Placenta 2012; 33 Suppl 2:e3-10. [PMID: 22995735 DOI: 10.1016/j.placenta.2012.08.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 08/28/2012] [Accepted: 08/30/2012] [Indexed: 12/26/2022]
Abstract
Appropriate allocation of resources to the offspring is critical for successful reproduction, particularly in species that reproduce on more than one occasion. The offspring must be provisioned adequately to ensure its vigour, whereas the parent must not become so depleted such that its survival is endangered. In both flowering plants and mammals specialised structures have evolved to support the offspring during its development. In this review we consider common themes that may indicate conservation of nutrient transfer function and regulation by genomic imprinting across the two kingdoms.
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Affiliation(s)
- J F Gutierrez-Marcos
- School of Life Sciences, University of Warwick, Wellesbourne Campus, Coventry CV4 7AL, UK.
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32
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Calarco JP, Borges F, Donoghue MT, Van Ex F, Jullien PE, Lopes T, Gardner R, Berger F, Feijó JA, Becker JD, Martienssen RA. Reprogramming of DNA methylation in pollen guides epigenetic inheritance via small RNA. Cell 2012; 151:194-205. [PMID: 23000270 PMCID: PMC3697483 DOI: 10.1016/j.cell.2012.09.001] [Citation(s) in RCA: 390] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 08/14/2012] [Accepted: 08/30/2012] [Indexed: 11/20/2022]
Abstract
Epigenetic inheritance is more widespread in plants than in mammals, in part because mammals erase epigenetic information by germline reprogramming. We sequenced the methylome of three haploid cell types from developing pollen: the sperm cell, the vegetative cell, and their precursor, the postmeiotic microspore, and found that unlike in mammals the plant germline retains CG and CHG DNA methylation. However, CHH methylation is lost from retrotransposons in microspores and sperm cells and restored by de novo DNA methyltransferase guided by 24 nt small interfering RNA, both in the vegetative nucleus and in the embryo after fertilization. In the vegetative nucleus, CG methylation is lost from targets of DEMETER (DME), REPRESSOR OF SILENCING 1 (ROS1), and their homologs, which include imprinted loci and recurrent epialleles that accumulate corresponding small RNA and are premethylated in sperm. Thus genome reprogramming in pollen contributes to epigenetic inheritance, transposon silencing, and imprinting, guided by small RNA.
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Affiliation(s)
- Joseph P. Calarco
- Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Filipe Borges
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal
| | - Mark T.A. Donoghue
- Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Frédéric Van Ex
- Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Pauline E. Jullien
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore
| | - Telma Lopes
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal
| | - Rui Gardner
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal
| | - Frédéric Berger
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore
| | - José A. Feijó
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal
- Universidade de Lisboa, Faculdade de Ciências, Departamento de Biologia Vegetal, Campo Grande C2, 1749-016 Lisboa, Portugal
| | - Jörg D. Becker
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal
| | - Robert A. Martienssen
- Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
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33
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Rea M, Zheng W, Chen M, Braud C, Bhangu D, Rognan TN, Xiao W. Histone H1 affects gene imprinting and DNA methylation in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 71:776-86. [PMID: 22519754 PMCID: PMC3429642 DOI: 10.1111/j.1365-313x.2012.05028.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Imprinting, i.e. parent-of-origin expression of alleles, plays an important role in regulating development in mammals and plants. DNA methylation catalyzed by DNA methyltransferases plays a pivotal role in regulating imprinting by silencing parental alleles. DEMETER (DME), a DNA glycosylase functioning in the base-excision DNA repair pathway, can excise 5-methylcytosine from DNA and regulate genomic imprinting in Arabidopsis. DME demethylates the maternal MEDEA (MEA) promoter in endosperm, resulting in expression of the maternal MEA allele. However, it is not known whether DME interacts with other proteins in regulating gene imprinting. Here we report the identification of histone H1.2 as a DME-interacting protein in a yeast two-hybrid screen, and confirmation of their interaction by the in vitro pull-down assay. Genetic analysis of the loss-of-function histone h1 mutant showed that the maternal histone H1 allele is required for DME regulation of MEA, FWA and FIS2 imprinting in Arabidopsis endosperm but the paternal allele is dispensable. Furthermore, we show that mutations in histone H1 result in an increase of DNA methylation in the maternal MEA and FWA promoter in endosperm. Our results suggest that histone H1 is involved in DME-mediated DNA methylation and gene regulation at imprinted loci.
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Affiliation(s)
| | | | | | | | | | | | - Wenyan Xiao
- For correspondence: Fax, 314-977-3658; Tel, 314-977-2547;
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34
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Jiang H, Köhler C. Evolution, function, and regulation of genomic imprinting in plant seed development. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:4713-22. [PMID: 22922638 DOI: 10.1093/jxb/ers145] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Genomic imprinting is an epigenetic phenomenon whereby genetically identical alleles are differentially expressed dependent on their parent-of-origin. Genomic imprinting has independently evolved in flowering plants and mammals. In both organism classes, imprinting occurs in embryo-nourishing tissues, the placenta and the endosperm, respectively, and it has been proposed that imprinted genes regulate the transfer of nutrients to the developing progeny. Many imprinted genes are located in the vicinity of DNA-methylated transposon or repeat sequences, implying that transposon insertions are associated with the evolution of imprinted loci. The antagonistic action of DNA methylation and Polycomb group-mediated histone methylation seems important for the regulation of many imprinted plant genes, whereby the position of such epigenetic modifications can determine whether a gene will be mainly expressed from either the maternally or paternally inherited alleles. Furthermore, long non-coding RNAs seem to play an as yet underappreciated role for the regulation of imprinted plant genes. Imprinted expression of a number of genes is conserved between monocots and dicots, suggesting that long-term selection can maintain imprinted expression at some loci.
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Affiliation(s)
- Hua Jiang
- Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center of Plant Biology, 750 07 Uppsala, Sweden
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35
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Wöhrmann HJP, Gagliardini V, Raissig MT, Wehrle W, Arand J, Schmidt A, Tierling S, Page DR, Schöb H, Walter J, Grossniklaus U. Identification of a DNA methylation-independent imprinting control region at the Arabidopsis MEDEA locus. Genes Dev 2012; 26:1837-50. [PMID: 22855791 DOI: 10.1101/gad.195123.112] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Genomic imprinting is exclusive to mammals and seed plants and refers to parent-of-origin-dependent, differential transcription. As previously shown in mammals, studies in Arabidopsis have implicated DNA methylation as an important hallmark of imprinting. The current model suggests that maternally expressed imprinted genes, such as MEDEA (MEA), are activated by the DNA glycosylase DEMETER (DME), which removes DNA methylation established by the DNA methyltransferase MET1. We report the systematic functional dissection of the MEA cis-regulatory region, resulting in the identification of a 200-bp fragment that is necessary and sufficient to mediate MEA activation and imprinted expression, thus containing the imprinting control region (ICR). Notably, imprinted MEA expression mediated by this ICR is independent of DME and MET1, consistent with the lack of any significant DNA methylation in this region. This is the first example of an ICR without differential DNA methylation, suggesting that factors other than DME and MET1 are required for imprinting at the MEA locus.
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Affiliation(s)
- Heike J P Wöhrmann
- Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
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36
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Ikeda Y. Plant imprinted genes identified by genome-wide approaches and their regulatory mechanisms. PLANT & CELL PHYSIOLOGY 2012; 53:809-816. [PMID: 22492232 DOI: 10.1093/pcp/pcs049] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Genomic imprinting is an epigenetic phenomenon found in mammals and flowering plants that leads to differential allelic gene expression depending on their parent of origin. In plants, genomic imprinting primarily occurs in the endosperm, and it is associated with seed development. The imprinted expression is driven by the epigenetic memory programmed in each lineage of female and male germlines. Several imprinted genes have been identified based on genetic studies in maize and Arabidopsis. Recent advances in genome-wide analyses made it possible to identify multiple imprinted genes including many nuclear proteins, such as transcription factors and chromatin-related proteins in different plant species. Some of these genes are conserved in Arabidopsis, rice and maize, but many are species specific. Genome-wide analyses also clarified the regulation mechanism of imprinted genes orchestrated by DNA methylation and histone methylation marks. Additionally, genetic analyses using Arabidopsis revealed new regulatory factors of DNA demethylation and imprinting and shed light on the more precise mechanisms.
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Affiliation(s)
- Yoko Ikeda
- Plant Reproductive Genetics, GCOE Research Group, Graduate School of Biological Science, Nara Institute of Science and Technology, Japan.
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37
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Köhler C, Wolff P, Spillane C. Epigenetic mechanisms underlying genomic imprinting in plants. ANNUAL REVIEW OF PLANT BIOLOGY 2012; 63:331-52. [PMID: 22404470 DOI: 10.1146/annurev-arplant-042811-105514] [Citation(s) in RCA: 126] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Genomic imprinting, the differential expression of an autosomal gene that is dependent on its parent of origin, has independently evolved in flowering plants and mammals. In both of these organism classes, imprinting occurs in embryo-nourishing tissues-the placenta and the endosperm, respectively. It has been proposed that some imprinted genes control nutrient flow from the mother to the offspring. Genome-wide analyses of imprinted genes in plants have revealed that many imprinted genes are located in the vicinity of transposon or repeat sequences, implying that transposon insertions are associated with the evolution of imprinted loci. Imprinted expression of a number of genes is conserved between monocots and dicots, suggesting that long-term selection can maintain imprinted expression at some loci. In terms of epigenetic mechanisms, imprinted expression is largely controlled by an antagonistic action of DNA methylation and Polycomb group-mediated histone methylation in the vicinity of imprinted genes, whereby the position of such epigenetic modifications can determine whether a gene will be expressed mainly from either the maternally or paternally inherited alleles.
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Affiliation(s)
- Claudia Köhler
- Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden.
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38
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Singer TM, Moll C, Groß-Hardt R. When Double is not Twice as Much. FRONTIERS IN PLANT SCIENCE 2011; 2:94. [PMID: 22645557 PMCID: PMC3355729 DOI: 10.3389/fpls.2011.00094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Accepted: 11/22/2011] [Indexed: 06/01/2023]
Abstract
Gene and genome duplications provide a playground for various selective pressures and contribute significantly to genome complexity. It is assumed that the genomes of all major eukaryotic lineages possess duplicated regions that result from gene and genome duplication. There is evidence that the model plant Arabidopsis has been subjected to at least three whole-genome duplication events over the last 150-200 million years. As a result, many cellular processes are governed by redundantly acting gene families. Plants pass through two distinct life phases with a haploid gametophytic alternating with a diploid sporophytic generation. This ontogenetic difference in gene copy number has important implications for the outcome of deleterious mutations, which are masked by the second gene copy in diploid systems but expressed in a dominant fashion in haploid organisms. As a consequence, maintaining the activity of duplicated genes might be particularly advantageous during the haploid gametophytic generation. Here, we describe the distinctive features associated with the alteration of generations and discuss how activity profiles of duplicated genes might get modulated in a life phase dependent fashion.
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Affiliation(s)
- Theresa Maria Singer
- Cell and Developmental Genetics, Center for Plant Molecular Biology, University of TuebingenTuebingen, Germany
| | - Cordula Moll
- Cell and Developmental Genetics, Center for Plant Molecular Biology, University of TuebingenTuebingen, Germany
| | - Rita Groß-Hardt
- Cell and Developmental Genetics, Center for Plant Molecular Biology, University of TuebingenTuebingen, Germany
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39
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Waters AJ, Makarevitch I, Eichten SR, Swanson-Wagner RA, Yeh CT, Xu W, Schnable PS, Vaughn MW, Gehring M, Springer NM. Parent-of-origin effects on gene expression and DNA methylation in the maize endosperm. THE PLANT CELL 2011; 23:4221-33. [PMID: 22198147 PMCID: PMC3269861 DOI: 10.1105/tpc.111.092668] [Citation(s) in RCA: 149] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Revised: 11/17/2011] [Accepted: 11/30/2011] [Indexed: 05/18/2023]
Abstract
Imprinting describes the differential expression of alleles based on their parent of origin. Deep sequencing of RNAs from maize (Zea mays) endosperm and embryo tissue 14 d after pollination was used to identify imprinted genes among a set of ~12,000 genes that were expressed and contained sequence polymorphisms between the B73 and Mo17 genotypes. The analysis of parent-of-origin patterns of expression resulted in the identification of 100 putative imprinted genes in maize endosperm, including 54 maternally expressed genes (MEGs) and 46 paternally expressed genes (PEGs). Three of these genes have been previously identified as imprinted, while the remaining 97 genes represent novel imprinted maize genes. A genome-wide analysis of DNA methylation identified regions with reduced endosperm DNA methylation in, or near, 19 of the 100 imprinted genes. The reduced levels of DNA methylation in endosperm are caused by hypomethylation of the maternal allele for both MEGs and PEGs in all cases tested. Many of the imprinted genes with reduced DNA methylation levels also show endosperm-specific expression patterns. The imprinted maize genes were compared with imprinted genes identified in genome-wide screens of rice (Oryza sativa) and Arabidopsis thaliana, and at least 10 examples of conserved imprinting between maize and each of the other species were identified.
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Affiliation(s)
- Amanda J. Waters
- Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, Minnesota 55108
| | - Irina Makarevitch
- Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, Minnesota 55108
- Department of Biology, Hamline University, Saint Paul, Minnesota 55114
| | - Steve R. Eichten
- Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, Minnesota 55108
| | - Ruth A. Swanson-Wagner
- Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, Minnesota 55108
| | - Cheng-Ting Yeh
- Center for Plant Genomics, Iowa State University, Ames, Iowa 50011
| | - Wayne Xu
- Minnesota Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, Minnesota 55455
| | | | - Matthew W. Vaughn
- Texas Advanced Computing Center, University of Texas, Austin, Texas 78758
| | - Mary Gehring
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Nathan M. Springer
- Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, Minnesota 55108
- Address correspondence to
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