1
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Soliman HK, Coughlan JM. United by Conflict: Convergent Signatures of Parental Conflict in Angiosperms and Placental Mammals. J Hered 2024:esae009. [PMID: 38366852 DOI: 10.1093/jhered/esae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Indexed: 02/18/2024] Open
Abstract
Endosperm in angiosperms and placenta in eutherians are convergent innovations for efficient embryonic nutrient transfer. Despite advantages, this reproductive strategy incurs metabolic costs that maternal parents disproportionately shoulder, leading to potential inter-parental conflict over optimal offspring investment. Genomic imprinting-parent-of-origin-biased gene expression-is fundamental for endosperm and placenta development and has convergently evolved in angiosperms and mammals, in part, to resolve parental conflict. Here, we review the mechanisms of genomic imprinting in these taxa. Despite differences in the timing and spatial extent of imprinting, these taxa exhibit remarkable convergence in the molecular machinery and genes governing imprinting. We then assess the role of parental conflict in shaping evolution within angiosperms and eutherians using four criteria: (1) Do differences in the extent of sibling relatedness cause differences in the inferred strength of parental conflict? (2) Do reciprocal crosses between taxa with different inferred histories of parental conflict exhibit parent-of-origin growth effects? (3) Are these parent-of-origin growth effects caused by dosage-sensitive mechanisms and do these loci exhibit signals of positive selection? (4) Can normal development be restored by genomic perturbations that restore stoichiometric balance in the endosperm/placenta? Although we find evidence for all criteria in angiosperms and eutherians, suggesting that parental conflict may help shape their evolution, many questions remain. Additionally, myriad differences between the two taxa suggest that their respective biologies may shape how/when/where/to what extent parental conflict manifests. Lastly, we discuss outstanding questions, highlighting the power of comparative work in quantifying the role of parental conflict in evolution.
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Affiliation(s)
- Hagar K Soliman
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, 06511, United States
- Department of Biotechnology, Faculty of Science, Cairo University, Giza, 12613, Egypt
| | - Jenn M Coughlan
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, 06511, United States
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2
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John RM, Higgs MJ, Isles AR. Imprinted genes and the manipulation of parenting in mammals. Nat Rev Genet 2023; 24:783-796. [PMID: 37714957 DOI: 10.1038/s41576-023-00644-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/24/2023] [Indexed: 09/17/2023]
Abstract
Genomic imprinting refers to the parent-of-origin expression of genes, which originates from epigenetic events in the mammalian germ line. The evolution of imprinting may reflect a conflict over resource allocation early in life, with silencing of paternal genes in offspring soliciting increased maternal provision and silencing of maternal genes limiting demands on the mother. Parental caregiving has been identified as an area of potential conflict, with several imprinted genes serendipitously found to directly influence the quality of maternal care. Recent systems biology approaches, based on single-cell RNA sequencing data, support a more deliberate relationship, which is reinforced by the finding that imprinted genes expressed in the offspring influence the quality of maternal caregiving. These bidirectional, reiterative relationships between parents and their offspring are critical both for short-term survival and for lifelong wellbeing, with clear implications for human health.
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3
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Reifová R, Ament-Velásquez SL, Bourgeois Y, Coughlan J, Kulmuni J, Lipinska AP, Okude G, Stevison L, Yoshida K, Kitano J. Mechanisms of Intrinsic Postzygotic Isolation: From Traditional Genic and Chromosomal Views to Genomic and Epigenetic Perspectives. Cold Spring Harb Perspect Biol 2023; 15:a041607. [PMID: 37696577 PMCID: PMC10547394 DOI: 10.1101/cshperspect.a041607] [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: 09/13/2023]
Abstract
Intrinsic postzygotic isolation typically appears as reduced viability or fertility of interspecific hybrids caused by genetic incompatibilities between diverged parental genomes. Dobzhansky-Muller interactions among individual genes, and chromosomal rearrangements causing problems with chromosome synapsis and recombination in meiosis, have both long been considered as major mechanisms behind intrinsic postzygotic isolation. Recent research has, however, suggested that the genetic basis of intrinsic postzygotic isolation can be more complex and involves, for example, overall divergence of the DNA sequence or epigenetic changes. Here, we review the mechanisms of intrinsic postzygotic isolation from genic, chromosomal, genomic, and epigenetic perspectives across diverse taxa. We provide empirical evidence for these mechanisms, discuss their importance in the speciation process, and highlight questions that remain unanswered.
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Affiliation(s)
- Radka Reifová
- Department of Zoology, Faculty of Science, Charles University, 128 00 Prague, Czech Republic
| | | | - Yann Bourgeois
- DIADE, University of Montpellier, CIRAD, IRD, 34090 Montpellier, France
| | - Jenn Coughlan
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA
| | - Jonna Kulmuni
- Institute for Biodiversity and Ecosystem Dynamics, Department of Evolutionary and Population Biology, University of Amsterdam, 1012 Amsterdam, The Netherlands
- Organismal & Evolutionary Biology Research Programme, University of Helsinki, 00100 Helsinki, Finland
| | - Agnieszka P Lipinska
- Department of Algal Development and Evolution, Max Planck Institute for Biology, 72076 Tuebingen, Germany
- CNRS, UMR 8227, Integrative Biology of Marine Models, Sorbonne Université, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Genta Okude
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Laurie Stevison
- Department of Biological Sciences, Auburn University, Auburn, Alabama 36849, USA
| | - Kohta Yoshida
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Jun Kitano
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
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4
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Patten MM, Schenkel MA, Ågren JA. Adaptation in the face of internal conflict: the paradox of the organism revisited. Biol Rev Camb Philos Soc 2023; 98:1796-1811. [PMID: 37203364 DOI: 10.1111/brv.12983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/20/2023]
Abstract
The paradox of the organism refers to the observation that organisms appear to function as coherent purposeful entities, despite the potential for within-organismal components like selfish genetic elements and cancer cells to erode them from within. While it is commonly accepted that organisms may pursue fitness maximisation and can be thought to hold particular agendas, there is a growing recognition that genes and cells do so as well. This can lead to evolutionary conflicts between an organism and the parts that reside within it. Here, we revisit the paradox of the organism. We first outline its conception and relationship to debates about adaptation in evolutionary biology. Second, we review the ways selfish elements may exploit organisms, and the extent to which this threatens organismal integrity. To this end, we introduce a novel classification scheme that distinguishes between selfish elements that seek to distort transmission versus those that seek to distort phenotypic traits. Our classification scheme also highlights how some selfish elements elude a multi-level selection decomposition using the Price equation. Third, we discuss how the organism can retain its status as the primary fitness-maximising agent in the face of selfish elements. The success of selfish elements is often constrained by their strategy and further limited by a combination of fitness alignment and enforcement mechanisms controlled by the organism. Finally, we argue for the need for quantitative measures of both internal conflicts and organismality.
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Affiliation(s)
- Manus M Patten
- Department of Biology, Georgetown University, 37th and O St. NW, Washington, DC, 20057, USA
| | - Martijn A Schenkel
- Department of Biology, Georgetown University, 37th and O St. NW, Washington, DC, 20057, USA
- Groningen Institute of Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - J Arvid Ågren
- Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, Uppsala, 752 36, Sweden
- Lerner Research Institute, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH, 44195, USA
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5
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Alaniz-Fabián J, Orozco-Nieto A, Abreu-Goodger C, Gillmor CS. Hybridization alters maternal and paternal genome contributions to early plant embryogenesis. Development 2022; 149:281772. [PMID: 36314727 DOI: 10.1242/dev.201025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022]
Abstract
After fertilization, zygotic genome activation results in a transcriptionally competent embryo. Hybrid transcriptome experiments in Arabidopsis have concluded that the maternal and paternal genomes make equal contributions to zygotes and embryos, yet embryo defective (emb) mutants in the Columbia (Col) ecotype display early maternal effects. Here, we show that hybridization of Col with Landsberg erecta (Ler) or Cape Verde Islands (Cvi) ecotypes decreases the maternal effects of emb mutants. Reanalysis of Col/Ler and Col/Cvi transcriptomes confirmed equal parental contributions in Col/Cvi early embryos. By contrast, thousands of genes in Col/Ler zygotes and one-cell embryos were biallelic in one cross and monoallelic in the reciprocal cross, with analysis of intron reads pointing to active transcription as responsible for this parent-of-origin bias. Our analysis shows that, contrary to previous conclusions, the maternal and paternal genomes in Col/Ler zygotes are activated in an asymmetric manner. The decrease in maternal effects in hybrid embryos compared with those in isogenic Col along with differences in genome activation between Col/Cvi and Col/Ler suggest that neither of these hybrids accurately reflects the general trends of parent-of-origin regulation in Arabidopsis embryogenesis.
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Affiliation(s)
- Jaime Alaniz-Fabián
- Langebio, Unidad de Genómica Avanzada, CINVESTAV-IPN, Irapuato 36824, México
| | - Axel Orozco-Nieto
- Langebio, Unidad de Genómica Avanzada, CINVESTAV-IPN, Irapuato 36824, México
| | - Cei Abreu-Goodger
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - C Stewart Gillmor
- Langebio, Unidad de Genómica Avanzada, CINVESTAV-IPN, Irapuato 36824, México
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RNA Pol IV induces antagonistic parent-of-origin effects on Arabidopsis endosperm. PLoS Biol 2022; 20:e3001602. [PMID: 35389984 PMCID: PMC9017945 DOI: 10.1371/journal.pbio.3001602] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 04/19/2022] [Accepted: 03/11/2022] [Indexed: 12/14/2022] Open
Abstract
Gene expression in endosperm-a seed tissue that mediates transfer of maternal resources to offspring-is under complex epigenetic control. We show here that plant-specific RNA polymerase IV (Pol IV) mediates parental control of endosperm gene expression. Pol IV is required for the production of small interfering RNAs that typically direct DNA methylation. We compared small RNAs (sRNAs), DNA methylation, and mRNAs in Arabidopsis thaliana endosperm from heterozygotes produced by reciprocally crossing wild-type (WT) plants to Pol IV mutants. We find that maternally and paternally acting Pol IV induce distinct effects on endosperm. Loss of maternal or paternal Pol IV impacts sRNAs and DNA methylation at different genomic sites. Strikingly, maternally and paternally acting Pol IV have antagonistic impacts on gene expression at some loci, divergently promoting or repressing endosperm gene expression. Antagonistic parent-of-origin effects have only rarely been described and are consistent with a gene regulatory system evolving under parental conflict.
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Zhang Z, Yu S, Li J, Zhu Y, Jiang S, Xia H, Zhou Y, Sun D, Liu M, Li C, Zhu Y, Ruan Y, Dong X. Epigenetic modifications potentially controlling the allelic expression of imprinted genes in sunflower endosperm. BMC PLANT BIOLOGY 2021; 21:570. [PMID: 34863098 PMCID: PMC8642925 DOI: 10.1186/s12870-021-03344-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 10/26/2021] [Indexed: 06/02/2023]
Abstract
BACKGROUND Genomic imprinting is an epigenetic phenomenon mainly occurs in endosperm of flowering plants. Genome-wide identification of imprinted genes have been completed in several dicot Cruciferous plant and monocot crops. RESULTS Here, we analyzed global patterns of allelic gene expression in developing endosperm of sunflower which belongs to the composite family. Totally, 691 imprinted loci candidates were identified in 12 day-after-pollination sunflower endosperm including 79 maternally expressed genes (MEG) and 596 paternally expressed genes (PEG), 6 maternally expressed noncoding RNAs (MNC) and 10 paternally expressed noncoding RNAs (PNC). And a clear clustering of imprinted genes throughout the rapeseed genome was identified. Generally, imprinting in sunflower is conserved within a species, but intraspecific variation also was detected. Limited loci in sunflower are imprinted in other several different species. The DNA methylation pattern around imprinted genes were investigated in embryo and endosperm tissues. In CG context, the imprinted genes were significantly associated with differential methylated regions exhibiting hypomethylation in endosperm and hypermethylation in embryo, which indicated that the maternal demethylation in CG context potentially induce the genomic imprinting in endosperm. CONCLUSION Our study would be helpful for understanding of genomic imprinting in plants and provide potential basis for further research in imprinting in sunflower.
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Affiliation(s)
- Zhichao Zhang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China
| | - Shuai Yu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China
| | - Jing Li
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, China
| | - Yanbin Zhu
- State Key Laboratory of Maize Bio-Breeding, Shenyang, China
- State Key Laboratory of the Northeast Crop Genetics and Breeding, Shenyang, China
| | - Siqi Jiang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China
| | - Haoran Xia
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China
| | - Yue Zhou
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China
| | - Daqiu Sun
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China
| | - Meiling Liu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China
| | - Cong Li
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China
| | - Yanshu Zhu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China
| | - Yanye Ruan
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China
| | - Xiaomei Dong
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China.
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China.
- State Key Laboratory of Maize Bio-Breeding, Shenyang, China.
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8
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Rodrigues JA, Hsieh PH, Ruan D, Nishimura T, Sharma MK, Sharma R, Ye X, Nguyen ND, Nijjar S, Ronald PC, Fischer RL, Zilberman D. Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting. Proc Natl Acad Sci U S A 2021; 118:e2104445118. [PMID: 34272287 PMCID: PMC8307775 DOI: 10.1073/pnas.2104445118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Parent-of-origin-dependent gene expression in mammals and flowering plants results from differing chromatin imprints (genomic imprinting) between maternally and paternally inherited alleles. Imprinted gene expression in the endosperm of seeds is associated with localized hypomethylation of maternally but not paternally inherited DNA, with certain small RNAs also displaying parent-of-origin-specific expression. To understand the evolution of imprinting mechanisms in Oryza sativa (rice), we analyzed imprinting divergence among four cultivars that span both japonica and indica subspecies: Nipponbare, Kitaake, 93-11, and IR64. Most imprinted genes are imprinted across cultivars and enriched for functions in chromatin and transcriptional regulation, development, and signaling. However, 4 to 11% of imprinted genes display divergent imprinting. Analyses of DNA methylation and small RNAs revealed that endosperm-specific 24-nt small RNA-producing loci show weak RNA-directed DNA methylation, frequently overlap genes, and are imprinted four times more often than genes. However, imprinting divergence most often correlated with local DNA methylation epimutations (9 of 17 assessable loci), which were largely stable within subspecies. Small insertion/deletion events and transposable element insertions accompanied 4 of the 9 locally epimutated loci and associated with imprinting divergence at another 4 of the remaining 8 loci. Correlating epigenetic and genetic variation occurred at key regulatory regions-the promoter and transcription start site of maternally biased genes, and the promoter and gene body of paternally biased genes. Our results reinforce models for the role of maternal-specific DNA hypomethylation in imprinting of both maternally and paternally biased genes, and highlight the role of transposition and epimutation in rice imprinting evolution.
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Affiliation(s)
- Jessica A Rodrigues
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Ping-Hung Hsieh
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Deling Ruan
- Department of Plant Pathology, University of California, Davis, CA 95616
| | - Toshiro Nishimura
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Manoj K Sharma
- Department of Plant Pathology, University of California, Davis, CA 95616
| | - Rita Sharma
- Department of Plant Pathology, University of California, Davis, CA 95616
| | - XinYi Ye
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Nicholas D Nguyen
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Sukhranjan Nijjar
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Pamela C Ronald
- Department of Plant Pathology, University of California, Davis, CA 95616
- The Genome Center, University of California, Davis, CA 95616
| | - Robert L Fischer
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720;
| | - Daniel Zilberman
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720;
- Department of Cell and Developmental Biology, The John Innes Centre, Norwich NR4 7UH, United Kingdom
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9
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Simonini S, Bemer M, Bencivenga S, Gagliardini V, Pires ND, Desvoyes B, van der Graaff E, Gutierrez C, Grossniklaus U. The Polycomb group protein MEDEA controls cell proliferation and embryonic patterning in Arabidopsis. Dev Cell 2021; 56:1945-1960.e7. [PMID: 34192526 PMCID: PMC8279741 DOI: 10.1016/j.devcel.2021.06.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 04/22/2021] [Accepted: 06/07/2021] [Indexed: 12/13/2022]
Abstract
Establishing the embryonic body plan of multicellular organisms relies on precisely orchestrated cell divisions coupled with pattern formation, which, in animals, are regulated by Polycomb group (PcG) proteins. The conserved Polycomb Repressive Complex 2 (PRC2) mediates H3K27 trimethylation and comes in different flavors in Arabidopsis. The PRC2 catalytic subunit MEDEA is required for seed development; however, a role for PRC2 in embryonic patterning has been dismissed. Here, we demonstrate that embryos derived from medea eggs abort because MEDEA is required for patterning and cell lineage determination in the early embryo. Similar to PcG proteins in mammals, MEDEA regulates embryonic patterning and growth by controlling cell-cycle progression through repression of CYCD1;1, which encodes a core cell-cycle component. Thus, Arabidopsis embryogenesis is epigenetically regulated by PcG proteins, revealing that the PRC2-dependent modulation of cell-cycle progression was independently recruited to control embryonic cell proliferation and patterning in animals and plants.
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Affiliation(s)
- Sara Simonini
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - Marian Bemer
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - Stefano Bencivenga
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - Valeria Gagliardini
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - Nuno D Pires
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - Bénédicte Desvoyes
- Centro de Biología Molecular Severo Ochoa CSIC-UAM, Nicolás Cabrera 1, Cantoblanco 28049, Madrid, Spain
| | - Eric van der Graaff
- BIOSS Centre for Biological Signaling Studies, Faculty of Biology, Albert-Ludwigs-Universität Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Crisanto Gutierrez
- Centro de Biología Molecular Severo Ochoa CSIC-UAM, Nicolás Cabrera 1, Cantoblanco 28049, Madrid, Spain
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland.
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10
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Xu X, E Z, Zhang D, Yun Q, Zhou Y, Niu B, Chen C. OsYUC11-mediated auxin biosynthesis is essential for endosperm development of rice. PLANT PHYSIOLOGY 2021; 185:934-950. [PMID: 33793908 PMCID: PMC8133553 DOI: 10.1093/plphys/kiaa057] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 11/18/2020] [Indexed: 05/06/2023]
Abstract
Auxin is a phytohormone essential for plant development. However, our understanding of auxin-regulated endosperm development remains limited. Here, we described rice YUCCA (YUC) flavin-containing monooxygenase encoding gene OsYUC11 as a key contributor to auxin biosynthesis in rice (Oryza sativa) endosperm. Grain filling or storage product accumulation was halted by mutation of OsYUC11, but the deficiencies could be recovered by the exogenous application of auxin. A rice transcription factor (TF) yeast library was screened, and 41 TFs that potentially bind to the OsYUC11 promoter were identified, of which OsNF-YB1, a member of the nuclear factor Y family, is predominantly expressed in the endosperm. Both osyuc11 and osnf-yb1 mutants exhibited reduced seed size and increased chalkiness, accompanied by a reduction in indole-3-acetic acid biosynthesis. OsNF-YB1 can bind the OsYUC11 promoter to induce gene expression in vivo. We also found that OsYUC11 was a dynamically imprinted gene that predominantly expressed the paternal allele in the endosperm up to 10 d after fertilization (DAF) but then became a non-imprinted gene at 15 DAF. A functional maternal allele of OsYUC11 was able to recover the paternal defects of this gene. Overall, the findings indicate that OsYUC11-mediated auxin biosynthesis is essential for endosperm development in rice.
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Affiliation(s)
- Xinyu Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Zhiguo E
- Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Dongping Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Qianbin Yun
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Yong Zhou
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Baixiao Niu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Chen Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Author for communication:
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Liu Y, Jing X, Zhang H, Xiong J, Qiao Y. Identification of Imprinted Genes Based on Homology: An Example of Fragaria vesca. Genes (Basel) 2021; 12:genes12030380. [PMID: 33800118 PMCID: PMC7999015 DOI: 10.3390/genes12030380] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/28/2021] [Accepted: 03/04/2021] [Indexed: 01/04/2023] Open
Abstract
Genomic imprinting has drawn increasing attention in plant biology in recent years. At present, hundreds of imprinted genes have been identified in various plants, and some of them have been reported to be evolutionarily conserved in plant species. In this research, 17 candidate genes in Fragaria vesca were obtained based on the homologous imprinted genes in Arabidopsis thaliana and other species. We further constructed reciprocal crosses of diploid strawberry (F. vesca) using the varieties 10-41 and 18-86 as the parents to investigate the conservation of these imprinted genes. Potentially informative single nucleotide polymorphisms (SNPs) were used as molecular markers of two parents obtained from candidate imprinted genes which have been cloned and sequenced. Meanwhile, we analyzed the SNP site variation ratios and parent-of-origin expression patterns of candidate imprinted genes at 10 days after pollination (DAP) endosperm and embryo for the hybrids of reciprocal cross, respectively. A total of five maternally expressed genes (MEGs), i.e., FvARI8, FvKHDP-2, FvDRIP2, FvBRO1, and FvLTP3, were identified in the endosperm, which did not show imprinting in the embryo. Finally, tissues expression analysis indicated that the five imprinted genes excluding FvDRIP2 mainly expressed in the endosperm. This is the first report on imprinted genes of Fragaria, and we provide a simple and rapid method based on homologous conservation to screen imprinted genes. The present study will provide a basis for further study of function and mechanism of genomic imprinting in F. vesca.
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12
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Abstract
In this review, Batista and Köhler revisit the current models explaining imprinting regulation in plants, and discuss novel regulatory mechanisms that could function independently of parental DNA methylation asymmetries in the establishment of imprinting. Genomic imprinting is an epigenetic phenomenon leading to parentally biased gene expression. Throughout the years, extensive efforts have been made to characterize the epigenetic marks underlying imprinting in animals and plants. As a result, DNA methylation asymmetries between parental genomes emerged as the primary factor controlling the imprinting status of many genes. Nevertheless, the data accumulated so far suggest that this process cannot solely explain the imprinting of all genes. In this review, we revisit the current models explaining imprinting regulation in plants, and discuss novel regulatory mechanisms that could function independently of parental DNA methylation asymmetries in the establishment of imprinting.
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Affiliation(s)
- Rita A Batista
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, Uppsala SE-750 07, Sweden
| | - Claudia Köhler
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, Uppsala SE-750 07, Sweden
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13
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Abstract
Genomic imprinting is a phenomenon that occurs in flowering plants and mammals, whereby a gene is expressed in a parent-of-origin-specific manner. Although imprinting has now been examined genome-wide in a number of species using RNA-seq, the analyses used to assess imprinting vary between studies, making consistent comparisons between species difficult. Here we present a simple, easy-to-use bioinformatic pipeline for imprinting analyses suitable for any tissue, including plant endosperm. All relevant scripts can be downloaded. As an illustrative example, we reanalyze published data from A. thaliana and Z. mays endosperm using the pipeline and then demonstrate how to use the results to assess the conservation of imprinting between these species. We also introduce the Plant Imprinting Database, a repository for published imprinting datasets in plants that can be used to view, compare, and download data.
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Affiliation(s)
- Colette L Picard
- Computational and Systems Biology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Mary Gehring
- Computational and Systems Biology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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14
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Millership SJ, Van de Pette M, Withers DJ. Genomic imprinting and its effects on postnatal growth and adult metabolism. Cell Mol Life Sci 2019; 76:4009-4021. [PMID: 31270580 PMCID: PMC6785587 DOI: 10.1007/s00018-019-03197-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 06/10/2019] [Accepted: 06/17/2019] [Indexed: 12/25/2022]
Abstract
Imprinted genes display parent-of-origin-specific expression with this epigenetic system of regulation found exclusively in therian mammals. Historically, defined imprinted gene functions were almost solely focused on pregnancy and the influence on the growth parameters of the developing embryo and placenta. More recently, a number of postnatal functions have been identified which converge on resource allocation, both for animals in the nest and in adults. While many of the prenatal functions of imprinted genes that have so far been described adhere to the "parental conflict" hypothesis, no clear picture has yet emerged on the functional role of imprints on postnatal metabolism. As these roles are uncovered, interest in the potential for these genes to influence postnatal metabolism and associated adult-onset disease outcomes when dysregulated has gathered pace. Here, we review the published data on imprinted genes and their influence on postnatal metabolism, starting in the nest, and then progressing through to adulthood. When observing the functional effects of these genes on adult metabolism, we must always be careful to acknowledge the influence both of direct expression in the relevant metabolic tissue, but also indirect metabolic programming effects caused by their modulation of both in utero and postnatal growth trajectories.
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Affiliation(s)
- Steven J Millership
- MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK.
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK.
| | - Mathew Van de Pette
- MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Dominic J Withers
- MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK.
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK.
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15
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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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16
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Baroux C, Grossniklaus U. Seeds-An evolutionary innovation underlying reproductive success in flowering plants. Curr Top Dev Biol 2018; 131:605-642. [PMID: 30612632 DOI: 10.1016/bs.ctdb.2018.11.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
"Seeds nourish, seeds unite, seeds endure, seeds defend, seeds travel," explains the science writer Thor Hanson in his book The Triumph of Seeds (2015). The seed is an ultimate product of land plant evolution. The nursing and protective organization of the seed enable a unique parental care of the progeny that has fueled seed plant radiation. Seeds promote dispersal and optimize offspring production and thus reproductive fitness through biological adaptations that integrate environmental and developmental cues. The composite structure of seeds, uniting tissues that originate from three distinct organisms, enables the partitioning of tasks during development, maturation, and storage, while a sophisticated interplay between the compartments allows the fine-tuning of embryonic growth, as well as seed maturation, dormancy, and germination. In this review, we will highlight peculiarities in the development and evolution of the different seed compartments and focus on the molecular mechanisms underlying the interactions between them.
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Affiliation(s)
- Célia Baroux
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland.
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
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17
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Chen C, Li T, Zhu S, Liu Z, Shi Z, Zheng X, Chen R, Huang J, Shen Y, Luo S, Wang L, Liu QQ, E Z. Characterization of Imprinted Genes in Rice Reveals Conservation of Regulation and Imprinting with Other Plant Species. PLANT PHYSIOLOGY 2018; 177:1754-1771. [PMID: 29914891 PMCID: PMC6084669 DOI: 10.1104/pp.17.01621] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Accepted: 06/07/2018] [Indexed: 05/08/2023]
Abstract
Genomic imprinting is an epigenetic phenomenon by which certain genes display differential expression in a parent-of-origin-dependent manner. Hundreds of imprinted genes have been identified from several plant species. Here, we identified, with a high level of confidence, 208 imprinted gene candidates from rice (Oryza sativa). Imprinted genes of rice showed limited association with the transposable elements, which contrasts with findings from Arabidopsis (Arabidopsis thaliana). Generally, imprinting in rice is conserved within a species, but intraspecific variation also was detected. The imprinted rice genes do not show signatures of selection, which suggests that domestication has had a limited evolutionary consequence on genomic imprinting. Although conservation of imprinting in plants is limited, we show that some loci are imprinted in several different species. Moreover, our results suggest that different types of epigenetic regulation can be established either before or after fertilization. Imprinted 24-nucleotide small RNAs and their neighboring genes tend to express alleles from different parents. This association was not observed between 21-nucleotide small RNAs and their neighboring genes. Together, our findings suggest that the regulation of imprinting can be diverse, and genomic imprinting has evolutionary and biological significance.
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Affiliation(s)
- Chen Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, China, 225009
| | - Tingting Li
- China National Rice Research Institute, Hangzhou, China, 311401
| | - Shan Zhu
- Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, China, 330200
| | - Zehou Liu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China, 610041
| | - Zhenyuan Shi
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, China, 225009
| | - Xiaoming Zheng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Key Facilities for Crop Gene Resources and Genetic Improvement, Beijing, China, 100081
| | - Rui Chen
- Tianjin Institute of Agricultural Quality Standard and Testing Technology, Tianjin Academy of Agricultural Sciences, Tianjin, China, 300381
| | - Jianfeng Huang
- Shanghai Biotechnology Corporation, Shanghai, China, 201203
| | - Yi Shen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China, 210014
| | - Shiyou Luo
- Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, China, 330200
| | - Lei Wang
- China National Rice Research Institute, Hangzhou, China, 311401
| | - Qiao-Quan Liu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, China, 225009
| | - Zhiguo E
- China National Rice Research Institute, Hangzhou, China, 311401
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18
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Abstract
ABSTRACT
In the 1980s, mouse nuclear transplantation experiments revealed that both male and female parental genomes are required for successful development to term (McGrath and Solter, 1983; Surani and Barton, 1983). This non-equivalence of parental genomes is because imprinted genes are predominantly expressed from only one parental chromosome. Uniparental inheritance of these genomic regions causes paediatric growth disorders such as Beckwith–Wiedemann and Silver–Russell syndromes (reviewed in Peters, 2014). More than 100 imprinted genes have now been discovered and the functions of many of these genes have been assessed in murine models. The first such genes described were the fetal growth factor insulin-like growth factor 2 (Igf2) and its inhibitor Igf2 receptor (Igf2r) (DeChiara et al., 1991; Lau et al., 1994; Wang et al., 1994). Since then, it has emerged that most imprinted genes modulate fetal growth and resource acquisition in a variety of ways. First, imprinted genes are required for the development of a functional placenta, the organ that mediates the exchange of nutrients between mother and fetus. Second, these genes act in an embryo-autonomous manner to affect the growth rate and organogenesis. Finally, imprinted genes can signal the nutritional status between mother and fetus, and can modulate levels of maternal care. Importantly, many imprinted genes have been shown to affect postnatal growth and energy homeostasis. Given that abnormal birthweight correlates with adverse adult metabolic health, including obesity and cardiovascular disease, it is crucial to understand how the modulation of this dosage-sensitive, epigenetically regulated class of genes can contribute to fetal and postnatal growth, with implications for lifelong health and disease.
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Affiliation(s)
- Féaron C. Cassidy
- Queen Mary University of London, Charterhouse Square, LondonEC1M 6BQ, UK
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19
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Yang G, Liu Z, Gao L, Yu K, Feng M, Yao Y, Peng H, Hu Z, Sun Q, Ni Z, Xin M. Genomic Imprinting Was Evolutionarily Conserved during Wheat Polyploidization. THE PLANT CELL 2018; 30:37-47. [PMID: 29298834 PMCID: PMC5810578 DOI: 10.1105/tpc.17.00837] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 12/11/2017] [Accepted: 01/02/2018] [Indexed: 05/06/2023]
Abstract
Genomic imprinting is an epigenetic phenomenon that causes genes to be differentially expressed depending on their parent of origin. To evaluate the evolutionary conservation of genomic imprinting and the effects of ploidy on this process, we investigated parent-of-origin-specific gene expression patterns in the endosperm of diploid (Aegilops spp), tetraploid, and hexaploid wheat (Triticum spp) at various stages of development via high-throughput transcriptome sequencing. We identified 91, 135, and 146 maternally or paternally expressed genes (MEGs or PEGs, respectively) in diploid, tetraploid, and hexaploid wheat, respectively, 52.7% of which exhibited dynamic expression patterns at different developmental stages. Gene Ontology enrichment analysis suggested that MEGs and PEGs were involved in metabolic processes and DNA-dependent transcription, respectively. Nearly half of the imprinted genes exhibited conserved expression patterns during wheat hexaploidization. In addition, 40% of the homoeolog pairs originating from whole-genome duplication were consistently maternally or paternally biased in the different subgenomes of hexaploid wheat. Furthermore, imprinted expression was found for 41.2% and 50.0% of homolog pairs that evolved by tandem duplication after genome duplication in tetraploid and hexaploid wheat, respectively. These results suggest that genomic imprinting was evolutionarily conserved between closely related Triticum and Aegilops species and in the face of polyploid hybridization between species in these genera.
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Affiliation(s)
- Guanghui Yang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhenshan Liu
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Lulu Gao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Kuohai Yu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Man Feng
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
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20
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Inoue A, Jiang L, Lu F, Suzuki T, Zhang Y. Maternal H3K27me3 controls DNA methylation-independent imprinting. Nature 2017; 547:419-424. [PMID: 28723896 PMCID: PMC9674007 DOI: 10.1038/nature23262] [Citation(s) in RCA: 284] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 06/01/2017] [Indexed: 12/22/2022]
Abstract
Mammalian sperm and oocytes have different epigenetic landscapes and are organized in different fashion. Following fertilization, the initially distinct parental epigenomes become largely equalized with the exception of certain loci including imprinting control regions (ICRs). How parental chromatin becomes equalized and how ICRs escape from this reprogramming is largely unknown. Here we profiled parental allele-specific DNase I hypersensitive sites (DHSs) in mouse zygotes and morula embryos, and investigated the epigenetic mechanisms underlying allelic DHSs. Integrated analyses of DNA methylome and H3K27me3 ChIP-seq data sets revealed 76 genes with paternal allele-specific DHSs that are devoid of DNA methylation but harbor maternal allele-specific H3K27me3. Interestingly, these genes are paternally expressed in preimplantation embryos, and ectopic removal of H3K27me3 induces maternal allele expression. H3K27me3-dependent imprinting is largely lost in the embryonic cell lineage, but at least 5 genes maintain their imprinting in the extra-embryonic cell lineage. The 5 genes include all previously identified DNA methylation-independent imprinted autosomal genes. Thus, our study identifies maternal H3K27me3 as a DNA methylation-independent imprinting mechanism.
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21
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Xiao J, Jin R, Wagner D. Developmental transitions: integrating environmental cues with hormonal signaling in the chromatin landscape in plants. Genome Biol 2017; 18:88. [PMID: 28490341 PMCID: PMC5425979 DOI: 10.1186/s13059-017-1228-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Plant development is predominantly postembryonic and tuned in to respond to environmental cues. All living plant cells can be triggered to de-differentiate, assume different cell identities, or form a new organism. This developmental plasticity is thought to be an adaptation to the sessile lifestyle of plants. Recent discoveries have advanced our understanding of the orchestration of plant developmental switches by transcriptional master regulators, chromatin state changes, and hormone response pathways. Here, we review these recent advances with emphasis on the earliest stages of plant development and on the switch from pluripotency to differentiation in different plant organ systems.
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Affiliation(s)
- Jun Xiao
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Run Jin
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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22
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O'Brien EK, Wolf JB. The coadaptation theory for genomic imprinting. Evol Lett 2017; 1:49-59. [PMID: 30283638 PMCID: PMC6121825 DOI: 10.1002/evl3.5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 02/23/2017] [Accepted: 03/21/2017] [Indexed: 12/14/2022] Open
Abstract
Imprinted genes are peculiar in that expression of the two copies differs depending on whether the copy was maternally or paternally inherited. The discovery of this striking pattern of gene expression inspired myriad evolutionary theories, the most successful of which identify scenarios that create an asymmetry between the maternally and paternally inherited gene copies that favors silencing of one of the copies. Most notably, imprinting can evolve when gene dosage affects kin interactions (typically involving conflict) or when silencing enhances coadaptation by coordinating traits expressed by interacting kin. Although we have a well-established theory for the former process (the "Kinship Theory"), the coadaptation process has only been explored for the specific case of interactions between mothers and offspring. Here, we fill this critical gap in our understanding by developing a general "Coadaptation Theory" that explains how imprinting can evolve to coordinate interactions between all types of relatives. Using a simple model in which fitness of an individual is determined by an interaction between its own phenotype (and hence genotype) and that of its social partner(s), we find that when the relatedness of interactants differs through their maternally versus paternally inherited gene copies, then selection favors expression of the allele through which relatedness is higher. The predictions of this Coadaptation Theory potentially apply whenever a gene underlies traits that mediate the outcome of conspecific interactions, regardless of their mechanism or the type of organism, and therefore provide a potential explanation for enigmatic patterns of imprinting, including those underlying adult traits. By providing simple testable predictions that often directly contrast with those derived from alternative theories, our model should play an important role in consolidating our understanding of the evolution of imprinting across genes and species, which will ultimately provide crucial insights into imprinted gene function and dysfunction.
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Affiliation(s)
- Eleanor K. O'Brien
- Milner Centre for Evolution and Department of Biology & BiochemistryUniversity of BathClaverton DownBathBA2 7AYUnited Kingdom
| | - Jason B. Wolf
- Milner Centre for Evolution and Department of Biology & BiochemistryUniversity of BathClaverton DownBathBA2 7AYUnited Kingdom
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23
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Nakamura S, Pourkheirandish M, Morishige H, Sameri M, Sato K, Komatsuda T. Quantitative Trait Loci and Maternal Effects Affecting the Strong Grain Dormancy of Wild Barley ( Hordeum vulgare ssp. spontaneum). FRONTIERS IN PLANT SCIENCE 2017; 8:1840. [PMID: 29163576 PMCID: PMC5674934 DOI: 10.3389/fpls.2017.01840] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 10/10/2017] [Indexed: 05/05/2023]
Abstract
Wild barley (Hordeum vulgare ssp. spontaneum) has strong grain dormancy, a trait that may enhance its survival in non-cultivated environments; by contrast, cultivated barley (Hordeum vulgare ssp. vulgare) has weaker dormancy, allowing uniform germination in cultivation. Malting barley cultivars have been bred for especially weak dormancy to optimize their use in malt production. Here, we analyzed the genetic mechanism of this difference in seed dormancy, using recombinant inbred lines (RILs) derived from a cross between the wild barley accession 'H602' and the malting barley cultivar 'Kanto Nakate Gold (KNG)'. Grains of H602 and KNG harvested at physiological maturity and dried at 30°C for 7 days had germination of approximately 0 and 100%, respectively. Analysis of quantitative trait loci (QTL) affecting grain dormancy identified the well-known major dormancy QTL SD1 and SD2 (located near the centromeric region and at the distal end of the long arm of chromosome 5H, respectively), and QTL at the end of the long arm of chromosome 4H and in the middle of the long arm of chromosome 5H. We designated these four QTL Qsd1-OK, Qsd2-OK, Qsdw-4H, and Qsdw-5H, and they explained approximately 6, 38, 3, and 13% of the total phenotypic variation, respectively. RILs carrying H602 alleles showed increased dormancy levels for all QTL. The QTL acted additively and did not show epistasis or QTL-environment interactions. Comparison of QTL locations indicated that all QTL except Qsdw-5H are likely the same as the QTL previously detected in the doubled haploid population from a cross between the malting cultivar 'Haruna Nijo' and 'H602.' We further examined Qsd2-OK and Qsdw-5H by analyzing the segregation of phenotypes and genotypes of F2 progenies derived from crosses between RILs carrying specific segments of chromosome 5H from H602 in the KNG background. This analysis confirmed that the two genomic regions corresponding to these QTL are involved in the regulation of grain dormancy. Germination tests of F1 grains derived from reciprocal crosses between H602 and KNG revealed that the H602 strong dormancy phenotype shows maternal inheritance with incomplete dominance. These results provide new insight into the mechanisms regulating grain dormancy in barley.
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Affiliation(s)
- Shingo Nakamura
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Japan
- *Correspondence: Shingo Nakamura,
| | - Mohammad Pourkheirandish
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Japan
- Plant Breeding Institute, The University of Sydney, Sydney, NSW, Australia
| | - Hiromi Morishige
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Mohammad Sameri
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Takao Komatsuda
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Japan
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24
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Piskurewicz U, Iwasaki M, Susaki D, Megies C, Kinoshita T, Lopez-Molina L. Dormancy-specific imprinting underlies maternal inheritance of seed dormancy in Arabidopsis thaliana. eLife 2016; 5. [PMID: 28005006 PMCID: PMC5243116 DOI: 10.7554/elife.19573] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 12/21/2016] [Indexed: 01/31/2023] Open
Abstract
Mature seed dormancy is a vital plant trait that prevents germination out of season. In Arabidopsis, the trait can be maternally regulated but the underlying mechanisms sustaining this regulation, its general occurrence and its biological significance among accessions are poorly understood. Upon seed imbibition, the endosperm is essential to repress the germination of dormant seeds. Investigation of genomic imprinting in the mature seed endosperm led us to identify a novel set of imprinted genes that are expressed upon seed imbibition. Remarkably, programs of imprinted gene expression are adapted according to the dormancy status of the seed. We provide direct evidence that imprinted genes play a role in regulating germination processes and that preferential maternal allelic expression can implement maternal inheritance of seed dormancy levels. DOI:http://dx.doi.org/10.7554/eLife.19573.001
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Affiliation(s)
- Urszula Piskurewicz
- Department of Plant Biology, University of Geneva, Geneva, Switzerland.,Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Mayumi Iwasaki
- Department of Plant Biology, University of Geneva, Geneva, Switzerland.,Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Daichi Susaki
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Christian Megies
- Department of Plant Biology, University of Geneva, Geneva, Switzerland.,Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Tetsu Kinoshita
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Luis Lopez-Molina
- Department of Plant Biology, University of Geneva, Geneva, Switzerland.,Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
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Florez-Rueda AM, Paris M, Schmidt A, Widmer A, Grossniklaus U, Städler T. Genomic Imprinting in the Endosperm Is Systematically Perturbed in Abortive Hybrid Tomato Seeds. Mol Biol Evol 2016; 33:2935-2946. [PMID: 27601611 PMCID: PMC5062328 DOI: 10.1093/molbev/msw175] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Hybrid seed failure represents an important postzygotic barrier to interbreeding among species of wild tomatoes (Solanum section Lycopersicon) and other flowering plants. We studied genome-wide changes associated with hybrid seed abortion in the closely related Solanum peruvianum and S. chilense where hybrid crosses yield high proportions of inviable seeds due to endosperm failure and arrested embryo development. Based on differences of seed size in reciprocal hybrid crosses and developmental evidence implicating endosperm failure, we hypothesized that perturbed genomic imprinting is involved in this strong postzygotic barrier. Consequently, we surveyed the transcriptomes of developing endosperms from intra- and inter-specific crosses using tissues isolated by laser-assisted microdissection. We implemented a novel approach to estimate parent-of-origin–specific expression using both homozygous and heterozygous nucleotide differences between parental individuals and identified candidate imprinted genes. Importantly, we uncovered systematic shifts of “normal” (intraspecific) maternal:paternal transcript proportions in hybrid endosperms; the average maternal proportion of gene expression increased in both crossing directions but was stronger with S. peruvianum in the maternal role. These genome-wide shifts almost entirely eliminated paternally expressed imprinted genes in S. peruvianum hybrid endosperm but also affected maternally expressed imprinted genes and all other assessed genes. These profound, systematic changes in parental expression proportions suggest that core processes of transcriptional regulation are functionally compromised in hybrid endosperm and contribute to hybrid seed failure.
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Affiliation(s)
- Ana M Florez-Rueda
- Plant Ecological Genetics, Institute of Integrative Biology & Zurich-Basel Plant Science Center, ETH Zurich, Zurich, Switzerland
| | - Margot Paris
- Plant Ecological Genetics, Institute of Integrative Biology & Zurich-Basel Plant Science Center, ETH Zurich, Zurich, Switzerland
| | - Anja Schmidt
- Plant Developmental Genetics, Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Alex Widmer
- Plant Ecological Genetics, Institute of Integrative Biology & Zurich-Basel Plant Science Center, ETH Zurich, Zurich, Switzerland
| | - Ueli Grossniklaus
- Plant Developmental Genetics, Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Thomas Städler
- Plant Ecological Genetics, Institute of Integrative Biology & Zurich-Basel Plant Science Center, ETH Zurich, Zurich, Switzerland
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Hatorangan MR, Laenen B, Steige KA, Slotte T, Köhler C. Rapid Evolution of Genomic Imprinting in Two Species of the Brassicaceae. THE PLANT CELL 2016; 28:1815-27. [PMID: 27465027 PMCID: PMC5006707 DOI: 10.1105/tpc.16.00304] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 06/16/2016] [Accepted: 07/21/2016] [Indexed: 05/21/2023]
Abstract
Genomic imprinting is an epigenetic phenomenon occurring in mammals and flowering plants that causes genes to adopt a parent-of-origin-specific mode of expression. While the imprinting status of genes is well conserved in mammals, clear estimates for the degree of conservation were lacking in plants. We therefore analyzed the genome-wide imprinting status of Capsella rubella, which shared a common recent ancestor with Arabidopsis thaliana ∼10 to 14 million years ago. However, only ∼14% of maternally expressed genes (MEGs) and ∼29% of paternally expressed genes (PEGs) in C. rubella were commonly imprinted in both species, revealing that genomic imprinting is a rapidly evolving phenomenon in plants. Nevertheless, conserved PEGs exhibited signs of selection, suggesting that a subset of imprinted genes play an important functional role and are therefore maintained in plants. Like in Arabidopsis, PEGs in C. rubella are frequently associated with the presence of transposable elements that preferentially belong to helitron and MuDR families. Our data further reveal that MEGs and PEGs differ in their targeting by 24-nucleotide small RNAs and asymmetric DNA methylation, suggesting different mechanisms establishing DNA methylation at MEGs and PEGs.
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Affiliation(s)
- Marcelinus R Hatorangan
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 750 07 Uppsala, Sweden
| | - Benjamin Laenen
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden
| | - Kim A Steige
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden
| | - Tanja Slotte
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden
| | - Claudia Köhler
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 750 07 Uppsala, Sweden
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27
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Abstract
Genomic imprinting, an inherently epigenetic phenomenon defined by parent of origin-dependent gene expression, is observed in mammals and flowering plants. Genome-scale surveys of imprinted expression and the underlying differential epigenetic marks have led to the discovery of hundreds of imprinted plant genes and confirmed DNA and histone methylation as key regulators of plant imprinting. However, the biological roles of the vast majority of imprinted plant genes are unknown, and the evolutionary forces shaping plant imprinting remain rather opaque. Here, we review the mechanisms of plant genomic imprinting and discuss theories of imprinting evolution and biological significance in light of recent findings.
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Affiliation(s)
- Jessica A Rodrigues
- Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, California 94720, USA
| | - Daniel Zilberman
- Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, California 94720, USA
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28
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Remnant EJ, Ashe A, Young PE, Buchmann G, Beekman M, Allsopp MH, Suter CM, Drewell RA, Oldroyd BP. Parent-of-origin effects on genome-wide DNA methylation in the Cape honey bee (Apis mellifera capensis) may be confounded by allele-specific methylation. BMC Genomics 2016; 17:226. [PMID: 26969617 PMCID: PMC4788913 DOI: 10.1186/s12864-016-2506-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 02/19/2016] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Intersexual genomic conflict sometimes leads to unequal expression of paternal and maternal alleles in offspring, resulting in parent-of-origin effects. In honey bees reciprocal crosses can show strong parent-of-origin effects, supporting theoretical predictions that genomic imprinting occurs in this species. Mechanisms behind imprinting in honey bees are unclear but differential DNA methylation in eggs and sperm suggests that DNA methylation could be involved. Nonetheless, because DNA methylation is multifunctional, it is difficult to separate imprinting from other roles of methylation. Here we use a novel approach to investigate parent-of-origin DNA methylation in honey bees. In the subspecies Apis mellifera capensis, reproduction of females occurs either sexually by fertilization of eggs with sperm, or via thelytokous parthenogenesis, producing female embryos derived from two maternal genomes. RESULTS We compared genome-wide methylation patterns of sexually-produced, diploid embryos laid by a queen, with parthenogenetically-produced diploid embryos laid by her daughters. Thelytokous embryos inheriting two maternal genomes had fewer hypermethylated genes compared to fertilized embryos, supporting the prediction that fertilized embryos have increased methylation due to inheritance of a paternal genome. However, bisulfite PCR and sequencing of a differentially methylated gene, Stan (GB18207) showed strong allele-specific methylation that was maintained in both fertilized and thelytokous embryos. For this gene, methylation was associated with haplotype, not parent of origin. CONCLUSIONS The results of our study are consistent with predictions from the kin theory of genomic imprinting. However, our demonstration of allele-specific methylation based on sequence shows that genome-wide differential methylation studies can potentially confound imprinting and allele-specific methylation. It further suggests that methylation patterns are heritable or that specific sequence motifs are targets for methylation in some genes.
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Affiliation(s)
- Emily J. Remnant
- />Behavior and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences A12, University of Sydney, Room 248, Macleay Building (A12), Sydney, NSW 2006 Australia
| | - Alyson Ashe
- />School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006 Australia
| | - Paul E. Young
- />Victor Chang Cardiac Research Institute, Lowy Packer Building, 405 Liverpool Street, Darlinghurst, NSW 2010 Australia
- />University of New South Wales, Kensington, NSW 2033 Australia
| | - Gabriele Buchmann
- />Behavior and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences A12, University of Sydney, Room 248, Macleay Building (A12), Sydney, NSW 2006 Australia
| | - Madeleine Beekman
- />Behavior and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences A12, University of Sydney, Room 248, Macleay Building (A12), Sydney, NSW 2006 Australia
| | - Michael H. Allsopp
- />Honey Bee Research Section, ARC-Plant Protection Research Institute, Private Bag X5017, Stellenbosch, South Africa
| | - Catherine M. Suter
- />Victor Chang Cardiac Research Institute, Lowy Packer Building, 405 Liverpool Street, Darlinghurst, NSW 2010 Australia
- />University of New South Wales, Kensington, NSW 2033 Australia
| | - Robert A. Drewell
- />Biology Department, Clark University, 950 Main Street, Worcester, MA 01610 USA
| | - Benjamin P. Oldroyd
- />Behavior and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences A12, University of Sydney, Room 248, Macleay Building (A12), Sydney, NSW 2006 Australia
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Quantitative Genetics Identifies Cryptic Genetic Variation Involved in the Paternal Regulation of Seed Development. PLoS Genet 2016; 12:e1005806. [PMID: 26811909 PMCID: PMC4727937 DOI: 10.1371/journal.pgen.1005806] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/21/2015] [Indexed: 12/19/2022] Open
Abstract
Embryonic development requires a correct balancing of maternal and paternal genetic information. This balance is mediated by genomic imprinting, an epigenetic mechanism that leads to parent-of-origin-dependent gene expression. The parental conflict (or kinship) theory proposes that imprinting can evolve due to a conflict between maternal and paternal alleles over resource allocation during seed development. One assumption of this theory is that paternal alleles can regulate seed growth; however, paternal effects on seed size are often very low or non-existent. We demonstrate that there is a pool of cryptic genetic variation in the paternal control of Arabidopsis thaliana seed development. Such cryptic variation can be exposed in seeds that maternally inherit a medea mutation, suggesting that MEA acts as a maternal buffer of paternal effects. Genetic mapping using recombinant inbred lines, and a novel method for the mapping of parent-of-origin effects using whole-genome sequencing of segregant bulks, indicate that there are at least six loci with small, paternal effects on seed development. Together, our analyses reveal the existence of a pool of hidden genetic variation on the paternal control of seed development that is likely shaped by parental conflict.
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Cis-acting determinants of paramutation. Semin Cell Dev Biol 2015; 44:22-32. [DOI: 10.1016/j.semcdb.2015.08.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 08/20/2015] [Indexed: 11/23/2022]
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31
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Yudin NS, Voevoda MI. Molecular genetic markers of economically important traits in dairy cattle. RUSS J GENET+ 2015. [DOI: 10.1134/s1022795415050087] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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32
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Bai F, Settles AM. Imprinting in plants as a mechanism to generate seed phenotypic diversity. FRONTIERS IN PLANT SCIENCE 2014; 5:780. [PMID: 25674092 PMCID: PMC4307191 DOI: 10.3389/fpls.2014.00780] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 12/16/2014] [Indexed: 05/21/2023]
Abstract
Normal plant development requires epigenetic regulation to enforce changes in developmental fate. Genomic imprinting is a type of epigenetic regulation in which identical alleles of genes are expressed in a parent-of-origin dependent manner. Deep sequencing of transcriptomes has identified hundreds of imprinted genes with scarce evidence for the developmental importance of individual imprinted loci. Imprinting is regulated through global DNA demethylation in the central cell prior to fertilization and directed repression of individual loci with the Polycomb Repressive Complex 2 (PRC2). There is significant evidence for transposable elements and repeat sequences near genes acting as cis-elements to determine imprinting status of a gene, implying that imprinted gene expression patterns may evolve randomly and at high frequency. Detailed genetic analysis of a few imprinted loci suggests an imprinted pattern of gene expression is often dispensable for seed development. Few genes show conserved imprinted expression within or between plant species. These data are not fully explained by current models for the evolution of imprinting in plant seeds. We suggest that imprinting may have evolved to provide a mechanism for rapid neofunctionalization of genes during seed development to increase phenotypic diversity of seeds.
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Affiliation(s)
| | - A. M. Settles
- *Correspondence: A. M. Settles, Horticultural Sciences Department and Plant Molecular and Cellular Biology Program, University of Florida, P. O. Box 110690, Gainesville, FL 32611-0690, USA e-mail:
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