1
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Vigneau J, Martinho C, Godfroy O, Zheng M, Haas FB, Borg M, Coelho SM. Interactions between U and V sex chromosomes during the life cycle of Ectocarpus. Development 2024; 151:dev202677. [PMID: 38512707 PMCID: PMC11057875 DOI: 10.1242/dev.202677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 03/01/2024] [Indexed: 03/23/2024]
Abstract
In many animals and flowering plants, sex determination occurs in the diploid phase of the life cycle with XX/XY or ZW/ZZ sex chromosomes. However, in early diverging plants and most macroalgae, sex is determined by female (U) or male (V) sex chromosomes in a haploid phase called the gametophyte. Once the U and V chromosomes unite at fertilization to produce a diploid sporophyte, sex determination no longer occurs, raising key questions about the fate of the U and V sex chromosomes in the sporophyte phase. Here, we investigate genetic and molecular interactions of the UV sex chromosomes in both the haploid and diploid phases of the brown alga Ectocarpus. We reveal extensive developmental regulation of sex chromosome genes across its life cycle and implicate the TALE-HD transcription factor OUROBOROS in suppressing sex determination in the diploid phase. Small RNAs may also play a role in the repression of a female sex-linked gene, and transition to the diploid sporophyte coincides with major reconfiguration of histone H3K79me2, suggesting a more intricate role for this histone mark in Ectocarpus development than previously appreciated.
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Affiliation(s)
| | | | - Olivier Godfroy
- Roscoff Biological Station, CNRS-Sorbonne University, Place Georges Teissier, Roscoff 29680, France
| | - Min Zheng
- Max Planck Institute for Biology, 72076 Tübingen, Germany
| | - Fabian B. Haas
- Max Planck Institute for Biology, 72076 Tübingen, Germany
| | - Michael Borg
- Max Planck Institute for Biology, 72076 Tübingen, Germany
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2
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Kerckhofs E, Schubert D. Conserved functions of chromatin regulators in basal Archaeplastida. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1301-1311. [PMID: 37680033 DOI: 10.1111/tpj.16446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 08/15/2023] [Accepted: 08/18/2023] [Indexed: 09/09/2023]
Abstract
Chromatin is a dynamic network that regulates genome organization and gene expression. Different types of chromatin regulators are highly conserved among Archaeplastida, including unicellular algae, while some chromatin genes are only present in land plant genomes. Here, we review recent advances in understanding the function of conserved chromatin factors in basal land plants and algae. We focus on the role of Polycomb-group genes which mediate H3K27me3-based silencing and play a role in balancing gene dosage and regulating haploid-to-diploid transitions by tissue-specific repression of the transcription factors KNOX and BELL in many representatives of the green lineage. Moreover, H3K27me3 predominantly occupies repetitive elements which can lead to their silencing in a unicellular alga and basal land plants, while it covers mostly protein-coding genes in higher land plants. In addition, we discuss the role of nuclear matrix constituent proteins as putative functional lamin analogs that are highly conserved among land plants and might have an ancestral function in stress response regulation. In summary, our review highlights the importance of studying chromatin regulation in a wide range of organisms in the Archaeplastida.
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Affiliation(s)
- Elise Kerckhofs
- Epigenetics of Plants, Institute for Biology, Freie Universität Berlin, Berlin, Germany
| | - Daniel Schubert
- Epigenetics of Plants, Institute for Biology, Freie Universität Berlin, Berlin, Germany
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3
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Montgomery SA, Berger F. Paternal imprinting in Marchantia polymorpha. THE NEW PHYTOLOGIST 2024; 241:1000-1006. [PMID: 37936346 DOI: 10.1111/nph.19377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 10/09/2023] [Indexed: 11/09/2023]
Abstract
We are becoming aware of a growing number of organisms that do not express genetic information equally from both parents as a result of an epigenetic phenomenon called genomic imprinting. Recently, it was shown that the entire paternal genome is repressed during the diploid phase of the life cycle of the liverwort Marchantia polymorpha. The deposition of the repressive epigenetic mark H3K27me3 on the male pronucleus is responsible for the imprinted state, which is reset by the end of meiosis. Here, we put these recent reports in perspective of other forms of imprinting and discuss the potential mechanisms of imprinting in bryophytes and the causes of its evolution.
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Affiliation(s)
- Sean A Montgomery
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), C/ del Dr Aiguader, 88, 08003, Barcelona, Spain
| | - Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr Bohr-Gasse 3, 1030, Vienna, Austria
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4
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Wang M, Tabeta H, Ohtaka K, Kuwahara A, Nishihama R, Ishikawa T, Toyooka K, Sato M, Wakazaki M, Akashi H, Tsugawa H, Shoji T, Okazaki Y, Yoshida K, Sato R, Ferjani A, Kohchi T, Hirai MY. The phosphorylated pathway of serine biosynthesis affects sperm, embryo, and sporophyte development, and metabolism in Marchantia polymorpha. Commun Biol 2024; 7:102. [PMID: 38267515 PMCID: PMC10808223 DOI: 10.1038/s42003-023-05746-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 12/27/2023] [Indexed: 01/26/2024] Open
Abstract
Serine metabolism is involved in various biological processes. Here we investigate primary functions of the phosphorylated pathway of serine biosynthesis in a non-vascular plant Marchantia polymorpha by analyzing knockout mutants of MpPGDH encoding 3-phosphoglycerate dehydrogenase in this pathway. Growth phenotypes indicate that serine from the phosphorylated pathway in the dark is crucial for thallus growth. Sperm development requires serine from the phosphorylated pathway, while egg formation does not. Functional MpPGDH in the maternal genome is necessary for embryo and sporophyte development. Under high CO2 where the glycolate pathway of serine biosynthesis is inhibited, suppressed thallus growth of the mutants is not fully recovered by exogenously-supplemented serine, suggesting the importance of serine homeostasis involving the phosphorylated and glycolate pathways. Metabolomic phenotypes indicate that the phosphorylated pathway mainly influences the tricarboxylic acid cycle, the amino acid and nucleotide metabolism, and lipid metabolism. These results indicate the importance of the phosphorylated pathway of serine biosynthesis in the dark, in the development of sperm, embryo, and sporophyte, and metabolism in M. polymorpha.
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Affiliation(s)
- Mengyao Wang
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Hiromitsu Tabeta
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
- Department of Biology, Tokyo Gakugei University, Tokyo, Japan
| | - Kinuka Ohtaka
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
- Department of Chemical and Biological Sciences, Japan Women's University, Tokyo, Japan
| | - Ayuko Kuwahara
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Tokyo, Japan
| | - Toshiki Ishikawa
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | | | - Mayuko Sato
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Mayumi Wakazaki
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | | | - Hiroshi Tsugawa
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Tsubasa Shoji
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Yozo Okazaki
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Bioresource, Mie University, Tsushi, Japan
| | - Keisuke Yoshida
- Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Ryoichi Sato
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Ali Ferjani
- Department of Biology, Tokyo Gakugei University, Tokyo, Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Masami Yokota Hirai
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan.
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan.
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5
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McDaniel SF. Divergent outcomes of genetic conflict on the UV sex chromosomes of Marchantia polymorpha and Ceratodon purpureus. Curr Opin Genet Dev 2023; 83:102129. [PMID: 37864936 DOI: 10.1016/j.gde.2023.102129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 09/22/2023] [Accepted: 09/24/2023] [Indexed: 10/23/2023]
Abstract
In species with separate sexes, the genome must produce two distinct developmental programs. Sexually dimorphic development may be controlled by either sex-limited loci or biased expression of loci transmitted through both sexes. Variation in the gene content of sex-limited chromosomes demonstrates that eukaryotic species differ markedly in the roles of these two mechanisms in governing sexual dimorphism. The bryophyte model systems Marchantia polymorpha and Ceratodon purpureus provide a particularly striking contrast. Although both species possess a haploid UV sex chromosome system, in which females carry a U chromosome and males carry a V, M. polymorpha relies on biased autosomal expression, while in C. purpureus, sex-linked genes drive dimorphism. Framing these genetic architectures as divergent outcomes of genetic conflict highlights comparative genomic analyses to better understand the evolution of sexual dimorphism.
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Affiliation(s)
- Stuart F McDaniel
- Biology Department, University of Florida, Gainesville, FL 32611-8525, USA.
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6
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Sandler G, Agrawal AF, Wright SI. Population Genomics of the Facultatively Sexual Liverwort Marchantia polymorpha. Genome Biol Evol 2023; 15:evad196. [PMID: 37883717 PMCID: PMC10667032 DOI: 10.1093/gbe/evad196] [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: 12/16/2022] [Revised: 10/15/2023] [Accepted: 10/18/2023] [Indexed: 10/28/2023] Open
Abstract
The population genomics of facultatively sexual organisms are understudied compared with their abundance across the tree of life. We explore patterns of genetic diversity in two subspecies of the facultatively sexual liverwort Marchantia polymorpha using samples from across Southern Ontario, Canada. Despite the ease with which M. polymorpha should be able to propagate asexually, we find no evidence of strictly clonal descent among our samples and little to no signal of isolation by distance. Patterns of identity-by-descent tract sharing further showed evidence of recent recombination and close relatedness between geographically distant isolates, suggesting long distance gene flow and at least a modest frequency of sexual reproduction. However, the M. polymorpha genome contains overall very low levels of nucleotide diversity and signs of inefficient selection evidenced by a relatively high fraction of segregating deleterious variants. We interpret these patterns as possible evidence of the action of linked selection and a small effective population size due to past generations of asexual propagation. Overall, the M. polymorpha genome harbors signals of a complex history of both sexual and asexual reproduction.
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Affiliation(s)
- George Sandler
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Aneil F Agrawal
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
- Center for Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
- Center for Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
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7
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Hisanaga T, Romani F, Wu S, Kowar T, Wu Y, Lintermann R, Fridrich A, Cho CH, Chaumier T, Jamge B, Montgomery SA, Axelsson E, Akimcheva S, Dierschke T, Bowman JL, Fujiwara T, Hirooka S, Miyagishima SY, Dolan L, Tirichine L, Schubert D, Berger F. The Polycomb repressive complex 2 deposits H3K27me3 and represses transposable elements in a broad range of eukaryotes. Curr Biol 2023; 33:4367-4380.e9. [PMID: 37738971 DOI: 10.1016/j.cub.2023.08.073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 06/19/2023] [Accepted: 08/24/2023] [Indexed: 09/24/2023]
Abstract
The mobility of transposable elements (TEs) contributes to evolution of genomes. Their uncontrolled activity causes genomic instability; therefore, expression of TEs is silenced by host genomes. TEs are marked with DNA and H3K9 methylation, which are associated with silencing in flowering plants, animals, and fungi. However, in distantly related groups of eukaryotes, TEs are marked by H3K27me3 deposited by the Polycomb repressive complex 2 (PRC2), an epigenetic mark associated with gene silencing in flowering plants and animals. The direct silencing of TEs by PRC2 has so far only been shown in one species of ciliates. To test if PRC2 silences TEs in a broader range of eukaryotes, we generated mutants with reduced PRC2 activity and analyzed the role of PRC2 in extant species along the lineage of Archaeplastida and in the diatom P. tricornutum. In this diatom and the red alga C. merolae, a greater proportion of TEs than genes were repressed by PRC2, whereas a greater proportion of genes than TEs were repressed by PRC2 in bryophytes. In flowering plants, TEs contained potential cis-elements recognized by transcription factors and associated with neighbor genes as transcriptional units repressed by PRC2. Thus, silencing of TEs by PRC2 is observed not only in Archaeplastida but also in diatoms and ciliates, suggesting that PRC2 deposited H3K27me3 to silence TEs in the last common ancestor of eukaryotes. We hypothesize that during the evolution of Archaeplastida, TE fragments marked with H3K27me3 were selected to shape transcriptional regulation, controlling networks of genes regulated by PRC2.
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Affiliation(s)
- Tetsuya Hisanaga
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Facundo Romani
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Shuangyang Wu
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Teresa Kowar
- Epigenetics of Plants, Institute of Biology, Freie Universität Berlin, 14195 Berlin, Germany
| | - Yue Wu
- Nantes Université, CNRS, US2B, UMR 6286, 44000 Nantes, France
| | - Ruth Lintermann
- Epigenetics of Plants, Institute of Biology, Freie Universität Berlin, 14195 Berlin, Germany
| | - Arie Fridrich
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Chung Hyun Cho
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria; Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, South Korea
| | | | - Bhagyshree Jamge
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Sean A Montgomery
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Elin Axelsson
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Svetlana Akimcheva
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Tom Dierschke
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
| | - John L Bowman
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia; ARC Centre of Excellence for Plant Success in Nature and Agriculture, Monash University, Clayton, Melbourne, VIC 3800, Australia
| | - Takayuki Fujiwara
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan; Department of Genetics, Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
| | - Shunsuke Hirooka
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan; Department of Genetics, Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
| | - Shin-Ya Miyagishima
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan; Department of Genetics, Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
| | - Liam Dolan
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Leila Tirichine
- Nantes Université, CNRS, US2B, UMR 6286, 44000 Nantes, France
| | - Daniel Schubert
- Epigenetics of Plants, Institute of Biology, Freie Universität Berlin, 14195 Berlin, Germany.
| | - Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
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8
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Wang N, Wang Z, Tzourtzou S, Wang X, Bi X, Leimeister J, Xu L, Sakamoto T, Matsunaga S, Schaller A, Jiang H, Liu C. The plant nuclear lamina disassembles to regulate genome folding in stress conditions. NATURE PLANTS 2023:10.1038/s41477-023-01457-2. [PMID: 37400513 PMCID: PMC10356608 DOI: 10.1038/s41477-023-01457-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 06/07/2023] [Indexed: 07/05/2023]
Abstract
The nuclear lamina is a complex network of nuclear lamins and lamin-associated nuclear membrane proteins, which scaffold the nucleus to maintain structural integrity. In Arabidopsis thaliana, nuclear matrix constituent proteins (NMCPs) are essential components of the nuclear lamina and are required to maintain the structural integrity of the nucleus and specific perinuclear chromatin anchoring. At the nuclear periphery, suppressed chromatin overlapping with repetitive sequences and inactive protein-coding genes are enriched. At a chromosomal level, plant chromatin organization in interphase nuclei is flexible and responds to various developmental cues and environmental stimuli. On the basis of these observations in Arabidopsis, and given the role of NMCP genes (CRWN1 and CRWN4) in organizing chromatin positioning at the nuclear periphery, one can expect considerable changes in chromatin-nuclear lamina interactions when the global chromatin organization patterns are being altered in plants. Here we report the highly flexible nature of the plant nuclear lamina, which disassembles substantially under various stress conditions. Focusing on heat stress, we reveal that chromatin domains, initially tethered to the nuclear envelope, remain largely associated with CRWN1 and become scattered in the inner nuclear space. By investigating the three-dimensional chromatin contact network, we further reveal that CRWN1 proteins play a structural role in shaping the changes in genome folding under heat stress. Also, CRWN1 acts as a negative transcriptional coregulator to modulate the shift of the plant transcriptome profile in response to heat stress.
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Affiliation(s)
- Nan Wang
- Department of Epigenetics, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Zhidan Wang
- Department of Epigenetics, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Sofia Tzourtzou
- Department of Epigenetics, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Xu Wang
- Department of Plant Physiology and Biochemistry, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Xiuli Bi
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
- Shandong Provincial Hospital, Shandong First Medical University, Jinan, China
| | - Julia Leimeister
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Linhao Xu
- Applied Chromosome Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Takuya Sakamoto
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Japan
| | - Sachihiro Matsunaga
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Andreas Schaller
- Department of Plant Physiology and Biochemistry, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Hua Jiang
- Applied Chromosome Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Chang Liu
- Department of Epigenetics, Institute of Biology, University of Hohenheim, Stuttgart, Germany.
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9
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Inoue A. Noncanonical imprinting: intergenerational epigenetic inheritance mediated by Polycomb complexes. Curr Opin Genet Dev 2023; 78:102015. [PMID: 36577293 DOI: 10.1016/j.gde.2022.102015] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 11/06/2022] [Accepted: 11/22/2022] [Indexed: 12/27/2022]
Abstract
Genomic imprinting is illustrative of intergenerational epigenetic inheritance. The passage of parental genomes into the embryo is accompanied by epigenetic modifications, resulting in imprinted monoallelic gene expression in mammals. Some imprinted genes are regulated by maternal inheritance of H3K27me3, which is termed noncanonical imprinting. Noncanonical imprinting is established by Polycomb repressive complexes during oogenesis and maintained in preimplantation embryos and extraembryonic tissues, including the placenta. Recent studies of noncanonical imprinting have contributed to our understanding of chromatin regulation in oocytes and early embryos, imprinted X-chromosome inactivation, secondary differentially DNA-methylated regions, and the anomalies of cloned mice. Here, I summarize the current knowledge of noncanonical imprinting and remark on analogous mechanisms in invertebrates and plants.
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Affiliation(s)
- Azusa Inoue
- Laboratory for Epigenome Inheritance, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan; Tokyo Metropolitan University, Hachioji 192-0397, Japan.
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10
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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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11
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Montgomery SA, Hisanaga T, Wang N, Axelsson E, Akimcheva S, Sramek M, Liu C, Berger F. Polycomb-mediated repression of paternal chromosomes maintains haploid dosage in diploid embryos of Marchantia. eLife 2022; 11:79258. [PMID: 35996955 PMCID: PMC9402228 DOI: 10.7554/elife.79258] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/18/2022] [Indexed: 02/06/2023] Open
Abstract
Complex mechanisms regulate gene dosage throughout eukaryotic life cycles. Mechanisms controlling gene dosage have been extensively studied in animals, however it is unknown how generalizable these mechanisms are to diverse eukaryotes. Here, we use the haploid plant Marchantia polymorpha to assess gene dosage control in its short-lived diploid embryo. We show that throughout embryogenesis, paternal chromosomes are repressed resulting in functional haploidy. The paternal genome is targeted for genomic imprinting by the Polycomb mark H3K27me3 starting at fertilization, rendering the maternal genome in control of embryogenesis. Maintaining haploid gene dosage by this new form of imprinting is essential for embryonic development. Our findings illustrate how haploid-dominant species can regulate gene dosage through paternal chromosome inactivation and initiates the exploration of the link between life cycle history and gene dosage in a broader range of organisms.
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Affiliation(s)
- Sean Akira Montgomery
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria.,Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Tetsuya Hisanaga
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Nan Wang
- Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Elin Axelsson
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Svetlana Akimcheva
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Milos Sramek
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Chang Liu
- Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
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