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Mencia R. A place for everything and everything in its place: linker histone H1 controls heterochromatic condensation through phase separation. Plant Cell 2024; 36:1584-1585. [PMID: 38428945 DOI: 10.1093/plcell/koae032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 01/11/2024] [Indexed: 03/03/2024]
Affiliation(s)
- Regina Mencia
- Assistant Features Editor, The Plant Cell, American Society of Plant Biologists, USA
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
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2
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He S, Yu Y, Wang L, Zhang J, Bai Z, Li G, Li P, Feng X. Linker histone H1 drives heterochromatin condensation via phase separation in Arabidopsis. Plant Cell 2024; 36:1829-1843. [PMID: 38309957 DOI: 10.1093/plcell/koae034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/01/2023] [Accepted: 11/25/2023] [Indexed: 02/05/2024]
Abstract
In the eukaryotic nucleus, heterochromatin forms highly condensed, visible foci known as heterochromatin foci (HF). These HF are enriched with linker histone H1, a key player in heterochromatin condensation and silencing. However, it is unknown how H1 aggregates HF and condenses heterochromatin. In this study, we established that H1 facilitates heterochromatin condensation by enhancing inter- and intrachromosomal interactions between and within heterochromatic regions of the Arabidopsis (Arabidopsis thaliana) genome. We demonstrated that H1 drives HF formation via phase separation, which requires its C-terminal intrinsically disordered region (C-IDR). A truncated H1 lacking the C-IDR fails to form foci or recover HF in the h1 mutant background, whereas C-IDR with a short stretch of the globular domain (18 out of 71 amino acids) is sufficient to rescue both defects. In addition, C-IDR is essential for H1's roles in regulating nucleosome repeat length and DNA methylation in Arabidopsis, indicating that phase separation capability is required for chromatin functions of H1. Our data suggest that bacterial H1-like proteins, which have been shown to condense DNA, are intrinsically disordered and capable of mediating phase separation. Therefore, we propose that phase separation mediated by H1 or H1-like proteins may represent an ancient mechanism for condensing chromatin and DNA.
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Affiliation(s)
- Shengbo He
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Yiming Yu
- Institute of Science and Technology Austria (ISTA), Am Campus 1, Klosterneuburg 3400, Austria
| | - Liang Wang
- Institute of Biophysics, Chinese Academy of Science, 15 Datun Road, Chaoyang District, Beijing 100101, China
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jingyi Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Zhengyong Bai
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Guohong Li
- Institute of Biophysics, Chinese Academy of Science, 15 Datun Road, Chaoyang District, Beijing 100101, China
| | - Pilong Li
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaoqi Feng
- Institute of Science and Technology Austria (ISTA), Am Campus 1, Klosterneuburg 3400, Austria
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3
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Zeng Y, Somers J, Bell HS, Dawe RK, Fowler JE, Nelms B, Gent JI. Potent pollen gene regulation by DNA glycosylases in maize. bioRxiv 2024:2024.02.13.580204. [PMID: 38405940 PMCID: PMC10888782 DOI: 10.1101/2024.02.13.580204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Although DNA methylation primarily represses transposable elements (TEs) in plants, it also represses select endosperm and pollen genes. These genes, or their cis-regulatory elements, are methylated in plant body tissues but are demethylated by DNA glycosylases (DNGs) in endosperm and pollen, enabling their transcription. Activity of either one of two DNGs, MDR1 or DNG102, is essential for pollen viability in maize. Using single-pollen mRNA sequencing on pollen segregating mutations in both genes, we identified 58 candidate DNG target genes, whose expression is strongly decreased in double mutant pollen (124-fold decrease on average). These genes account for 11.1% of the wild-type pollen polyadenylated transcriptome, but they are silent or barely detectable in the plant body. They are unusual in their tendency to lack introns but even more so in their having TE-like methylation in their coding DNA sequence. Moreover, they are strongly enriched for predicted functions in cell wall modification. While some may support development of the pollen grain cell wall, expansins and pectinases in this set of genes suggest a function in cell wall loosening to support the rapid tip growth characteristic of pollen tubes as they carry the sperm cells through maternal apoplast and extracellular matrix of the pistil. These results suggest a critical role for DNA methylation and demethylation in regulating maize genes with potential for extremely high expression in pollen but constitutive silencing elsewhere.
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Affiliation(s)
- Yibing Zeng
- University of Georgia, Department of Genetics, Athens, GA 30602
| | - Julian Somers
- University of Georgia, Department of Genetics, Athens, GA 30602
| | - Harrison S Bell
- Oregon State University, Department of Botany and Plant Pathology, Corvallis, OR 97331
| | - R Kelly Dawe
- University of Georgia, Department of Genetics, Athens, GA 30602
- University of Georgia, Department of Plant Biology, Athens, GA 30602
| | - John E Fowler
- Oregon State University, Department of Botany and Plant Pathology, Corvallis, OR 97331
| | - Brad Nelms
- University of Georgia, Department of Plant Biology, Athens, GA 30602
| | - Jonathan I Gent
- University of Georgia, Department of Plant Biology, Athens, GA 30602
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4
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Takeuchi Y, Sato S, Nagasato C, Motomura T, Okuda S, Kasahara M, Takahashi F, Yoshikawa S. Sperm-specific histone H1 in highly condensed sperm nucleus of Sargassum horneri. Sci Rep 2024; 14:3387. [PMID: 38336896 PMCID: PMC10858212 DOI: 10.1038/s41598-024-53729-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 02/04/2024] [Indexed: 02/12/2024] Open
Abstract
Spermatogenesis is one of the most dramatic changes in cell differentiation. Remarkable chromatin condensation of the nucleus is observed in animal, plant, and algal sperm. Sperm nuclear basic proteins (SNBPs), such as protamine and sperm-specific histone, are involved in chromatin condensation of the sperm nucleus. Among brown algae, sperm of the oogamous Fucales algae have a condensed nucleus. However, the existence of sperm-specific SNBPs in Fucales algae was unclear. Here, we identified linker histone (histone H1) proteins in the sperm and analyzed changes in their gene expression pattern during spermatogenesis in Sargassum horneri. A search of transcriptomic data for histone H1 genes in showed six histone H1 genes, which we named ShH1.1a, ShH1b, ShH1.2, ShH1.3, ShH1.4, and ShH1.5. Analysis of SNBPs using SDS-PAGE and LC-MS/MS showed that sperm nuclei contain histone ShH1.2, ShH1.3, and ShH1.4 in addition to core histones. Both ShH1.2 and ShH1.3 genes were expressed in the vegetative thallus and the male and female receptacles (the organs producing antheridium or oogonium). Meanwhile, the ShH1.4 gene was expressed in the male receptacle but not in the vegetative thallus and female receptacles. From these results, ShH1.4 may be a sperm-specific histone H1 of S. horneri.
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Affiliation(s)
- Yu Takeuchi
- Faculty of Marine Science and Technology, Fukui Prefectural University, 1-1 Gakuencho, Obama, Fukui, 917-0003, Japan
| | - Shinya Sato
- Faculty of Marine Science and Technology, Fukui Prefectural University, 1-1 Gakuencho, Obama, Fukui, 917-0003, Japan
| | - Chikako Nagasato
- Field Science Center for Northern Biosphere, Muroran Marine Station, Hokkaido University, Muroran, 051-0013, Japan
| | - Taizo Motomura
- Field Science Center for Northern Biosphere, Muroran Marine Station, Hokkaido University, Muroran, 051-0013, Japan
| | - Shujiro Okuda
- Graduate School of Medical and Dental Science, Niigata University, 1-757 Asahimachi, Chuoku, Niigata, Niigata, 951-8501, Japan
| | - Masahiro Kasahara
- Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga, 525-8577, Japan
| | - Fumio Takahashi
- Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga, 525-8577, Japan
- Faculty of Pharmaceutical Sciences, Toho University, Funabashi, Chiba, 274-8510, Japan
| | - Shinya Yoshikawa
- Faculty of Marine Science and Technology, Fukui Prefectural University, 1-1 Gakuencho, Obama, Fukui, 917-0003, Japan.
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5
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Vivek Hari Sundar G, Madhu A, Archana A, Shivaprasad PV. Plant histone variants at the nexus of chromatin readouts, stress and development. Biochim Biophys Acta Gen Subj 2024; 1868:130539. [PMID: 38072208 DOI: 10.1016/j.bbagen.2023.130539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 11/21/2023] [Accepted: 12/05/2023] [Indexed: 12/17/2023]
Abstract
Histones are crucial proteins that are involved in packaging the DNA as condensed chromatin inside the eukaryotic cell nucleus. Rather than being static packaging units, these molecules undergo drastic variations spatially and temporally to facilitate accessibility of DNA to replication, transcription as well as wide range of gene regulatory machineries. In addition, incorporation of paralogous variants of canonical histones in the chromatin is ascribed to specific functions. Given the peculiar requirement of plants to rapidly modulate gene expression levels on account of their sessile nature, histones and their variants serve as additional layers of gene regulation. This review summarizes the mechanisms and implications of distribution, modifications and differential incorporation of histones and their variants across plant genomes, and outlines emerging themes.
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Affiliation(s)
- G Vivek Hari Sundar
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bangalore, India
| | - Aravind Madhu
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bangalore, India; SASTRA University, Thirumalaisamudram, Thanjavur 613 401, India
| | - A Archana
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bangalore, India; SASTRA University, Thirumalaisamudram, Thanjavur 613 401, India
| | - P V Shivaprasad
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bangalore, India.
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6
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Xu G, Law JA. Loops, crosstalk, and compartmentalization: it takes many layers to regulate DNA methylation. Curr Opin Genet Dev 2024; 84:102147. [PMID: 38176333 PMCID: PMC10922829 DOI: 10.1016/j.gde.2023.102147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 12/06/2023] [Accepted: 12/06/2023] [Indexed: 01/06/2024]
Abstract
DNA methylation is a conserved epigenetic modification associated with transposon silencing and gene regulation. The stability of this modification relies on intimate connections between DNA and histone modifications that generate self-reinforcing loops wherein the presence of one mark promotes the other. However, it is becoming increasingly clear that the efficiency of these loops is affected by cross-talk between pathways and by chromatin accessibility, which is heavily influenced by histone variants. Focusing primarily on plants, this review provides an update on the aforementioned self-reinforcing loops, highlights recent advances in understanding how DNA methylation pathways are restricted to prevent encroachment on genes, and discusses the roles of histone variants in compartmentalizing epigenetic pathways within the genome. This multilayered approach facilitates two essential, yet opposing functions, the ability to maintain heritable DNA methylation patterns while retaining the flexibility to modify these patterns during development.
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Affiliation(s)
- Guanghui Xu
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA. https://twitter.com/@GuanghuiXu1
| | - Julie A Law
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
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7
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Aggarwal B, Karlowski WM, Nuc P, Jarmolowski A, Szweykowska-Kulinska Z, Pietrykowska H. MiRNAs differentially expressed in vegetative and reproductive organs of Marchantia polymorpha - insights into their expression pattern, gene structures and function. RNA Biol 2024; 21:1-12. [PMID: 38303117 PMCID: PMC10841014 DOI: 10.1080/15476286.2024.2303555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/05/2024] [Indexed: 02/03/2024] Open
Abstract
MicroRNAs regulate gene expression affecting a variety of plant developmental processes. The evolutionary position of Marchantia polymorpha makes it a significant model to understand miRNA-mediated gene regulatory pathways in plants. Previous studies focused on conserved miRNA-target mRNA modules showed their critical role in Marchantia development. Here, we demonstrate that the differential expression of conserved miRNAs among land plants and their targets in selected organs of Marchantia additionally underlines their role in regulating fundamental developmental processes. The main aim of this study was to characterize selected liverwort-specific miRNAs, as there is a limited knowledge on their biogenesis, accumulation, targets, and function in Marchantia. We demonstrate their differential accumulation in vegetative and generative organs. We reveal that all liverwort-specific miRNAs examined are encoded by independent transcriptional units. MpmiR11737a, MpmiR11887 and MpmiR11796, annotated as being encoded within protein-encoding genes, have their own independent transcription start sites. The analysis of selected liverwort-specific miRNAs and their pri-miRNAs often reveal correlation in their levels, suggesting transcriptional regulation. However, MpmiR11796 shows a reverse correlation to its pri-miRNA level, suggesting post-transcriptional regulation. Moreover, we identify novel targets for selected liverwort-specific miRNAs and demonstrate an inverse correlation between their expression and miRNA accumulation. In the case of one miRNA precursor, we provide evidence that it encodes two functional miRNAs with two independent targets. Overall, our research sheds light on liverwort-specific miRNA gene structure, provides new data on their biogenesis and expression regulation. Furthermore, identifying their targets, we hypothesize the potential role of these miRNAs in early land plant development and functioning.
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Affiliation(s)
- Bharti Aggarwal
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Wojciech Maciej Karlowski
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Przemyslaw Nuc
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Halina Pietrykowska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
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8
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Wang Y, He S, Fang X. Emerging roles of phase separation in plant transcription and chromatin organization. Curr Opin Plant Biol 2023; 75:102387. [PMID: 37311366 DOI: 10.1016/j.pbi.2023.102387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/07/2023] [Accepted: 05/10/2023] [Indexed: 06/15/2023]
Abstract
Transcription is a core step in gene expression. Regulation of transcription is achieved at the level of transcription machinery, local chromatin environment as well as higher-order chromatin organization. Our understanding of transcriptional regulation was advanced by recent introduction of transcription and chromatin-associated condensates, which typically arise via phase separation of proteins and nucleic acids. While studies from mammalian cells are unveiling the mechanisms of phase separation in transcription regulation, those in plants further broaden and deepen our understanding of this process. In this review, we discuss recent progress in plants how phase separation operates in RNA-mediated chromatin silencing, transcription activity, and chromatin compartmentalization.
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Affiliation(s)
- Yunhe Wang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Shengbo He
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China.
| | - Xiaofeng Fang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
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9
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Teano G, Concia L, Wolff L, Carron L, Biocanin I, Adamusová K, Fojtová M, Bourge M, Kramdi A, Colot V, Grossniklaus U, Bowler C, Baroux C, Carbone A, Probst AV, Schrumpfová PP, Fajkus J, Amiard S, Grob S, Bourbousse C, Barneche F. Histone H1 protects telomeric repeats from H3K27me3 invasion in Arabidopsis. Cell Rep 2023; 42:112894. [PMID: 37515769 DOI: 10.1016/j.celrep.2023.112894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 12/02/2022] [Accepted: 07/13/2023] [Indexed: 07/31/2023] Open
Abstract
While the pivotal role of linker histone H1 in shaping nucleosome organization is well established, its functional interplays with chromatin factors along the epigenome are just starting to emerge. Here we show that, in Arabidopsis, as in mammals, H1 occupies Polycomb Repressive Complex 2 (PRC2) target genes where it favors chromatin condensation and H3K27me3 deposition. We further show that, contrasting with its conserved function in PRC2 activation at genes, H1 selectively prevents H3K27me3 accumulation at telomeres and large pericentromeric interstitial telomeric repeat (ITR) domains by restricting DNA accessibility to Telomere Repeat Binding (TRB) proteins, a group of H1-related Myb factors mediating PRC2 cis recruitment. This study provides a mechanistic framework by which H1 avoids the formation of gigantic H3K27me3-rich domains at telomeric sequences and contributes to safeguard nucleus architecture.
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Affiliation(s)
- Gianluca Teano
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France; Université Paris-Saclay, 91190 Orsay, France
| | - Lorenzo Concia
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Léa Wolff
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Léopold Carron
- Sorbonne Université, CNRS, IBPS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), 75005 Paris, France
| | - Ivona Biocanin
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France; Université Paris-Saclay, 91190 Orsay, France
| | - Kateřina Adamusová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Michael Bourge
- Cytometry Facility, Imagerie-Gif, Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Amira Kramdi
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Vincent Colot
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Chris Bowler
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Célia Baroux
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Alessandra Carbone
- Sorbonne Université, CNRS, IBPS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), 75005 Paris, France
| | - Aline V Probst
- CNRS UMR6293, Université Clermont Auvergne, INSERM U1103, GReD, CRBC, Clermont-Ferrand, France
| | - Petra Procházková Schrumpfová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Simon Amiard
- CNRS UMR6293, Université Clermont Auvergne, INSERM U1103, GReD, CRBC, Clermont-Ferrand, France
| | - Stefan Grob
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Clara Bourbousse
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Fredy Barneche
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France.
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10
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Auge G, Hankofer V, Groth M, Antoniou-Kourounioti R, Ratikainen I, Lampei C. Plant environmental memory: implications, mechanisms and opportunities for plant scientists and beyond. AoB Plants 2023; 15:plad032. [PMID: 37415723 PMCID: PMC10321398 DOI: 10.1093/aobpla/plad032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 06/01/2023] [Indexed: 07/08/2023]
Abstract
Plants are extremely plastic organisms. They continuously receive and integrate environmental information and adjust their growth and development to favour fitness and survival. When this integration of information affects subsequent life stages or the development of subsequent generations, it can be considered an environmental memory. Thus, plant memory is a relevant mechanism by which plants respond adaptively to different environments. If the cost of maintaining the response is offset by its benefits, it may influence evolutionary trajectories. As such, plant memory has a sophisticated underlying molecular mechanism with multiple components and layers. Nonetheless, when mathematical modelling is combined with knowledge of ecological, physiological, and developmental effects as well as molecular mechanisms as a tool for understanding plant memory, the combined potential becomes unfathomable for the management of plant communities in natural and agricultural ecosystems. In this review, we summarize recent advances in the understanding of plant memory, discuss the ecological requirements for its evolution, outline the multilayered molecular network and mechanisms required for accurate and fail-proof plant responses to variable environments, point out the direct involvement of the plant metabolism and discuss the tremendous potential of various types of models to further our understanding of the plant's environmental memory. Throughout, we emphasize the use of plant memory as a tool to unlock the secrets of the natural world.
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Affiliation(s)
| | - Valentin Hankofer
- Institute of Biochemical Plant Pathology, Helmholtz Munich, Ingolstädter Landstraße 1, 85764 Oberschleißheim, Neuherberg, Germany
| | - Martin Groth
- Institute of Functional Epigenetics, Helmholtz Munich, Ingolstädter Landstraße 1, 85764 Oberschleißheim, Neuherberg, Germany
| | - Rea Antoniou-Kourounioti
- School of Molecular Biosciences, University of Glasgow, Sir James Black Building, University Ave, Glasgow G12 8QQ, UK
| | - Irja Ratikainen
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Realfagbygget, NO-7491 Trondheim, Norway
| | - Christian Lampei
- Department of Biology (FB17), Plant Ecology and Geobotany Group, University of Marburg, Karl-von-Frisch-Straße 8, 35032 Marburg, Germany
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11
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Manavella PA, Godoy Herz MA, Kornblihtt AR, Sorenson R, Sieburth LE, Nakaminami K, Seki M, Ding Y, Sun Q, Kang H, Ariel FD, Crespi M, Giudicatti AJ, Cai Q, Jin H, Feng X, Qi Y, Pikaard CS. Beyond transcription: compelling open questions in plant RNA biology. Plant Cell 2023; 35:1626-1653. [PMID: 36477566 PMCID: PMC10226580 DOI: 10.1093/plcell/koac346] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/14/2022] [Accepted: 12/06/2022] [Indexed: 05/30/2023]
Abstract
The study of RNAs has become one of the most influential research fields in contemporary biology and biomedicine. In the last few years, new sequencing technologies have produced an explosion of new and exciting discoveries in the field but have also given rise to many open questions. Defining these questions, together with old, long-standing gaps in our knowledge, is the spirit of this article. The breadth of topics within RNA biology research is vast, and every aspect of the biology of these molecules contains countless exciting open questions. Here, we asked 12 groups to discuss their most compelling question among some plant RNA biology topics. The following vignettes cover RNA alternative splicing; RNA dynamics; RNA translation; RNA structures; R-loops; epitranscriptomics; long non-coding RNAs; small RNA production and their functions in crops; small RNAs during gametogenesis and in cross-kingdom RNA interference; and RNA-directed DNA methylation. In each section, we will present the current state-of-the-art in plant RNA biology research before asking the questions that will surely motivate future discoveries in the field. We hope this article will spark a debate about the future perspective on RNA biology and provoke novel reflections in the reader.
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Affiliation(s)
- Pablo A Manavella
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe 3000, Argentina
| | - Micaela A Godoy Herz
- Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Universidad de Buenos Aires (UBA), Buenos Aires C1428EHA, Argentina
| | - Alberto R Kornblihtt
- Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Universidad de Buenos Aires (UBA), Buenos Aires C1428EHA, Argentina
| | - Reed Sorenson
- School of Biological Sciences, University of UtahSalt Lake City 84112, USA
| | - Leslie E Sieburth
- School of Biological Sciences, University of UtahSalt Lake City 84112, USA
| | - Kentaro Nakaminami
- Center for Sustainable Resource Science, RIKEN, Kanagawa 230-0045, Japan
| | - Motoaki Seki
- Center for Sustainable Resource Science, RIKEN, Kanagawa 230-0045, Japan
- Cluster for Pioneering Research, RIKEN, Saitama 351-0198, Japan
- Kihara Institute for Biological Research, Yokohama City University, Kanagawa 244-0813, Japan
| | - Yiliang Ding
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Qianwen Sun
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Hunseung Kang
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea
| | - Federico D Ariel
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe 3000, Argentina
| | - Martin Crespi
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Evry, Université Paris-Saclay, Bâtiment 630, Orsay 91405, France
- Institute of Plant Sciences Paris-Saclay IPS2, Université de Paris, Bâtiment 630, Orsay 91405, France
| | - Axel J Giudicatti
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe 3000, Argentina
| | - Qiang Cai
- State Key Laboratory of Hybrid Rice, College of Life Science, Wuhan University, Wuhan 430072, China
| | - Hailing Jin
- Department of Microbiology and Plant Pathology and Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, California 92507, USA
| | - Xiaoqi Feng
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Yijun Qi
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Craig S Pikaard
- Howard Hughes Medical Institute, Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA
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12
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Flores-Tornero M, Becker JD. 50 years of sperm cell isolations: from structural to omic studies. J Exp Bot 2023:erad117. [PMID: 37025026 DOI: 10.1093/jxb/erad117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Indexed: 06/19/2023]
Abstract
The fusion of male and female gametes is a fundamental process in the perpetuation and diversification of species. During the last 50 years, significant efforts have been made to isolate and characterize sperm cells from flowering plants, and to identify how these cells interact with female gametes to achieve double fertilization. The first techniques and analytical approaches not only provided structural and biochemical characterizations of plant sperm cells but also paved the way for in vitro fertilization studies. Further technological advances then led to unique insights into sperm biology at transcriptomic, proteomic and epigenetic level. Starting with a historical overview of sperm cell isolation techniques, we provide examples of how these contributed to create our current knowledge of sperm cell biology, and point out remaining challenges.
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Affiliation(s)
- María Flores-Tornero
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, Oeiras, 2780-157 Portugal
| | - Jörg D Becker
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, Oeiras, 2780-157 Portugal
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13
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Feng X, Pan S, Tu H, Huang J, Xiao C, Shen X, You L, Zhao X, Chen Y, Xu D, Qu X, Hu H. IQ67 DOMAIN protein 21 is critical for indentation formation in pavement cell morphogenesis. J Integr Plant Biol 2023; 65:721-738. [PMID: 36263896 DOI: 10.1111/jipb.13393] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 10/15/2022] [Indexed: 05/26/2023]
Abstract
In plants, cortical microtubules anchor to the plasma membrane in arrays and play important roles in cell shape. However, the molecular mechanism of microtubule binding proteins, which connect the plasma membrane and cortical microtubules in cell morphology remains largely unknown. Here, we report that a plasma membrane and microtubule dual-localized IQ67 domain protein, IQD21, is critical for cotyledon pavement cell (PC) morphogenesis in Arabidopsis. iqd21 mutation caused increased indentation width, decreased lobe length, and similar lobe number of PCs, whereas IQD21 overexpression had a different effect on cotyledon PC shape. Weak overexpression led to increased lobe number, decreased indentation width, and similar lobe length, while moderate or great overexpression resulted in decreased lobe number, indentation width, and lobe length of PCs. Live-cell observations revealed that IQD21 accumulation at indentation regions correlates with lobe initiation and outgrowth during PC development. Cell biological and genetic approaches revealed that IQD21 promotes transfacial microtubules anchoring to the plasma membrane via its polybasic sites and bundling at the indentation regions in both periclinal and anticlinal walls. IQD21 controls cortical microtubule organization mainly through promoting Katanin 1-mediated microtubule severing during PC interdigitation. These findings provide the genetic evidence that transfacial microtubule arrays play a determinant role in lobe formation, and the insight into the molecular mechanism of IQD21 in transfacial microtubule organization at indentations and puzzle-shaped PC development.
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Affiliation(s)
- Xinhua Feng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shujuan Pan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Haifu Tu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Junjie Huang
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, 430070, China
| | - Chuanlei Xiao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xin Shen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lei You
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xinyan Zhao
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Yongqiang Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Danyun Xu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaolu Qu
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Honghong Hu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
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14
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Lyons DB, Briffa A, He S, Choi J, Hollwey E, Colicchio J, Anderson I, Feng X, Howard M, Zilberman D. Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons. Cell Rep 2023; 42:112132. [PMID: 36827183 DOI: 10.1016/j.celrep.2023.112132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 11/10/2022] [Accepted: 02/01/2023] [Indexed: 02/24/2023] Open
Abstract
Cytosine methylation within CG dinucleotides (mCG) can be epigenetically inherited over many generations. Such inheritance is thought to be mediated by a semiconservative mechanism that produces binary present/absent methylation patterns. However, we show here that, in Arabidopsis thaliana h1ddm1 mutants, intermediate heterochromatic mCG is stably inherited across many generations and is quantitatively associated with transposon expression. We develop a mathematical model that estimates the rates of semiconservative maintenance failure and de novo methylation at each transposon, demonstrating that mCG can be stably inherited at any level via a dynamic balance of these activities. We find that DRM2-the core methyltransferase of the RNA-directed DNA methylation pathway-catalyzes most of the heterochromatic de novo mCG, with de novo rates orders of magnitude higher than previously thought, whereas chromomethylases make smaller contributions. Our results demonstrate that stable epigenetic inheritance of mCG in plant heterochromatin is enabled by extensive de novo methylation.
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Affiliation(s)
| | | | | | | | - Elizabeth Hollwey
- John Innes Centre, Norwich NR4 7UH, UK; Institute of Science and Technology, 3400 Klosterneuburg, Austria
| | - Jack Colicchio
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ian Anderson
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Xiaoqi Feng
- John Innes Centre, Norwich NR4 7UH, UK; Institute of Science and Technology, 3400 Klosterneuburg, Austria
| | | | - Daniel Zilberman
- John Innes Centre, Norwich NR4 7UH, UK; Institute of Science and Technology, 3400 Klosterneuburg, Austria.
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15
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Abstract
DNA methylation plays essential homeostatic functions in eukaryotic genomes. In animals, DNA methylation is also developmentally regulated and, in turn, regulates development. In the past two decades, huge research effort has endorsed the understanding that DNA methylation plays a similar role in plant development, especially during sexual reproduction. The power of whole-genome sequencing and cell isolation techniques, as well as bioinformatics tools, have enabled recent studies to reveal dynamic changes in DNA methylation during germline development. Furthermore, the combination of these technological advances with genetics, developmental biology and cell biology tools has revealed functional methylation reprogramming events that control gene and transposon activities in flowering plant germlines. In this review, we discuss the major advances in our knowledge of DNA methylation dynamics during male and female germline development in flowering plants.
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Affiliation(s)
- Shengbo He
- Guangdong Laboratory for Lingnan Modern Agriculture, College of AgricultureSouth China Agricultural UniversityGuangzhou510642China
| | - Xiaoqi Feng
- John Innes Centre, Colney LaneNorwichNR4 7UHUK
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16
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Ichino L, Picard CL, Yun J, Chotai M, Wang S, Lin EK, Papareddy RK, Xue Y, Jacobsen SE. Single-nucleus RNA-seq reveals that MBD5, MBD6, and SILENZIO maintain silencing in the vegetative cell of developing pollen. Cell Rep 2022; 41:111699. [DOI: 10.1016/j.celrep.2022.111699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 09/28/2022] [Accepted: 10/28/2022] [Indexed: 11/23/2022] Open
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17
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Buttress T, He S, Wang L, Zhou S, Saalbach G, Vickers M, Li G, Li P, Feng X. Histone H2B.8 compacts flowering plant sperm through chromatin phase separation. Nature 2022; 611:614-622. [PMID: 36323776 PMCID: PMC9668745 DOI: 10.1038/s41586-022-05386-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 09/26/2022] [Indexed: 11/17/2022]
Abstract
Sperm chromatin is typically transformed by protamines into a compact and transcriptionally inactive state1,2. Sperm cells of flowering plants lack protamines, yet they have small, transcriptionally active nuclei with chromatin condensed through an unknown mechanism3,4. Here we show that a histone variant, H2B.8, mediates sperm chromatin and nuclear condensation in Arabidopsis thaliana. Loss of H2B.8 causes enlarged sperm nuclei with dispersed chromatin, whereas ectopic expression in somatic cells produces smaller nuclei with aggregated chromatin. This result demonstrates that H2B.8 is sufficient for chromatin condensation. H2B.8 aggregates transcriptionally inactive AT-rich chromatin into phase-separated condensates, which facilitates nuclear compaction without reducing transcription. Reciprocal crosses show that mutation of h2b.8 reduces male transmission, which suggests that H2B.8-mediated sperm compaction is important for fertility. Altogether, our results reveal a new mechanism of nuclear compaction through global aggregation of unexpressed chromatin. We propose that H2B.8 is an evolutionary innovation of flowering plants that achieves nuclear condensation compatible with active transcription.
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Affiliation(s)
- Toby Buttress
- Cell and Developmental Biology Department, John Innes Centre, Norwich, UK
| | - Shengbo He
- Cell and Developmental Biology Department, John Innes Centre, Norwich, UK
| | - Liang Wang
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.,Institute of Biophysics, Chinese Academy of Science, Beijing, China
| | - Shaoli Zhou
- Cell and Developmental Biology Department, John Innes Centre, Norwich, UK
| | - Gerhard Saalbach
- Cell and Developmental Biology Department, John Innes Centre, Norwich, UK
| | - Martin Vickers
- Cell and Developmental Biology Department, John Innes Centre, Norwich, UK
| | - Guohong Li
- Institute of Biophysics, Chinese Academy of Science, Beijing, China
| | - Pilong Li
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.
| | - Xiaoqi Feng
- Cell and Developmental Biology Department, John Innes Centre, Norwich, UK.
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18
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Tirot L, Jullien PE. Epigenetic dynamics during sexual reproduction: At the nexus of developmental control and genomic integrity. Curr Opin Plant Biol 2022; 69:102278. [PMID: 35970063 DOI: 10.1016/j.pbi.2022.102278] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/20/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
Epigenetic marks influence gene regulation and genomic stability via the repression of transposable elements. During sexual reproduction, tight regulation of the epigenome must take place to maintain the repression of transposable elements while still allowing changes in cell-specific transcriptional programs. In plants, epigenetic marks are reorganized during reproduction and a reinforcing mechanism takes place to ensure transposable elements silencing. In this review, we describe the latest advances in characterizing the cell-specific epigenetic changes occurring from sporogenesis to seed development, with a focus on DNA methylation. We highlight the epigenetic co-regulation between transposable elements and developmental genes at different stages of plant reproduction.
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Affiliation(s)
- Louis Tirot
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
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19
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Gent JI, Higgins KM, Swentowsky KW, Fu FF, Zeng Y, Kim DW, Dawe RK, Springer NM, Anderson SN. The maize gene maternal derepression of r1 encodes a DNA glycosylase that demethylates DNA and reduces siRNA expression in the endosperm. Plant Cell 2022; 34:3685-3701. [PMID: 35775949 PMCID: PMC9516051 DOI: 10.1093/plcell/koac199] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 06/27/2022] [Indexed: 06/01/2023]
Abstract
Demethylation of transposons can activate the expression of nearby genes and cause imprinted gene expression in the endosperm; this demethylation is hypothesized to lead to expression of transposon small interfering RNAs (siRNAs) that reinforce silencing in the next generation through transfer either into egg or embryo. Here we describe maize (Zea mays) maternal derepression of r1 (mdr1), which encodes a DNA glycosylase with homology to Arabidopsis thaliana DEMETER and which is partially responsible for demethylation of thousands of regions in endosperm. Instead of promoting siRNA expression in endosperm, MDR1 activity inhibits it. Methylation of most repetitive DNA elements in endosperm is not significantly affected by MDR1, with an exception of Helitrons. While maternally-expressed imprinted genes preferentially overlap with MDR1 demethylated regions, the majority of genes that overlap demethylated regions are not imprinted. Double mutant megagametophytes lacking both MDR1 and its close homolog DNG102 result in early seed failure, and double mutant microgametophytes fail pre-fertilization. These data establish DNA demethylation by glycosylases as essential in maize endosperm and pollen and suggest that neither transposon repression nor genomic imprinting is its main function in endosperm.
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Affiliation(s)
| | - Kaitlin M Higgins
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Kyle W Swentowsky
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Fang-Fang Fu
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
- Co‐Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Yibing Zeng
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
| | - Dong won Kim
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
| | - R Kelly Dawe
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota 55108, USA
| | - Sarah N Anderson
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
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20
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Méteignier LV, Lecampion C, Velay F, Vriet C, Dimnet L, Rougée M, Breuer C, Soubigou-Taconnat L, Sugimoto K, Barneche F, Laloi C. Topoisomerase VI participates in an insulator-like function that prevents H3K9me2 spreading. Proc Natl Acad Sci U S A 2022; 119:e2001290119. [PMID: 35759655 DOI: 10.1073/pnas.2001290119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The organization of the genome into transcriptionally active and inactive chromatin domains requires well-delineated chromatin boundaries and insulator functions in order to maintain the identity of adjacent genomic loci with antagonistic chromatin marks and functionality. In plants that lack known chromatin insulators, the mechanisms that prevent heterochromatin spreading into euchromatin remain to be identified. Here, we show that DNA Topoisomerase VI participates in a chromatin boundary function that safeguards the expression of genes in euchromatin islands within silenced heterochromatin regions. While some transposable elements are reactivated in mutants of the Topoisomerase VI complex, genes insulated in euchromatin islands within heterochromatic regions of the Arabidopsis thaliana genome are specifically down-regulated. H3K9me2 levels consistently increase at euchromatin island loci and decrease at some transposable element loci. We further show that Topoisomerase VI physically interacts with S-adenosylmethionine synthase methionine adenosyl transferase 3 (MAT3), which is required for H3K9me2. A Topoisomerase VI defect affects MAT3 occupancy on heterochromatic elements and its exclusion from euchromatic islands, thereby providing a possible mechanistic explanation to the essential role of Topoisomerase VI in the delimitation of chromatin domains.
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21
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Abstract
The basic unit of chromatin, the nucleosome, is an octamer of four core histone proteins (H2A, H2B, H3, and H4) and serves as a fundamental regulatory unit in all DNA-templated processes. The majority of nucleosome assembly occurs during DNA replication when these core histones are produced en masse to accommodate the nascent genome. In addition, there are a number of nonallelic sequence variants of H2A and H3 in particular, known as histone variants, that can be incorporated into nucleosomes in a targeted and replication-independent manner. By virtue of their sequence divergence from the replication-coupled histones, these histone variants can impart unique properties onto the nucleosomes they occupy and thereby influence transcription and epigenetic states, DNA repair, chromosome segregation, and other nuclear processes in ways that profoundly affect plant biology. In this review, we discuss the evolutionary origins of these variants in plants, their known roles in chromatin, and their impacts on plant development and stress responses. We focus on the individual and combined roles of histone variants in transcriptional regulation within euchromatic and heterochromatic genome regions. Finally, we highlight gaps in our understanding of plant variants at the molecular, cellular, and organismal levels, and we propose new directions for study in the field of plant histone variants.
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Affiliation(s)
| | - Dylan H Holder
- Department of Biology, Emory University, Atlanta, Georgia, USA;
- Graduate Program in Genetics and Molecular Biology, Emory University, Atlanta, Georgia, USA
| | - Roger B Deal
- Department of Biology, Emory University, Atlanta, Georgia, USA;
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22
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Gutschker S, Corral JM, Schmiedl A, Ludewig F, Koch W, Fiedler-Wiechers K, Czarnecki O, Harms K, Keller I, Martins Rodrigues C, Pommerrenig B, Neuhaus HE, Zierer W, Sonnewald U, Müdsam C. Multi-omics data integration reveals link between epigenetic modifications and gene expression in sugar beet (Beta vulgaris subsp. vulgaris) in response to cold. BMC Genomics 2022; 23:144. [PMID: 35176993 DOI: 10.1186/s12864-022-08312-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/13/2022] [Indexed: 12/19/2022] Open
Abstract
Background DNA methylation is thought to influence the expression of genes, especially in response to changing environmental conditions and developmental changes. Sugar beet (Beta vulgaris ssp. vulgaris), and other biennial or perennial plants are inevitably exposed to fluctuating temperatures throughout their lifecycle and might even require such stimulus to acquire floral competence. Therefore, plants such as beets, need to fine-tune their epigenetic makeup to ensure phenotypic plasticity towards changing environmental conditions while at the same time steering essential developmental processes. Different crop species may show opposing reactions towards the same abiotic stress, or, vice versa, identical species may respond differently depending on the specific kind of stress. Results In this study, we investigated common effects of cold treatment on genome-wide DNA methylation and gene expression of two Beta vulgaris accessions via multi-omics data analysis. Cold exposure resulted in a pronounced reduction of DNA methylation levels, which particularly affected methylation in CHH context (and to a lesser extent CHG) and was accompanied by transcriptional downregulation of the chromomethyltransferase CMT2 and strong upregulation of several genes mediating active DNA demethylation. Conclusion Integration of methylomic and transcriptomic data revealed that, rather than methylation having directly influenced expression, epigenetic modifications correlated with changes in expression of known players involved in DNA (de)methylation. In particular, cold triggered upregulation of genes putatively contributing to DNA demethylation via the ROS1 pathway. Our observations suggest that these transcriptional responses precede the cold-induced global DNA-hypomethylation in non-CpG, preparing beets for additional transcriptional alterations necessary for adapting to upcoming environmental changes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08312-2.
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23
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Abstract
In flowering plants, the female gametophyte (FG) initiates from the formation of the megaspore mother cell (MMC). Among a pool of the somatic cells in the ovule primordium, only one hypodermal cell undergoes a transition of cell fate to become the MMC. Subsequently, the MMC undergoes a series of meiosis and mitosis to form the mature FG harboring seven cells with eight nuclei. Although SPL/NZZ, the core transcription factor for MMC formation, was identified several decades ago, which and why only one somatic cell is chosen as the MMC have long remained mysterious. A growing body of evidence reveal that MMC formation is associated with epigenetic regulation at multiple layers, including dynamic distribution of histone variants and histone modifications, small RNAs, and DNA methylation. In this review, we summarize the progress of epigenetic regulation in the MMC formation, emphasizing the roles of chromosome condensation, histone variants, histone methylation, small RNAs, and DNA methylation.
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24
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Abstract
Plants and algae have a complex life history that transitions between distinct life forms called the sporophyte and the gametophyte. This phenomenon-called the alternation of generations-has fascinated botanists and phycologists for over 170 years. Despite the mesmerizing array of life histories described in plants and algae, we are only now beginning to learn about the molecular mechanisms controlling them and how they evolved. Epigenetic silencing plays an essential role in regulating gene expression during multicellular development in eukaryotes, raising questions about its impact on the life history strategy of plants and algae. Here, we trace the origin and function of epigenetic mechanisms across the plant kingdom, from unicellular green algae through to angiosperms, and attempt to reconstruct the evolutionary steps that influenced life history transitions during plant evolution. Central to this evolutionary scenario is the adaption of epigenetic silencing from a mechanism of genome defense to the repression and control of alternating generations. We extend our discussion beyond the green lineage and highlight the peculiar case of the brown algae. Unlike their unicellular diatom relatives, brown algae lack epigenetic silencing pathways common to animals and plants yet display complex life histories, hinting at the emergence of novel life history controls during stramenopile evolution.
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Affiliation(s)
- Jérômine Vigneau
- Department of Algal Development and Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Michael Borg
- Department of Algal Development and Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany.
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25
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Raboni S, Montalbano S, Stransky S, Garcia BA, Buschini A, Bettati S, Sidoli S, Mozzarelli A. A Key Silencing Histone Mark on Chromatin Is Lost When Colorectal Adenocarcinoma Cells Are Depleted of Methionine by Methionine γ-Lyase. Front Mol Biosci 2021; 8:735303. [PMID: 34660696 PMCID: PMC8517235 DOI: 10.3389/fmolb.2021.735303] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/02/2021] [Indexed: 12/12/2022] Open
Abstract
Methionine is an essential amino acid used, beyond protein synthesis, for polyamine formation and DNA/RNA/protein methylation. Cancer cells require particularly high methionine supply for their homeostasis. A successful approach for decreasing methionine concentration is based on the systemic delivery of methionine γ-lyase (MGL), with in vitro and in vivo studies demonstrating its efficacy in cancer therapy. However, the mechanisms explaining how cancer cells suffer from the absence of methionine more significantly than non-malignant cells are still unclear. We analyzed the outcome of the human colorectal adenocarcinoma cancer cell line HT29 to the exposure of MGL for up to 72 h by monitoring cell viability, proteome expression, histone post-translational modifications, and presence of spurious transcription. The rationale of this study was to verify whether reduced methionine supply would affect chromatin decondensation by changing the levels of histone methylation and therefore increasing genomic instability. MGL treatment showed a time-dependent cytotoxic effect on HT29 cancer cells, with an IC50 of 30 µg/ml, while Hs27 normal cells were less affected, with an IC50 of >460 µg/ml. Although the levels of total histone methylation were not altered, a loss of the silencing histone mark H3K9me2 was observed, as well as a decrease in H4K20me3. Since H3K9me2/3 decorate repetitive DNA elements, we proved by qRT-PCR that MGL treatment leads to an increased expression of major satellite units. Our data indicate that selected histone methylation marks may play major roles in the mechanism of methionine starvation in cancer cells, proving that MGL treatment directly impacts chromatin homeostasis.
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Affiliation(s)
- Samanta Raboni
- Interdepartmental Center SITEIA.PARMA, University of Parma, Parma, Italy.,Institute of Biophysics, National Research Center, Pisa, Italy
| | - Serena Montalbano
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Stephanie Stransky
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Annamaria Buschini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.,Interdepartmental Centre for Molecular and Translational Oncology COMT, University of Parma, Parma, Italy
| | - Stefano Bettati
- Interdepartmental Center SITEIA.PARMA, University of Parma, Parma, Italy.,Institute of Biophysics, National Research Center, Pisa, Italy.,Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Andrea Mozzarelli
- Institute of Biophysics, National Research Center, Pisa, Italy.,Department of Food and Drug, University of Parma, Parma, Italy
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26
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Huang J, Dong J, Qu LJ. From birth to function: Male gametophyte development in flowering plants. Curr Opin Plant Biol 2021; 63:102118. [PMID: 34625367 PMCID: PMC9039994 DOI: 10.1016/j.pbi.2021.102118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 08/13/2021] [Accepted: 08/25/2021] [Indexed: 05/08/2023]
Abstract
Male germline development in flowering plants involves two distinct and successive phases, microsporogenesis and microgametogenesis, which involve one meiosis followed by two rounds of mitosis. Many aspects of distinctions after mitosis between the vegetative cell and the male germ cells are seen, from morphology to structure, and the differential functions of the two cell types in the male gametophyte are differentially needed and required for double fertilization. The two sperm cells, carriers of the hereditary substances, depend on the vegetative cell/pollen tube to be delivered to the female gametophyte for double fertilization. Thus, the intercellular communication and coordinated activity within the male gametophyte probably represent the most subtle regulation in flowering plants to guarantee the success of reproduction. This review will focus on what we have known about the differentiation process and the functional diversification of the vegetative cell and the male germ cell, the most crucial cell types for plant fertility and crop production.
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Affiliation(s)
- Jiaying Huang
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at the College of Life Sciences, Peking University, Beijing 100871, People's Republic of China; Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA; Department of Plant Biology, Rutgers, the State University of New Jersey, Piscataway, NJ 08901, USA
| | - Juan Dong
- Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA; Department of Plant Biology, Rutgers, the State University of New Jersey, Piscataway, NJ 08901, USA.
| | - Li-Jia Qu
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at the College of Life Sciences, Peking University, Beijing 100871, People's Republic of China; The National Plant Gene Research Center (Beijing), Beijing 100101, People's Republic of China.
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27
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Wang Y, Wang T, Liu L. The rice VCS1 is identified as a molecular tool to mark and visualize the vegetative cell of pollen. Plant Signal Behav 2021; 16:1924502. [PMID: 33982648 PMCID: PMC8244767 DOI: 10.1080/15592324.2021.1924502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/25/2021] [Accepted: 04/27/2021] [Indexed: 06/12/2023]
Abstract
Cell-type-specific markers are valuable tools to reveal developmental processes underlying cell differentiation during plant reproduction. Here we report the pollen vegetative cell marker gene VCS1 (Vegetative Cell Specific 1) of rice (Oryza sativa japonica). VCS1 was expressed specifically in late pollen and was predicted to encode a small FAF domain-containing protein of 205 amino acid residues (aa). The expression of reporter fusion proteins showed that VCS1 was exclusively targeted to the vegetative nucleus of pollen. Upon pollen germination, VCS1 lost vegetative nucleus localization, and appeared diffused in the vegetative cytoplasm of pollen grain but not in the pollen tube. T-DNA insertional mutation which disrupted the carboxyl-terminal 21 aa of VCS1 did not affect plant vegetative growth and pollen development, while destruction of VCS1 by CRISPR/Cas9 only moderately affect pollen viability. VCS1 is evolutionally conserved in monocots but appeared absent in dicotyledons. This study reveals a molecular tool for visualizing the vegetative cell of rice and possible other monocots, which has potential values in the genetic engineering of male-sterile lines.
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Affiliation(s)
- Yanli Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Tai Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
- Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Lingtong Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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28
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Long J, Walker J, She W, Aldridge B, Gao H, Deans S, Vickers M, Feng X. Nurse cell--derived small RNAs define paternal epigenetic inheritance in Arabidopsis. Science 2021; 373:373/6550/eabh0556. [PMID: 34210850 DOI: 10.1126/science.abh0556] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 05/10/2021] [Indexed: 11/02/2022]
Abstract
The plant male germline undergoes DNA methylation reprogramming, which methylates genes de novo and thereby alters gene expression and regulates meiosis. Here, we reveal the molecular mechanism underlying this reprogramming. We demonstrate that genic methylation in the male germline, from meiocytes to sperm, is established by 24-nucleotide small interfering RNAs (siRNAs) transcribed from transposons with imperfect sequence homology. These siRNAs are synthesized by meiocyte nurse cells (tapetum) through activity of CLSY3, a chromatin remodeler absent in other anther cells. Tapetal siRNAs govern germline methylation throughout the genome, including the inherited methylation patterns in sperm. Tapetum-derived siRNAs also silence germline transposons, safeguarding genome integrity. Our results reveal that tapetal siRNAs are sufficient to reconstitute germline methylation patterns and drive functional methylation reprogramming throughout the male germline.
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Affiliation(s)
- Jincheng Long
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - James Walker
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Wenjing She
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Billy Aldridge
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Hongbo Gao
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Samuel Deans
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Martin Vickers
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Xiaoqi Feng
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK.
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29
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Bourguet P, Picard CL, Yelagandula R, Pélissier T, Lorković ZJ, Feng S, Pouch-Pélissier MN, Schmücker A, Jacobsen SE, Berger F, Mathieu O. The histone variant H2A.W and linker histone H1 co-regulate heterochromatin accessibility and DNA methylation. Nat Commun 2021; 12:2683. [PMID: 33976212 PMCID: PMC8113232 DOI: 10.1038/s41467-021-22993-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 04/09/2021] [Indexed: 12/12/2022] Open
Abstract
In flowering plants, heterochromatin is demarcated by the histone variant H2A.W, elevated levels of the linker histone H1, and specific epigenetic modifications, such as high levels of DNA methylation at both CG and non-CG sites. How H2A.W regulates heterochromatin organization and interacts with other heterochromatic features is unclear. Here, we create a h2a.w null mutant via CRISPR-Cas9, h2a.w-2, to analyze the in vivo function of H2A.W. We find that H2A.W antagonizes deposition of H1 at heterochromatin and that non-CG methylation and accessibility are moderately decreased in h2a.w-2 heterochromatin. Compared to H1 loss alone, combined loss of H1 and H2A.W greatly increases accessibility and facilitates non-CG DNA methylation in heterochromatin, suggesting co-regulation of heterochromatic features by H2A.W and H1. Our results suggest that H2A.W helps maintain optimal heterochromatin accessibility and DNA methylation by promoting chromatin compaction together with H1, while also inhibiting excessive H1 incorporation.
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Affiliation(s)
- Pierre Bourguet
- CNRS, Université Clermont Auvergne, Inserm, Institut Génétique Reproduction et Développement (iGReD), Clermont-Ferrand, France
| | - Colette L Picard
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Ramesh Yelagandula
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Thierry Pélissier
- CNRS, Université Clermont Auvergne, Inserm, Institut Génétique Reproduction et Développement (iGReD), Clermont-Ferrand, France
| | - Zdravko J Lorković
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Suhua Feng
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Marie-Noëlle Pouch-Pélissier
- CNRS, Université Clermont Auvergne, Inserm, Institut Génétique Reproduction et Développement (iGReD), Clermont-Ferrand, France
| | - Anna Schmücker
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Steven E Jacobsen
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA
- Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, CA, USA
| | - Frédéric Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Olivier Mathieu
- CNRS, Université Clermont Auvergne, Inserm, Institut Génétique Reproduction et Développement (iGReD), Clermont-Ferrand, France.
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30
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Liu L, Wang T. Male gametophyte development in flowering plants: A story of quarantine and sacrifice. J Plant Physiol 2021; 258-259:153365. [PMID: 33548696 DOI: 10.1016/j.jplph.2021.153365] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 01/06/2021] [Accepted: 01/06/2021] [Indexed: 05/19/2023]
Abstract
Over 160 years ago, scientists made the first microscopic observations of angiosperm pollen. Unlike in animals, male meiosis in angiosperms produces a haploid microspore that undergoes one asymmetric division to form a vegetative cell and a generative cell. These two cells have distinct fates: the vegetative cell exits the cell cycle and elongates to form a tip-growing pollen tube; the generative cell divides once more in the pollen grain or within the growing pollen tube to form a pair of sperm cells. The concept that male germ cells are less active than the vegetative cell came from biochemical analyses and pollen structure anatomy early in the last century and is supported by the pollen transcriptome data of the last decade. However, the mechanism of how and when the transcriptional repression in male germ cells occurs is still not fully understood. In this review, we provide a brief account of the cytological and metabolic differentiation between the vegetative cell and male germ cells, with emphasis on the role of temporary callose walls, dynamic nuclear pore density, transcription repression, and histone variants. We further discuss the intercellular movement of small interfering RNA (siRNA) derived from transposable elements (TEs) and reexamine the function of TE expression in male germ cells.
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Affiliation(s)
- Lingtong Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| | - Tai Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China; Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100093, China.
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31
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Huang X, Sun MX. Epigenetic regulation and intercellular communication during male gametophyte development. J Plant Physiol 2021; 258-259:153391. [PMID: 33647786 DOI: 10.1016/j.jplph.2021.153391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 02/12/2021] [Indexed: 06/12/2023]
Abstract
The male gametophyte of angiosperms has long been recognized as an ideal system for the study of the molecular mechanisms regulating cell fate determination. Recent findings on histone variants in two cell lineages, vegetative-cell-derived small interfering RNA and transposable element expression provide new power for relevant investigations.
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Affiliation(s)
- Xiaorong Huang
- College of Life Science, State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China
| | - Meng-Xiang Sun
- College of Life Science, State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China.
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32
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Wu W, Li L, Zhao Y, Zhao Y, Jiang T, McCormick S, Zheng B. Heterochromatic silencing is reinforced by ARID1-mediated small RNA movement in Arabidopsis pollen. New Phytol 2021; 229:3269-3280. [PMID: 32783185 DOI: 10.1111/nph.16871] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 07/27/2020] [Indexed: 06/11/2023]
Abstract
In the plant male germline, transposable elements (TEs) are reactivated in the companion vegetative nucleus, resulting in siRNA production and the intercellular movement of these siRNAs to reinforce TE silencing in sperm. However, the mechanism by which siRNA movement is regulated remains unexplored. Here we show that ARID1, a transcription factor which is constitutively expressed in the vegetative nucleus but dynamically accumulates in the generative cell (the progenitor of sperm) to promote the second pollen mitosis, mediates siRNA movement to reinforce heterochromatic silencing in the male germline. We looked for regulators involved in the accumulation of ARID1 in the generative cell, and found that AGO9, a germline-specific AGO in Arabidopsis, is required for the accumulation of ARID1 in the generative cell. Mutations in either ARID1 or AGO9 lead to the interruption of not only the second pollen mitosis but also the movement of siRNA from the vegetative nucleus to the male germline, resulting in the release of heterochromatic silencing in the male germline. Moreover, conditional knockdown of ARID1 in the generative cell causes reduced heterochromatic silencing in both bicellular and mature pollen. This study provides insights into how a spatiotemporal transcription factor coordinates heterochromatic silencing and male germline maturation.
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Affiliation(s)
- Wenye Wu
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Lei Li
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yi Zhao
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Youshang Zhao
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Ting Jiang
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Sheila McCormick
- Department of Plant and Microbial Biology, UC-Berkeley, Albany, CA, 94710, USA
| | - Binglian Zheng
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
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33
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Liu S, de Jonge J, Trejo‐Arellano MS, Santos‐González J, Köhler C, Hennig L. Role of H1 and DNA methylation in selective regulation of transposable elements during heat stress. New Phytol 2021; 229:2238-2250. [PMID: 33091182 PMCID: PMC7894476 DOI: 10.1111/nph.17018] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/09/2020] [Indexed: 05/03/2023]
Abstract
Heat-stressed Arabidopsis plants release heterochromatin-associated transposable element (TE) silencing, yet it is not accompanied by major reductions of epigenetic repressive modifications. In this study, we explored the functional role of histone H1 in repressing heterochromatic TEs in response to heat stress. We generated and analyzed RNA and bisulfite-sequencing data of wild-type and h1 mutant seedlings before and after heat stress. Loss of H1 caused activation of pericentromeric Gypsy elements upon heat treatment, despite these elements remaining highly methylated. By contrast, nonpericentromeric Copia elements became activated concomitantly with loss of DNA methylation. The same Copia elements became activated in heat-treated chromomethylase 2 (cmt2) mutants, indicating that H1 represses Copia elements through maintaining DNA methylation under heat. We discovered that H1 is required for TE repression in response to heat stress, but its functional role differs depending on TE location. Strikingly, H1-deficient plants treated with the DNA methyltransferase inhibitor zebularine were highly tolerant to heat stress, suggesting that both H1 and DNA methylation redundantly suppress the plant response to heat stress.
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Affiliation(s)
- Shujing Liu
- Department of Plant BiologySwedish University of Agricultural Sciences and Linnean Center for Plant BiologyUppsala75007Sweden
| | - Jennifer de Jonge
- Department of Plant BiologySwedish University of Agricultural Sciences and Linnean Center for Plant BiologyUppsala75007Sweden
| | - Minerva S. Trejo‐Arellano
- Department of Plant BiologySwedish University of Agricultural Sciences and Linnean Center for Plant BiologyUppsala75007Sweden
| | - Juan Santos‐González
- Department of Plant BiologySwedish University of Agricultural Sciences and Linnean Center for Plant BiologyUppsala75007Sweden
| | - Claudia Köhler
- Department of Plant BiologySwedish University of Agricultural Sciences and Linnean Center for Plant BiologyUppsala75007Sweden
| | - Lars Hennig
- Department of Plant BiologySwedish University of Agricultural Sciences and Linnean Center for Plant BiologyUppsala75007Sweden
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34
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Borg M, Papareddy RK, Dombey R, Axelsson E, Nodine MD, Twell D, Berger F. Epigenetic reprogramming rewires transcription during the alternation of generations in Arabidopsis. eLife 2021; 10:e61894. [PMID: 33491647 PMCID: PMC7920552 DOI: 10.7554/elife.61894] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 01/25/2021] [Indexed: 12/18/2022] Open
Abstract
Alternation between morphologically distinct haploid and diploid life forms is a defining feature of most plant and algal life cycles, yet the underlying molecular mechanisms that govern these transitions remain unclear. Here, we explore the dynamic relationship between chromatin accessibility and epigenetic modifications during life form transitions in Arabidopsis. The diploid-to-haploid life form transition is governed by the loss of H3K9me2 and DNA demethylation of transposon-associated cis-regulatory elements. This event is associated with dramatic changes in chromatin accessibility and transcriptional reprogramming. In contrast, the global loss of H3K27me3 in the haploid form shapes a chromatin accessibility landscape that is poised to re-initiate the transition back to diploid life after fertilisation. Hence, distinct epigenetic reprogramming events rewire transcription through major reorganisation of the regulatory epigenome to guide the alternation of generations in flowering plants.
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Affiliation(s)
- Michael Borg
- Gregor Mendel Institute (GMI), Austrian Academy of SciencesViennaAustria
| | | | - Rodolphe Dombey
- Gregor Mendel Institute (GMI), Austrian Academy of SciencesViennaAustria
| | - Elin Axelsson
- Gregor Mendel Institute (GMI), Austrian Academy of SciencesViennaAustria
| | - Michael D Nodine
- Gregor Mendel Institute (GMI), Austrian Academy of SciencesViennaAustria
| | - David Twell
- Gregor Mendel Institute (GMI), Austrian Academy of SciencesViennaAustria
- Department of Genetics, University of LeicesterLeicesterUnited Kingdom
| | - Frédéric Berger
- Gregor Mendel Institute (GMI), Austrian Academy of SciencesViennaAustria
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35
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Khouider S, Borges F, LeBlanc C, Ungru A, Schnittger A, Martienssen R, Colot V, Bouyer D. Male fertility in Arabidopsis requires active DNA demethylation of genes that control pollen tube function. Nat Commun 2021; 12:410. [PMID: 33462227 PMCID: PMC7813888 DOI: 10.1038/s41467-020-20606-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 12/11/2020] [Indexed: 12/31/2022] Open
Abstract
Active DNA demethylation is required for sexual reproduction in plants but the molecular determinants underlying this epigenetic control are not known. Here, we show in Arabidopsis thaliana that the DNA glycosylases DEMETER (DME) and REPRESSOR OF SILENCING 1 (ROS1) act semi-redundantly in the vegetative cell of pollen to demethylate DNA and ensure proper pollen tube progression. Moreover, we identify six pollen-specific genes with increased DNA methylation as well as reduced expression in dme and dme;ros1. We further show that for four of these genes, reinstalling their expression individually in mutant pollen is sufficient to improve male fertility. Our findings demonstrate an essential role of active DNA demethylation in regulating genes involved in pollen function.
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Affiliation(s)
- Souraya Khouider
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Ecole Normale Supérieure, PSL Research University, 75005, Paris, France
| | - Filipe Borges
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, 11724, USA.,Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - Chantal LeBlanc
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, 11724, USA.,Faculty of Arts and Sciences, Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, 06511, USA
| | - Alexander Ungru
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Arp Schnittger
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany.,Institut de Biologie Moleculaire des Plantes (IBMP), CNRS, University Strasbourg, 67084, Strasbourg, France.,University Hamburg, 22609, Hamburg, Germany
| | - Robert Martienssen
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, 11724, USA
| | - Vincent Colot
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Ecole Normale Supérieure, PSL Research University, 75005, Paris, France.
| | - Daniel Bouyer
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Ecole Normale Supérieure, PSL Research University, 75005, Paris, France. .,Institut de Biologie Moleculaire des Plantes (IBMP), CNRS, University Strasbourg, 67084, Strasbourg, France. .,Laboratoire Reproduction et Développement des Plantes (RDP), UnivLyon, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon1, CNRS, INRAE, 69342, Lyon, France.
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Rougée M, Quadrana L, Zervudacki J, Hure V, Colot V, Navarro L, Deleris A. Polycomb mutant partially suppresses DNA hypomethylation-associated phenotypes in Arabidopsis. Life Sci Alliance 2020; 4:4/2/e202000848. [PMID: 33443101 PMCID: PMC7756957 DOI: 10.26508/lsa.202000848] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 11/25/2020] [Accepted: 12/01/2020] [Indexed: 12/16/2022] Open
Abstract
A mutation in Arabidopsis polycomb repressive complex 2 partially suppresses the transposon activity observed in a DNA methylation mutant, challenging expectations. In plants and mammals, DNA methylation and histone H3 lysine 27 trimethylation (H3K27me3), which is deposited by the polycomb repressive complex 2, are considered as two specialized systems for the epigenetic silencing of transposable element (TE) and genes, respectively. Nevertheless, many TE sequences acquire H3K27me3 when DNA methylation is lost. Here, we show in Arabidopsis thaliana that the gain of H3K27me3 observed at hundreds of TEs in the ddm1 mutant defective in the maintenance of DNA methylation, essentially depends on CURLY LEAF (CLF), one of two partially redundant H3K27 methyltransferases active in vegetative tissues. Surprisingly, the complete loss of H3K27me3 in ddm1 clf double mutant plants was not associated with further reactivation of TE expression nor with a burst of transposition. Instead, ddm1 clf plants exhibited less activated TEs, and a chromatin recompaction as well as hypermethylation of linker DNA compared with ddm1. Thus, a mutation in polycomb repressive complex 2 does not aggravate the molecular phenotypes linked to ddm1 but instead partially suppresses them, challenging our assumptions of the relationship between two conserved epigenetic silencing pathways.
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Affiliation(s)
- Martin Rougée
- Université Paris-Saclay, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Leandro Quadrana
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, Sciences and Lettres (PSL) Research University, Paris, France
| | - Jérôme Zervudacki
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, Sciences and Lettres (PSL) Research University, Paris, France
| | - Valentin Hure
- Université Paris-Saclay, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Vincent Colot
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, Sciences and Lettres (PSL) Research University, Paris, France
| | - Lionel Navarro
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, Sciences and Lettres (PSL) Research University, Paris, France
| | - Angélique Deleris
- Université Paris-Saclay, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
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Papareddy RK, Páldi K, Paulraj S, Kao P, Lutzmayer S, Nodine MD. Chromatin regulates expression of small RNAs to help maintain transposon methylome homeostasis in Arabidopsis. Genome Biol 2020; 21:251. [PMID: 32943088 PMCID: PMC7499886 DOI: 10.1186/s13059-020-02163-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 09/04/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Eukaryotic genomes are partitioned into euchromatic and heterochromatic domains to regulate gene expression and other fundamental cellular processes. However, chromatin is dynamic during growth and development and must be properly re-established after its decondensation. Small interfering RNAs (siRNAs) promote heterochromatin formation, but little is known about how chromatin regulates siRNA expression. RESULTS We demonstrate that thousands of transposable elements (TEs) produce exceptionally high levels of siRNAs in Arabidopsis thaliana embryos. TEs generate siRNAs throughout embryogenesis according to two distinct patterns depending on whether they are located in euchromatic or heterochromatic regions of the genome. siRNA precursors are transcribed in embryos, and siRNAs are required to direct the re-establishment of DNA methylation on TEs from which they are derived in the new generation. Decondensed chromatin also permits the production of 24-nt siRNAs from heterochromatic TEs during post-embryogenesis, and siRNA production from bipartite-classified TEs is controlled by their chromatin states. CONCLUSIONS Decondensation of heterochromatin in response to developmental, and perhaps environmental, cues promotes the transcription and function of siRNAs in plants. Our results indicate that chromatin-mediated siRNA transcription provides a cell-autonomous homeostatic control mechanism to help reconstitute pre-existing chromatin states during growth and development including those that ensure silencing of TEs in the future germ line.
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Affiliation(s)
- Ranjith K. Papareddy
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Katalin Páldi
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Subramanian Paulraj
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Ping Kao
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Stefan Lutzmayer
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Michael D. Nodine
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
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Stransky S, Aguilan J, Lachowicz J, Madrid-Aliste C, Nieves E, Sidoli S. Mass Spectrometry to Study Chromatin Compaction. Biology (Basel) 2020; 9:E140. [PMID: 32604817 DOI: 10.3390/biology9060140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/19/2020] [Accepted: 06/23/2020] [Indexed: 12/26/2022]
Abstract
Chromatin accessibility is a major regulator of gene expression. Histone writers/erasers have a critical role in chromatin compaction, as they “flag” chromatin regions by catalyzing/removing covalent post-translational modifications on histone proteins. Anomalous chromatin decondensation is a common phenomenon in cells experiencing aging and viral infection. Moreover, about 50% of cancers have mutations in enzymes regulating chromatin state. Numerous genomics methods have evolved to characterize chromatin state, but the analysis of (in)accessible chromatin from the protein perspective is not yet in the spotlight. We present an overview of the most used approaches to generate data on chromatin accessibility and then focus on emerging methods that utilize mass spectrometry to quantify the accessibility of histones and the rest of the chromatin bound proteome. Mass spectrometry is currently the method of choice to quantify entire proteomes in an unbiased large-scale manner; accessibility on chromatin of proteins and protein modifications adds an extra quantitative layer to proteomics dataset that assist more informed data-driven hypotheses in chromatin biology. We speculate that this emerging new set of methods will enhance predictive strength on which proteins and histone modifications are critical in gene regulation, and which proteins occupy different chromatin states in health and disease.
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Sun L, Jing Y, Liu X, Li Q, Xue Z, Cheng Z, Wang D, He H, Qian W. Heat stress-induced transposon activation correlates with 3D chromatin organization rearrangement in Arabidopsis. Nat Commun 2020; 11:1886. [PMID: 32312999 DOI: 10.1038/s41467-020-15809-5] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 03/30/2020] [Indexed: 02/08/2023] Open
Abstract
In higher eukaryotes, heterochromatin is mainly composed of transposable elements (TEs) silenced by epigenetic mechanisms. But, the silencing of certain heterochromatin-associated TEs is disrupted by heat stress. By comparing genome-wide high-resolution chromatin packing patterns under normal or heat conditions obtained through Hi-C analysis, we show here that heat stress causes global rearrangement of the 3D genome in Arabidopsis thaliana. Contacts between pericentromeric regions and distal chromosome arms, as well as proximal intra-chromosomal interactions along the chromosomes, are enhanced. However, interactions within pericentromeres and those between distal intra-chromosomal regions are decreased. Many inter-chromosomal interactions, including those within the KNOT, are also reduced. Furthermore, heat activation of TEs exhibits a high correlation with the reduction of chromosomal interactions involving pericentromeres, the KNOT, the knob, and the upstream and downstream flanking regions of the activated TEs. Together, our results provide insights into the relationship between TE activation and 3D genome reorganization.
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40
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Wang Z, Butel N, Santos-González J, Borges F, Yi J, Martienssen RA, Martinez G, Köhler C. Polymerase IV Plays a Crucial Role in Pollen Development in Capsella. Plant Cell 2020; 32:950-966. [PMID: 31988265 PMCID: PMC7145478 DOI: 10.1105/tpc.19.00938] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/13/2020] [Accepted: 01/21/2020] [Indexed: 05/04/2023]
Abstract
In Arabidopsis (Arabidopsis thaliana), DNA-dependent RNA polymerase IV (Pol IV) is required for the formation of transposable element (TE)-derived small RNA transcripts. These transcripts are processed by DICER-LIKE3 into 24-nucleotide small interfering RNAs (siRNAs) that guide RNA-directed DNA methylation. In the pollen grain, Pol IV is also required for the accumulation of 21/22-nucleotide epigenetically activated siRNAs, which likely silence TEs via post-transcriptional mechanisms. Despite this proposed role of Pol IV, its loss of function in Arabidopsis does not cause a discernible pollen defect. Here, we show that the knockout of NRPD1, encoding the largest subunit of Pol IV, in the Brassicaceae species Capsella (Capsella rubella), caused postmeiotic arrest of pollen development at the microspore stage. As in Arabidopsis, all TE-derived siRNAs were depleted in Capsella nrpd1 microspores. In the wild-type background, the same TEs produced 21/22-nucleotide and 24-nucleotide siRNAs; these processes required Pol IV activity. Arrest of Capsella nrpd1 microspores was accompanied by the deregulation of genes targeted by Pol IV-dependent siRNAs. TEs were much closer to genes in Capsella compared with Arabidopsis, perhaps explaining the essential role of Pol IV in pollen development in Capsella. Our discovery that Pol IV is functionally required in Capsella microspores emphasizes the relevance of investigating different plant models.
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Affiliation(s)
- Zhenxing Wang
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden
| | - Nicolas Butel
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden
| | - Juan Santos-González
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden
| | - Filipe Borges
- Howard Hughes Medical Institute and Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | - Jun Yi
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden
| | - Robert A Martienssen
- Howard Hughes Medical Institute and Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | - German Martinez
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden
| | - Claudia Köhler
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden
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Warman C, Panda K, Vejlupkova Z, Hokin S, Unger-Wallace E, Cole RA, Chettoor AM, Jiang D, Vollbrecht E, Evans MMS, Slotkin RK, Fowler JE. High expression in maize pollen correlates with genetic contributions to pollen fitness as well as with coordinated transcription from neighboring transposable elements. PLoS Genet 2020; 16:e1008462. [PMID: 32236090 PMCID: PMC7112179 DOI: 10.1371/journal.pgen.1008462] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 02/27/2020] [Indexed: 12/20/2022] Open
Abstract
In flowering plants, gene expression in the haploid male gametophyte (pollen) is essential for sperm delivery and double fertilization. Pollen also undergoes dynamic epigenetic regulation of expression from transposable elements (TEs), but how this process interacts with gene expression is not clearly understood. To explore relationships among these processes, we quantified transcript levels in four male reproductive stages of maize (tassel primordia, microspores, mature pollen, and sperm cells) via RNA-seq. We found that, in contrast with vegetative cell-limited TE expression in Arabidopsis pollen, TE transcripts in maize accumulate as early as the microspore stage and are also present in sperm cells. Intriguingly, coordinate expression was observed between highly expressed protein-coding genes and their neighboring TEs, specifically in mature pollen and sperm cells. To investigate a potential relationship between elevated gene transcript level and pollen function, we measured the fitness cost (male-specific transmission defect) of GFP-tagged coding sequence insertion mutations in over 50 genes identified as highly expressed in the pollen vegetative cell, sperm cell, or seedling (as a sporophytic control). Insertions in seedling genes or sperm cell genes (with one exception) exhibited no difference from the expected 1:1 transmission ratio. In contrast, insertions in over 20% of vegetative cell genes were associated with significant reductions in fitness, showing a positive correlation of transcript level with non-Mendelian segregation when mutant. Insertions in maize gamete expressed2 (Zm gex2), the sole sperm cell gene with measured contributions to fitness, also triggered seed defects when crossed as a male, indicating a conserved role in double fertilization, given the similar phenotype previously demonstrated for the Arabidopsis ortholog GEX2. Overall, our study demonstrates a developmentally programmed and coordinated transcriptional activation of TEs and genes in pollen, and further identifies maize pollen as a model in which transcriptomic data have predictive value for quantitative phenotypes.
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Affiliation(s)
- Cedar Warman
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Kaushik Panda
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Zuzana Vejlupkova
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Sam Hokin
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, United States of America
| | - Erica Unger-Wallace
- Department of Genetics Development and Cell Biology, Iowa State University, Ames, Iowa, United States of America
| | - Rex A. Cole
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Antony M. Chettoor
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, United States of America
| | - Duo Jiang
- Department of Statistics, Oregon State University, Corvallis, Oregon, United States of America
| | - Erik Vollbrecht
- Department of Genetics Development and Cell Biology, Iowa State University, Ames, Iowa, United States of America
- Bioinformatics and Computational Biology, Iowa State University, Ames, Iowa, United States of America
- Interdepartmental Genetics, Iowa State University, Ames, Iowa, United States of America
| | - Matthew M. S. Evans
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, United States of America
| | - R. Keith Slotkin
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - John E. Fowler
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
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42
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Panda K, McCue AD, Slotkin RK. Arabidopsis RNA Polymerase IV generates 21-22 nucleotide small RNAs that can participate in RNA-directed DNA methylation and may regulate genes. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190417. [PMID: 32075560 DOI: 10.1098/rstb.2019.0417] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The plant-specific RNA Polymerase IV (Pol IV) transcribes heterochromatic regions, including many transposable elements (TEs), with the well-described role of generating 24 nucleotide (nt) small interfering RNAs (siRNAs). These siRNAs target DNA methylation back to TEs to reinforce the boundary between heterochromatin and euchromatin. In the male gametophytic phase of the plant life cycle, pollen, Pol IV switches to generating primarily 21-22 nt siRNAs, but the biogenesis and function of these siRNAs have been enigmatic. In contrast to being pollen-specific, we identified that Pol IV generates these 21-22 nt siRNAs in sporophytic tissues, likely from the same transcripts that are processed into the more abundant 24 nt siRNAs. The 21-22 nt forms are specifically generated by the combined activities of DICER proteins DCL2/DCL4 and can participate in RNA-directed DNA methylation. These 21-22 nt siRNAs are also loaded into ARGONAUTE1 (AGO1), which is known to function in post-transcriptional gene regulation. Like other plant siRNAs and microRNAs incorporated into AGO1, we find a signature of genic mRNA cleavage at the predicted target site of these siRNAs, suggesting that Pol IV-generated 21-22 nt siRNAs may function to regulate gene transcript abundance. Our data provide support for the existing model that in pollen Pol IV functions in gene regulation. This article is part of a discussion meeting issue 'Crossroads between transposons and gene regulation'.
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Affiliation(s)
- Kaushik Panda
- Donald Danforth Plant Science Center, St. Louis, MO 63132-2918, USA
| | - Andrea D McCue
- Donald Danforth Plant Science Center, St. Louis, MO 63132-2918, USA.,Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210-1214, USA
| | - R Keith Slotkin
- Donald Danforth Plant Science Center, St. Louis, MO 63132-2918, USA.,Division of Biological Sciences, University of Missouri, Columbia, MO 65211-7400, USA
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Choi J, Lyons DB, Kim MY, Moore JD, Zilberman D. DNA Methylation and Histone H1 Jointly Repress Transposable Elements and Aberrant Intragenic Transcripts. Mol Cell 2020; 77:310-323.e7. [DOI: 10.1016/j.molcel.2019.10.011] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 08/26/2019] [Accepted: 10/10/2019] [Indexed: 12/12/2022]
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44
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Han Q, Bartels A, Cheng X, Meyer A, An YQC, Hsieh TF, Xiao W. Epigenetics Regulates Reproductive Development in Plants. Plants (Basel) 2019; 8:plants8120564. [PMID: 31810261 PMCID: PMC6963493 DOI: 10.3390/plants8120564] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 11/23/2019] [Accepted: 11/27/2019] [Indexed: 12/20/2022]
Abstract
Seed, resulting from reproductive development, is the main nutrient source for human beings, and reproduction has been intensively studied through genetic, molecular, and epigenetic approaches. However, how different epigenetic pathways crosstalk and integrate to regulate seed development remains unknown. Here, we review the recent progress of epigenetic changes that affect chromatin structure, such as DNA methylation, polycomb group proteins, histone modifications, and small RNA pathways in regulating plant reproduction. In gametogenesis of flowering plants, epigenetics is dynamic between the companion cell and gametes. Cytosine DNA methylation occurs in CG, CHG, CHH contexts (H = A, C, or T) of genes and transposable elements, and undergoes dynamic changes during reproduction. Cytosine methylation in the CHH context increases significantly during embryogenesis, reaches the highest levels in mature embryos, and decreases as the seed germinates. Polycomb group proteins are important transcriptional regulators during seed development. Histone modifications and small RNA pathways add another layer of complexity in regulating seed development. In summary, multiple epigenetic pathways are pivotal in regulating seed development. It remains to be elucidated how these epigenetic pathways interplay to affect dynamic chromatin structure and control reproduction.
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Affiliation(s)
- Qiang Han
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA (A.B.); (X.C.)
| | - Arthur Bartels
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA (A.B.); (X.C.)
| | - Xi Cheng
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA (A.B.); (X.C.)
| | - Angela Meyer
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA (A.B.); (X.C.)
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Yong-Qiang Charles An
- US Department of Agriculture, Agricultural Research Service, Midwest Area, Plant Genetics Research Unit, Donald Danforth Plant Science Center, MO 63132, USA;
| | - Tzung-Fu Hsieh
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA;
- Plants for Human Health Institute, North Carolina State University, North Carolina Research Campus, Kannapolis, NC 28081, USA
| | - Wenyan Xiao
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA (A.B.); (X.C.)
- Correspondence: ; Tel.: +1-314-977-2547
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Rutowicz K, Lirski M, Mermaz B, Teano G, Schubert J, Mestiri I, Kroteń MA, Fabrice TN, Fritz S, Grob S, Ringli C, Cherkezyan L, Barneche F, Jerzmanowski A, Baroux C. Linker histones are fine-scale chromatin architects modulating developmental decisions in Arabidopsis. Genome Biol 2019; 20:157. [PMID: 31391082 PMCID: PMC6685187 DOI: 10.1186/s13059-019-1767-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 07/21/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Chromatin provides a tunable platform for gene expression control. Besides the well-studied core nucleosome, H1 linker histones are abundant chromatin components with intrinsic potential to influence chromatin function. Well studied in animals, little is known about the evolution of H1 function in other eukaryotic lineages for instance plants. Notably, in the model plant Arabidopsis, while H1 is known to influence heterochromatin and DNA methylation, its contribution to transcription, molecular, and cytological chromatin organization remains elusive. RESULTS We provide a multi-scale functional study of Arabidopsis linker histones. We show that H1-deficient plants are viable yet show phenotypes in seed dormancy, flowering time, lateral root, and stomata formation-complemented by either or both of the major variants. H1 depletion also impairs pluripotent callus formation. Fine-scale chromatin analyses combined with transcriptome and nucleosome profiling reveal distinct roles of H1 on hetero- and euchromatin: H1 is necessary to form heterochromatic domains yet dispensable for silencing of most transposable elements; H1 depletion affects nucleosome density distribution and mobility in euchromatin, spatial arrangement of nanodomains, histone acetylation, and methylation. These drastic changes affect moderately the transcription but reveal a subset of H1-sensitive genes. CONCLUSIONS H1 variants have a profound impact on the molecular and spatial (nuclear) chromatin organization in Arabidopsis with distinct roles in euchromatin and heterochromatin and a dual causality on gene expression. Phenotypical analyses further suggest the novel possibility that H1-mediated chromatin organization may contribute to the epigenetic control of developmental and cellular transitions.
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Affiliation(s)
- Kinga Rutowicz
- Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Maciej Lirski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Benoît Mermaz
- Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
- Department of Molecular, Cellular & Developmental Biology, Yale University, 352a Osborn memorial laboratories, New Haven, CT, 06511, USA
| | - Gianluca Teano
- Département de Biologie, IBENS, Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 46 rue d'Ulm, F-75005, Paris, France
| | - Jasmin Schubert
- Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Imen Mestiri
- Département de Biologie, IBENS, Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 46 rue d'Ulm, F-75005, Paris, France
| | - Magdalena A Kroteń
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089, Warsaw, Poland
| | - Tohnyui Ndinyanka Fabrice
- Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Simon Fritz
- Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Stefan Grob
- Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Christoph Ringli
- Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Lusik Cherkezyan
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Fredy Barneche
- Département de Biologie, IBENS, Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 46 rue d'Ulm, F-75005, Paris, France
| | - Andrzej Jerzmanowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland.
- Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland.
| | - Célia Baroux
- Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland.
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He S, Vickers M, Zhang J, Feng X. Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. eLife 2019; 8:42530. [PMID: 31135340 PMCID: PMC6594752 DOI: 10.7554/elife.42530] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 05/26/2019] [Indexed: 01/09/2023] Open
Abstract
Transposable elements (TEs), the movement of which can damage the genome, are epigenetically silenced in eukaryotes. Intriguingly, TEs are activated in the sperm companion cell - vegetative cell (VC) - of the flowering plant Arabidopsis thaliana. However, the extent and mechanism of this activation are unknown. Here we show that about 100 heterochromatic TEs are activated in VCs, mostly by DEMETER-catalyzed DNA demethylation. We further demonstrate that DEMETER access to some of these TEs is permitted by the natural depletion of linker histone H1 in VCs. Ectopically expressed H1 suppresses TEs in VCs by reducing DNA demethylation and via a methylation-independent mechanism. We demonstrate that H1 is required for heterochromatin condensation in plant cells and show that H1 overexpression creates heterochromatic foci in the VC progenitor cell. Taken together, our results demonstrate that the natural depletion of H1 during male gametogenesis facilitates DEMETER-directed DNA demethylation, heterochromatin relaxation, and TE activation.
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Affiliation(s)
- Shengbo He
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | - Martin Vickers
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | - Jingyi Zhang
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | - Xiaoqi Feng
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
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Abstract
Plants use solar radiation as energy source for photosynthesis. They also take advantage of the information provided by the varying properties of sunlight, such as wavelength, orientation, and periodicity, to trigger physiological and developmental adaptations to a changing environment. After more than a century of research efforts in plant photobiology, multiple light signaling pathways converging onto chromatin-based mechanisms have now been identified, which in some instances play critical roles in plant phenotypic plasticity. In addition to locus-specific changes linked to transcription regulation, light signals impact higher-order chromatin organization. Here, we summarize current knowledge on how light can affect the global composition and the spatial distribution of chromatin domains. We introduce emerging questions on the functional links between light signaling and the epigenome, and further discuss how different chromatin regulatory layers may interconnect during plant adaptive responses to light.
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Affiliation(s)
- Clara Bourbousse
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- *Correspondence: Clara Bourbousse, ; Fredy Barneche,
| | - Fredy Barneche
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- *Correspondence: Clara Bourbousse, ; Fredy Barneche,
| | - Christophe Laloi
- Aix Marseille Univ, CEA, CNRS, BIAM, Luminy Génétique et Biophysique des Plantes, Marseille, France
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