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Fal K, Berr A, Le Masson M, Faigenboim A, Pano E, Ishkhneli N, Moyal NL, Villette C, Tomkova D, Chabouté ME, Williams LE, Carles CC. Lysine 27 of histone H3.3 is a fine modulator of developmental gene expression and stands as an epigenetic checkpoint for lignin biosynthesis in Arabidopsis. New Phytol 2023; 238:1085-1100. [PMID: 36779574 DOI: 10.1111/nph.18666] [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: 10/20/2022] [Accepted: 11/28/2022] [Indexed: 06/18/2023]
Abstract
Chromatin is a dynamic platform within which gene expression is controlled by epigenetic modifications, notably targeting amino acid residues of histone H3. Among them is lysine 27 of H3 (H3K27), the trimethylation of which by the Polycomb Repressive Complex 2 (PRC2) is instrumental in regulating spatiotemporal patterns of key developmental genes. H3K27 is also subjected to acetylation and is found at sites of active transcription. Most information on the function of histone residues and their associated modifications in plants was obtained from studies of loss-of-function mutants for the complexes that modify them. To decrypt the genuine function of H3K27, we expressed a non-modifiable variant of H3 at residue K27 (H3.3K27A ) in Arabidopsis, and developed a multi-scale approach combining in-depth phenotypical and cytological analyses, with transcriptomics and metabolomics. We uncovered that the H3.3K27A variant causes severe developmental defects, part of them are reminiscent of PRC2 mutants, part of them are new. They include early flowering, increased callus formation and short stems with thicker xylem cell layer. This latest phenotype correlates with mis-regulation of phenylpropanoid biosynthesis. Overall, our results reveal novel roles of H3K27 in plant cell fates and metabolic pathways, and highlight an epigenetic control point for elongation and lignin composition of the stem.
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Affiliation(s)
- Kateryna Fal
- Plant and Cell Physiology Lab, IRIG-DBSCI-LPCV, CEA, Grenoble Alpes University - CNRS - INRAE - CEA, 17 rue des Martyrs, bât. C2, 38054, Grenoble Cedex 9, France
| | - Alexandre Berr
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084, Strasbourg Cedex, France
| | - Marie Le Masson
- Plant and Cell Physiology Lab, IRIG-DBSCI-LPCV, CEA, Grenoble Alpes University - CNRS - INRAE - CEA, 17 rue des Martyrs, bât. C2, 38054, Grenoble Cedex 9, France
| | - Adi Faigenboim
- Institute of Plant Sciences, ARO Volcani Center, PO Box 15159, Rishon LeZion, 7528809, Israel
| | - Emeline Pano
- Plant and Cell Physiology Lab, IRIG-DBSCI-LPCV, CEA, Grenoble Alpes University - CNRS - INRAE - CEA, 17 rue des Martyrs, bât. C2, 38054, Grenoble Cedex 9, France
| | - Nickolay Ishkhneli
- Robert H. Smith Institute of Plant Sciences & Genetics in Agriculture - Hebrew University of Jerusalem, Rehovot, 76100, Israel
| | - Netta-Lee Moyal
- Robert H. Smith Institute of Plant Sciences & Genetics in Agriculture - Hebrew University of Jerusalem, Rehovot, 76100, Israel
| | - Claire Villette
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084, Strasbourg Cedex, France
| | - Denisa Tomkova
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084, Strasbourg Cedex, France
| | - Marie-Edith Chabouté
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084, Strasbourg Cedex, France
| | - Leor Eshed Williams
- Robert H. Smith Institute of Plant Sciences & Genetics in Agriculture - Hebrew University of Jerusalem, Rehovot, 76100, Israel
| | - Cristel C Carles
- Plant and Cell Physiology Lab, IRIG-DBSCI-LPCV, CEA, Grenoble Alpes University - CNRS - INRAE - CEA, 17 rue des Martyrs, bât. C2, 38054, Grenoble Cedex 9, France
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Fal K, Tomkova D, Vachon G, Chabouté ME, Berr A, Carles CC. Chromatin Manipulation and Editing: Challenges, New Technologies and Their Use in Plants. Int J Mol Sci 2021; 22:E512. [PMID: 33419220 PMCID: PMC7825600 DOI: 10.3390/ijms22020512] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 12/10/2020] [Revised: 12/29/2020] [Accepted: 12/30/2020] [Indexed: 12/25/2022] Open
Abstract
An ongoing challenge in functional epigenomics is to develop tools for precise manipulation of epigenetic marks. These tools would allow moving from correlation-based to causal-based findings, a necessary step to reach conclusions on mechanistic principles. In this review, we describe and discuss the advantages and limits of tools and technologies developed to impact epigenetic marks, and which could be employed to study their direct effect on nuclear and chromatin structure, on transcription, and their further genuine role in plant cell fate and development. On one hand, epigenome-wide approaches include drug inhibitors for chromatin modifiers or readers, nanobodies against histone marks or lines expressing modified histones or mutant chromatin effectors. On the other hand, locus-specific approaches consist in targeting precise regions on the chromatin, with engineered proteins able to modify epigenetic marks. Early systems use effectors in fusion with protein domains that recognize a specific DNA sequence (Zinc Finger or TALEs), while the more recent dCas9 approach operates through RNA-DNA interaction, thereby providing more flexibility and modularity for tool designs. Current developments of "second generation", chimeric dCas9 systems, aiming at better targeting efficiency and modifier capacity have recently been tested in plants and provided promising results. Finally, recent proof-of-concept studies forecast even finer tools, such as inducible/switchable systems, that will allow temporal analyses of the molecular events that follow a change in a specific chromatin mark.
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Affiliation(s)
- Kateryna Fal
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000 Grenoble, France; (K.F.); (G.V.)
| | - Denisa Tomkova
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg CEDEX, France; (D.T.); (M.-E.C.)
| | - Gilles Vachon
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000 Grenoble, France; (K.F.); (G.V.)
| | - Marie-Edith Chabouté
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg CEDEX, France; (D.T.); (M.-E.C.)
| | - Alexandre Berr
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg CEDEX, France; (D.T.); (M.-E.C.)
| | - Cristel C. Carles
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000 Grenoble, France; (K.F.); (G.V.)
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Fal K, Cortes M, Liu M, Collaudin S, Das P, Hamant O, Trehin C. Paf1c defects challenge the robustness of flower meristem termination in Arabidopsis thaliana. Development 2019; 146:dev.173377. [PMID: 31540913 PMCID: PMC6826038 DOI: 10.1242/dev.173377] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 09/11/2019] [Indexed: 11/20/2022]
Abstract
Although accumulating evidence suggests that gene regulation is highly stochastic, genetic screens have successfully uncovered master developmental regulators, questioning the relationship between transcriptional noise and intrinsic robustness of development. To identify developmental modules that are more or less resilient to large-scale genetic perturbations, we used the Arabidopsis polymerase II-associated factor 1 complex (Paf1c) mutant vip3, which is impaired in several RNA polymerase II-dependent transcriptional processes. We found that the control of flower termination was not as robust as classically pictured. In angiosperms, the floral female organs, called carpels, display determinate growth: their development requires the arrest of stem cell maintenance. In vip3 mutant flowers, carpels displayed a highly variable morphology, with different degrees of indeterminacy defects up to wild-type size inflorescence emerging from carpels. This phenotype was associated with variable expression of two key regulators of flower termination and stem cell maintenance in flowers, WUSCHEL and AGAMOUS. The phenotype was also dependent on growth conditions. Together, these results highlight the surprisingly plastic nature of stem cell maintenance in plants and its dependence on Paf1c. Summary: Using a mutant with increased transcriptional noise, we reveal that stem cell maintenance is not as robust as anticipated in plants, even leading to major defects in essential developmental processes such as flower indeterminacy.
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Affiliation(s)
- Kateryna Fal
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, UCB Lyon 1, ENS de Lyon, INRA, CNRS, 46 Allée d'Italie, 69364 Lyon Cedex 07, France
| | - Matthieu Cortes
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, UCB Lyon 1, ENS de Lyon, INRA, CNRS, 46 Allée d'Italie, 69364 Lyon Cedex 07, France
| | - Mengying Liu
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, UCB Lyon 1, ENS de Lyon, INRA, CNRS, 46 Allée d'Italie, 69364 Lyon Cedex 07, France
| | - Sam Collaudin
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, UCB Lyon 1, ENS de Lyon, INRA, CNRS, 46 Allée d'Italie, 69364 Lyon Cedex 07, France
| | - Pradeep Das
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, UCB Lyon 1, ENS de Lyon, INRA, CNRS, 46 Allée d'Italie, 69364 Lyon Cedex 07, France
| | - Olivier Hamant
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, UCB Lyon 1, ENS de Lyon, INRA, CNRS, 46 Allée d'Italie, 69364 Lyon Cedex 07, France
| | - Christophe Trehin
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, UCB Lyon 1, ENS de Lyon, INRA, CNRS, 46 Allée d'Italie, 69364 Lyon Cedex 07, France
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Fal K, Liu M, Duisembekova A, Refahi Y, Haswell ES, Hamant O. Phyllotactic regularity requires the Paf1 complex in Arabidopsis. Development 2017; 144:4428-4436. [PMID: 28982682 PMCID: PMC5769633 DOI: 10.1242/dev.154369] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 09/25/2017] [Indexed: 12/19/2022]
Abstract
In plants, aerial organs are initiated at stereotyped intervals, both spatially (every 137° in a pattern called phyllotaxis) and temporally (at prescribed time intervals called plastochrons). To investigate the molecular basis of such regularity, mutants with altered architecture have been isolated. However, most of them only exhibit plastochron defects and/or produce a new, albeit equally reproducible, phyllotactic pattern. This leaves open the question of a molecular control of phyllotaxis regularity. Here, we show that phyllotaxis regularity depends on the function of VIP proteins, components of the RNA polymerase II-associated factor 1 complex (Paf1c). Divergence angles between successive organs along the stem exhibited increased variance in vip3-1 and vip3-2 compared with the wild type, in two different growth conditions. Similar results were obtained with the weak vip3-6 allele and in vip6, a mutant for another Paf1c subunit. Mathematical analysis confirmed that these defects could not be explained solely by plastochron defects. Instead, increased variance in phyllotaxis in vip3 was observed at the meristem and related to defects in spatial patterns of auxin activity. Thus, the regularity of spatial, auxin-dependent, patterning at the meristem requires Paf1c.
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Affiliation(s)
- Kateryna Fal
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342, Lyon, France
| | - Mengying Liu
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342, Lyon, France
| | - Assem Duisembekova
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342, Lyon, France
| | - Yassin Refahi
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK
| | - Elizabeth S Haswell
- Department of Biology, Mailbox 1137, Washington University in Saint Louis, Saint Louis, MO 63130, USA
| | - Olivier Hamant
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342, Lyon, France
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Abstract
Thigmomorphogenesis is a stereotypical developmental alteration in the plant body plan that can be induced by repeatedly touching plant organs. To unravel how plants sense and record multiple touch stimuli we performed a novel forward genetic screen based on the development of a shorter stem in response to repetitive touch. The touch insensitive (ths1) mutant identified in this screen is defective in some aspects of shoot and root thigmomorphogenesis. The ths1 mutant is an intermediate loss-of-function allele of VERNALIZATION INDEPENDENCE 3 (VIP3), a previously characterized gene whose product is part of the RNA polymerase II-associated factor 1 (Paf1) complex. The Paf1 complex is found in yeast, plants and animals, and has been implicated in histone modification and RNA processing. Several components of the Paf1 complex are required for reduced stem height in response to touch and normal root slanting and coiling responses. Global levels of histone H3K36 trimethylation are reduced in VIP3 mutants. In addition, THS1/VIP3 is required for wild type histone H3K36 trimethylation at the TOUCH3 (TCH3) and TOUCH4 (TCH4) loci and for rapid touch-induced upregulation of TCH3 and TCH4 transcripts. Thus, an evolutionarily conserved chromatin-modifying complex is required for both short- and long-term responses to mechanical stimulation, providing insight into how plants record mechanical signals for thigmomorphogenesis.
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Affiliation(s)
- Gregory S Jensen
- Department of Biology, Washington University in Saint Louis, Saint Louis, MO, USA
| | - Kateryna Fal
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, Lyon, France
| | - Olivier Hamant
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, Lyon, France
| | - Elizabeth S Haswell
- Department of Biology, Washington University in Saint Louis, Saint Louis, MO, USA
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Fal K, Landrein B, Hamant O. Interplay between miRNA regulation and mechanical stress for CUC gene expression at the shoot apical meristem. Plant Signal Behav 2016; 11:e1127497. [PMID: 26653277 PMCID: PMC4883852 DOI: 10.1080/15592324.2015.1127497] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [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: 11/19/2015] [Accepted: 11/26/2015] [Indexed: 05/18/2023]
Abstract
The shoot apical meristem is the central organizer of plant aerial organogenesis. The molecular bases of its functions involve several cross-talks between transcription factors, hormones and microRNAs. We recently showed that the expression of the homeobox transcription factor STM is induced by mechanical perturbations, adding another layer of complexity to this regulation. Here we provide additional evidence that mechanical perturbations impact the promoter activity of CUC3, an important regulator of boundary formation at the shoot meristem. Interestingly, we did not detect such an effect for CUC1. This suggests that the robustness of expression patterns and developmental programs is controlled via a combined action of molecular factors as well as mechanical cues in the shoot apical meristem.
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Affiliation(s)
- Kateryna Fal
- Laboratoire de Reproduction et Développement des Plantes, INRA-CNRS-UCBL-ENS Lyon, Lyon, France
- Laboratoire Joliot Curie, CNRS-ENS Lyon, Lyon, France
| | - Benoit Landrein
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Olivier Hamant
- Laboratoire de Reproduction et Développement des Plantes, INRA-CNRS-UCBL-ENS Lyon, Lyon, France
- Laboratoire Joliot Curie, CNRS-ENS Lyon, Lyon, France
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Hristova E, Fal K, Klemme L, Windels D, Bucher E. HISTONE DEACETYLASE6 Controls Gene Expression Patterning and DNA Methylation-Independent Euchromatic Silencing. Plant Physiol 2015; 168:1298-308. [PMID: 25918117 PMCID: PMC4528735 DOI: 10.1104/pp.15.00177] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 04/23/2015] [Indexed: 05/24/2023]
Abstract
To investigate the role of chromatin regulators in patterning gene expression, we employed a unique epigenetically controlled and highly tissue-specific green fluorescent protein reporter line in Arabidopsis (Arabidopsis thaliana). Using a combination of forward and reverse genetic approaches on this line, we show here that distinct epigenetic regulators are involved in silencing the transgene in different tissues. The forward genetic screen led to the identification of a novel HISTONE DEACETYLASE6 (HDA6) mutant allele (epigenetic control1, hda6-8). This allele differs from the previously reported alleles, as it did not affect DNA methylation and only had a very modest effect on the release of transposable elements and other heterochromatic transcripts. Overall, our data shows that HDA6 has at least two clearly separable activities in different genomic regions. In addition, we present an unexpected role for HDA6 in the control of DNA methylation at CG dinucleotides.
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Affiliation(s)
- Emilija Hristova
- Botanical Institute, Zürich-Basel Plant Science Center, University of Basel, CH-4056 Basel, Switzerland (E.H., K.F., L.K., E.B.); andUniversité d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, 49071 Beaucouzé, France (D.W., E.B.)
| | - Kateryna Fal
- Botanical Institute, Zürich-Basel Plant Science Center, University of Basel, CH-4056 Basel, Switzerland (E.H., K.F., L.K., E.B.); andUniversité d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, 49071 Beaucouzé, France (D.W., E.B.)
| | - Laurin Klemme
- Botanical Institute, Zürich-Basel Plant Science Center, University of Basel, CH-4056 Basel, Switzerland (E.H., K.F., L.K., E.B.); andUniversité d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, 49071 Beaucouzé, France (D.W., E.B.)
| | - David Windels
- Botanical Institute, Zürich-Basel Plant Science Center, University of Basel, CH-4056 Basel, Switzerland (E.H., K.F., L.K., E.B.); andUniversité d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, 49071 Beaucouzé, France (D.W., E.B.)
| | - Etienne Bucher
- Botanical Institute, Zürich-Basel Plant Science Center, University of Basel, CH-4056 Basel, Switzerland (E.H., K.F., L.K., E.B.); andUniversité d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, 49071 Beaucouzé, France (D.W., E.B.)
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Henriet S, Sumic S, Doufoundou-Guilengui C, Jensen MF, Grandmougin C, Fal K, Thompson E, Volff JN, Chourrout D. Embryonic expression of endogenous retroviral RNAs in somatic tissues adjacent to the Oikopleura germline. Nucleic Acids Res 2015; 43:3701-11. [PMID: 25779047 PMCID: PMC4402516 DOI: 10.1093/nar/gkv169] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [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: 11/11/2014] [Accepted: 02/20/2015] [Indexed: 11/19/2022] Open
Abstract
Selective pressure to maintain small genome size implies control of transposable elements, and most old classes of retrotransposons are indeed absent from the very compact genome of the tunicate Oikopleura dioica. Nonetheless, two families of retrotransposons are present, including the Tor elements. The gene organization within Tor elements is similar to that of LTR retrotransposons and retroviruses. In addition to gag and pol, many Tor elements carry a third gene encoding viral envelope-like proteins (Env) that may mediate infection. We show that the Tor family contains distinct classes of elements. In some classes, env mRNA is transcribed from the 5′LTR as in retroviruses. In others, env is transcribed from an additional promoter located downstream of the 5′LTR. Tor Env proteins are membrane-associated glycoproteins which exhibit some features of viral membrane fusion proteins. Whereas some elements are expressed in the adult testis, many others are specifically expressed in embryonic somatic cells adjacent to primordial germ cells. Such embryonic expression depends on determinants present in the Tor elements and not on their surrounding genomic environment. Our study shows that unusual modes of transcription and expression close to the germline may contribute to the proliferation of Tor elements.
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Affiliation(s)
- Simon Henriet
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, N-5008, Norway
| | - Sara Sumic
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, N-5008, Norway
| | | | - Marit Flo Jensen
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, N-5008, Norway
| | - Camille Grandmougin
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, N-5008, Norway
| | - Kateryna Fal
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, N-5008, Norway
| | - Eric Thompson
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, N-5008, Norway Department of Biology, University of Bergen, Bergen, N-5020, Norway
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon - CNRS UMR 5242 - INRA USC 1370, Lyon, 69364 Lyon cedex 07, France
| | - Daniel Chourrout
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, N-5008, Norway
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