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Morao AK, Kim J, Obaji D, Sun S, Ercan S. Topoisomerases I and II facilitate condensin DC translocation to organize and repress X chromosomes in C. elegans. Mol Cell 2022; 82:4202-4217.e5. [PMID: 36302374 PMCID: PMC9837612 DOI: 10.1016/j.molcel.2022.10.002] [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: 11/29/2021] [Revised: 05/24/2022] [Accepted: 10/03/2022] [Indexed: 11/18/2022]
Abstract
Condensins are evolutionarily conserved molecular motors that translocate along DNA and form loops. To address how DNA topology affects condensin translocation, we applied auxin-inducible degradation of topoisomerases I and II and analyzed the binding and function of an interphase condensin that mediates X chromosome dosage compensation in C. elegans. TOP-2 depletion reduced long-range spreading of condensin-DC (dosage compensation) from its recruitment sites and shortened 3D DNA contacts measured by Hi-C. TOP-1 depletion did not affect long-range spreading but resulted in condensin-DC accumulation within expressed gene bodies. Both TOP-1 and TOP-2 depletion resulted in X chromosome derepression, indicating that condensin-DC translocation at both scales is required for its function. Together, the distinct effects of TOP-1 and TOP-2 suggest two distinct modes of condensin-DC association with chromatin: long-range DNA loop extrusion that requires decatenation/unknotting of DNA and short-range translocation across genes that requires resolution of transcription-induced supercoiling.
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Affiliation(s)
- Ana Karina Morao
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA.
| | - Jun Kim
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Daniel Obaji
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Siyu Sun
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Sevinç Ercan
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA.
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2
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Ragipani B, Albritton SE, Morao AK, Mesquita D, Kramer M, Ercan S. Increased gene dosage and mRNA expression from chromosomal duplications in Caenorhabditis elegans. G3 (Bethesda) 2022; 12:jkac151. [PMID: 35731207 PMCID: PMC9339279 DOI: 10.1093/g3journal/jkac151] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 06/09/2022] [Indexed: 11/14/2022]
Abstract
Isolation of copy number variations and chromosomal duplications at high frequency in the laboratory suggested that Caenorhabditis elegans tolerates increased gene dosage. Here, we addressed if a general dosage compensation mechanism acts at the level of mRNA expression in C. elegans. We characterized gene dosage and mRNA expression in 3 chromosomal duplications and a fosmid integration strain using DNA-seq and mRNA-seq. Our results show that on average, increased gene dosage leads to increased mRNA expression, pointing to a lack of genome-wide dosage compensation. Different genes within the same chromosomal duplication show variable levels of mRNA increase, suggesting feedback regulation of individual genes. Somatic dosage compensation and germline repression reduce the level of mRNA increase from X chromosomal duplications. Together, our results show a lack of genome-wide dosage compensation mechanism acting at the mRNA level in C. elegans and highlight the role of epigenetic and individual gene regulation contributing to the varied consequences of increased gene dosage.
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Affiliation(s)
- Bhavana Ragipani
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Sarah Elizabeth Albritton
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Ana Karina Morao
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Diogo Mesquita
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Maxwell Kramer
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Sevinç Ercan
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
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3
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Breimann L, Morao AK, Kim J, Jimenez DS, Maryn N, Bikkasani K, Carrozza MJ, Albritton SE, Kramer M, Street LA, Cerimi K, Schumann VF, Bahry E, Preibisch S, Woehler A, Ercan S. The H4K20 demethylase DPY-21 regulates the dynamics of condensin DC binding. J Cell Sci 2021; 135:273768. [PMID: 34918745 PMCID: PMC8917352 DOI: 10.1242/jcs.258818] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 11/29/2021] [Indexed: 11/26/2022] Open
Abstract
Condensin is a multi-subunit structural maintenance of chromosomes (SMC) complex that binds to and compacts chromosomes. Here, we addressed the regulation of condensin binding dynamics using Caenorhabditis elegans condensin DC, which represses X chromosomes in hermaphrodites for dosage compensation. We established fluorescence recovery after photobleaching (FRAP) using the SMC4 homolog DPY-27 and showed that a well-characterized ATPase mutation abolishes DPY-27 binding to X chromosomes. Next, we performed FRAP in the background of several chromatin modifier mutants that cause varying degrees of X chromosome derepression. The greatest effect was in a null mutant of the H4K20me2 demethylase DPY-21, where the mobile fraction of condensin DC reduced from ∼30% to 10%. In contrast, a catalytic mutant of dpy-21 did not regulate condensin DC mobility. Hi-C sequencing data from the dpy-21 null mutant showed little change compared to wild-type data, uncoupling Hi-C-measured long-range DNA contacts from transcriptional repression of the X chromosomes. Taken together, our results indicate that DPY-21 has a non-catalytic role in regulating the dynamics of condensin DC binding, which is important for transcription repression. Summary: The histone demethylase DPY-21 has catalytic and non-catalytic roles in condensin DC-mediated X chromosome repression. The non-catalytic activity regulates dynamics of condensin DC binding to X chromosomes.
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Affiliation(s)
- Laura Breimann
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA.,Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Institute for Biology, Humboldt University of Berlin, Berlin, Germany
| | - Ana Karina Morao
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Jun Kim
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - David Sebastian Jimenez
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Nina Maryn
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Krishna Bikkasani
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Michael J Carrozza
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Sarah E Albritton
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Maxwell Kramer
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Lena Annika Street
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Kustrim Cerimi
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Vic-Fabienne Schumann
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Ella Bahry
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Stephan Preibisch
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Andrew Woehler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Sevinç Ercan
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
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Morao AK, Ercan S. Hatched and starved: Two chromatin compaction mechanisms join forces to silence germ cell genome. J Cell Biol 2021; 220:212550. [PMID: 34383014 PMCID: PMC8366712 DOI: 10.1083/jcb.202107026] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Indexed: 11/24/2022] Open
Abstract
Animals evolved in environments with variable nutrient availability and one form of adaptation is the delay of reproduction in food shortage conditions. Belew et al. (2021. J. Cell Biol.https://doi.org/10.1083/jcb.202009197) report that in the nematode C. elegans, starvation-induced transcriptional quiescence in germ cells is achieved through a pathway that combines two well-known chromatin compaction mechanisms.
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Affiliation(s)
- Ana Karina Morao
- Department of Biology, Center for Genomics and System Biology, New York University, New York, NY
| | - Sevinc Ercan
- Department of Biology, Center for Genomics and System Biology, New York University, New York, NY
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5
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Street LA, Morao AK, Winterkorn LH, Jiao CY, Albritton SE, Sadic M, Kramer M, Ercan S. Binding of an X-Specific Condensin Correlates with a Reduction in Active Histone Modifications at Gene Regulatory Elements. Genetics 2019; 212:729-742. [PMID: 31123040 PMCID: PMC6614895 DOI: 10.1534/genetics.119.302254] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 01/22/2019] [Accepted: 05/20/2019] [Indexed: 12/13/2022] Open
Abstract
Condensins are evolutionarily conserved protein complexes that are required for chromosome segregation during cell division and genome organization during interphase. In Caenorhabditis elegans, a specialized condensin, which forms the core of the dosage compensation complex (DCC), binds to and represses X chromosome transcription. Here, we analyzed DCC localization and the effect of DCC depletion on histone modifications, transcription factor binding, and gene expression using chromatin immunoprecipitation sequencing and mRNA sequencing. Across the X, the DCC accumulates at accessible gene regulatory sites in active chromatin and not heterochromatin. The DCC is required for reducing the levels of activating histone modifications, including H3K4me3 and H3K27ac, but not repressive modification H3K9me3. In X-to-autosome fusion chromosomes, DCC spreading into the autosomal sequences locally reduces gene expression, thus establishing a direct link between DCC binding and repression. Together, our results indicate that DCC-mediated transcription repression is associated with a reduction in the activity of X chromosomal gene regulatory elements.
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Affiliation(s)
- Lena Annika Street
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York 10003
| | - Ana Karina Morao
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York 10003
| | - Lara Heermans Winterkorn
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York 10003
| | - Chen-Yu Jiao
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York 10003
| | | | - Mohammed Sadic
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York 10003
| | - Maxwell Kramer
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York 10003
| | - Sevinç Ercan
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York 10003
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Abstract
Progression of a cell along a differentiation path is characterized by changes in gene expression profiles. Alterations of these transcriptional programs result from cell type-specific transcription factors that act in a dynamic chromatin environment. Understanding the precise contribution of these molecular factors during the differentiation process requires accessing specific cell types within a developing organ. This chapter describes a streamlined and alternative version of INTACT, a method enabling the isolation of specific cell populations by affinity-purification of tagged nuclei and the subsequent analysis of gene expression, transcription factor binding profiles, as well as chromatin state at a genome-wide scale. In particular, modifications of the nuclei isolation, capture, and purification procedures are proposed that improve time scale, yield, and purity. In addition, the combination of different tags enables the analysis of distinct cell populations from a single transgenic line and the subtractive purification of subpopulations of cells, including those for which no specific promoter is available. Finally, we describe a chromatin immunoprecipitation protocol that has been successfully used to profile histone modifications and other chromatin-associated proteins such as RNA Polymerase II in different cell populations of the Arabidopsis root, including the quiescent center of the stem cell niche.
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Affiliation(s)
- Ana Karina Morao
- Centre National de la Recherche Scientifique (CNRS) UMR8197, Institut de Biologie de l'Ecole Normale Supérieure, Institut National de la Santé et de la Recherche Médicale (INSERM) U1024, Ecole Normale Supérieure, 46 rue d'Ulm, 75230, Paris Cedex 05, France
| | - Erwann Caillieux
- Centre National de la Recherche Scientifique (CNRS) UMR8197, Institut de Biologie de l'Ecole Normale Supérieure, Institut National de la Santé et de la Recherche Médicale (INSERM) U1024, Ecole Normale Supérieure, 46 rue d'Ulm, 75230, Paris Cedex 05, France
| | - Vincent Colot
- Centre National de la Recherche Scientifique (CNRS) UMR8197, Institut de Biologie de l'Ecole Normale Supérieure, Institut National de la Santé et de la Recherche Médicale (INSERM) U1024, Ecole Normale Supérieure, 46 rue d'Ulm, 75230, Paris Cedex 05, France
| | - François Roudier
- Centre National de la Recherche Scientifique (CNRS) UMR8197, Institut de Biologie de l'Ecole Normale Supérieure, Institut National de la Santé et de la Recherche Médicale (INSERM) U1024, Ecole Normale Supérieure, 46 rue d'Ulm, 75230, Paris Cedex 05, France.
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342, Lyon, France.
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7
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Morao AK, Bouyer D, Roudier F. Emerging concepts in chromatin-level regulation of plant cell differentiation: timing, counting, sensing and maintaining. Curr Opin Plant Biol 2016; 34:27-34. [PMID: 27522467 DOI: 10.1016/j.pbi.2016.07.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Revised: 07/26/2016] [Accepted: 07/30/2016] [Indexed: 05/04/2023]
Abstract
Plants are characterized by a remarkable phenotypic plasticity that meets the constraints of a sessile lifestyle and the need to adjust constantly to the environment. Recent studies have begun to reveal how chromatin dynamics participate in coordinating cell proliferation and differentiation in response to developmental cues as well as environmental fluctuations. In this review, we discuss the pivotal function of chromatin-based mechanisms in cell fate acquisition and maintenance, within as well as outside meristems. In particular, we highlight the emerging role of specific epigenomic factors and chromatin pathways in timing the activity of stem cells, counting cell divisions and positioning cell fate transitions by sensing phytohormone gradients.
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Affiliation(s)
- Ana Karina Morao
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique (CNRS) UMR8197, Institut National de la Santé et de la Recherche Médicale (INSERM) U1024, Ecole Normale Supérieure, 46 rue d'Ulm, 75230 Paris Cedex 05, France
| | - Daniel Bouyer
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique (CNRS) UMR8197, Institut National de la Santé et de la Recherche Médicale (INSERM) U1024, Ecole Normale Supérieure, 46 rue d'Ulm, 75230 Paris Cedex 05, France.
| | - François Roudier
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique (CNRS) UMR8197, Institut National de la Santé et de la Recherche Médicale (INSERM) U1024, Ecole Normale Supérieure, 46 rue d'Ulm, 75230 Paris Cedex 05, France; Laboratoire de Reproduction et Développement des Plantes, Centre National de la Recherche Scientifique (CNRS) UMR5667, Institut National de la Recherche Agronomique (INRA) UMR879, Ecole Normale Supérieure de Lyon, Université Lyon 1 (UCBL), 46 Allée d'Italie, 69364 Lyon Cedex 07, France.
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de Lucas M, Pu L, Turco G, Gaudinier A, Morao AK, Harashima H, Kim D, Ron M, Sugimoto K, Roudier F, Brady SM. Transcriptional Regulation of Arabidopsis Polycomb Repressive Complex 2 Coordinates Cell-Type Proliferation and Differentiation. Plant Cell 2016; 28:2616-2631. [PMID: 27650334 PMCID: PMC5134969 DOI: 10.1105/tpc.15.00744] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 08/29/2016] [Accepted: 09/14/2016] [Indexed: 05/21/2023]
Abstract
Spatiotemporal regulation of transcription is fine-tuned at multiple levels, including chromatin compaction. Polycomb Repressive Complex 2 (PRC2) catalyzes the trimethylation of Histone 3 at lysine 27 (H3K27me3), which is the hallmark of a repressive chromatin state. Multiple PRC2 complexes have been reported in Arabidopsis thaliana to control the expression of genes involved in developmental transitions and maintenance of organ identity. Here, we show that PRC2 member genes display complex spatiotemporal gene expression patterns and function in root meristem and vascular cell proliferation and specification. Furthermore, PRC2 gene expression patterns correspond with vascular and nonvascular tissue-specific H3K27me3-marked genes. This tissue-specific repression via H3K27me3 regulates the balance between cell proliferation and differentiation. Using enhanced yeast one-hybrid analysis, upstream regulators of the PRC2 member genes are identified, and genetic analysis demonstrates that transcriptional regulation of some PRC2 genes plays an important role in determining PRC2 spatiotemporal activity within a developing organ.
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Affiliation(s)
- Miguel de Lucas
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Li Pu
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Gina Turco
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Allison Gaudinier
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Ana Karina Morao
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8197, Institut National de la Santé et de la Recherche Médicale, U1024 Paris, France
| | - Hirofumi Harashima
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan
| | - Dahae Kim
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Mily Ron
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Keiko Sugimoto
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan
| | - Francois Roudier
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8197, Institut National de la Santé et de la Recherche Médicale, U1024 Paris, France
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
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9
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Marquès-Bueno MDM, Morao AK, Cayrel A, Platre MP, Barberon M, Caillieux E, Colot V, Jaillais Y, Roudier F, Vert G. A versatile Multisite Gateway-compatible promoter and transgenic line collection for cell type-specific functional genomics in Arabidopsis. Plant J 2016; 85:320-333. [PMID: 26662936 PMCID: PMC4880041 DOI: 10.1111/tpj.13099] [Citation(s) in RCA: 78] [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] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 11/20/2015] [Accepted: 11/24/2015] [Indexed: 05/03/2023]
Abstract
Multicellular organisms are composed of many cell types that acquire their specific fate through a precisely controlled pattern of gene expression in time and space dictated in part by cell type-specific promoter activity. Understanding the contribution of highly specialized cell types in the development of a whole organism requires the ability to isolate or analyze different cell types separately. We have characterized and validated a large collection of root cell type-specific promoters and have generated cell type-specific marker lines. These benchmarked promoters can be readily used to evaluate cell type-specific complementation of mutant phenotypes, or to knockdown gene expression using targeted expression of artificial miRNA. We also generated vectors and characterized transgenic lines for cell type-specific induction of gene expression and cell type-specific isolation of nuclei for RNA and chromatin profiling. Vectors and seeds from transgenic Arabidopsis plants will be freely available, and will promote rapid progress in cell type-specific functional genomics. We demonstrate the power of this promoter set for analysis of complex biological processes by investigating the contribution of root cell types in the IRT1-dependent root iron uptake. Our findings revealed the complex spatial expression pattern of IRT1 in both root epidermis and phloem companion cells and the requirement for IRT1 to be expressed in both cell types for proper iron homeostasis.
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Affiliation(s)
- Maria del Mar Marquès-Bueno
- Laboratoire de Reproduction et Développement des Plantes, UMR 5667 CNRS/INRA/ENS-Lyon/Université de Lyon, 46 allée d’Italie, 69364 Lyon Cedex 07, France
| | - Ana Karina Morao
- Institut de Biologie de l'Ecole Normale Supérieure, UMR 8197 CNRS/INSERM, Paris 75005, France
| | - Anne Cayrel
- Institute for Integrative Biology of the Cell, UMR 9198 CNRS/CEA/University Paris-Sud, Avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Matthieu Pierre Platre
- Laboratoire de Reproduction et Développement des Plantes, UMR 5667 CNRS/INRA/ENS-Lyon/Université de Lyon, 46 allée d’Italie, 69364 Lyon Cedex 07, France
| | - Marie Barberon
- University of Lausanne, Department of Plant Molecular Biology, UNIL-Sorge, 1015 Lausanne, Switzerland
| | - Erwann Caillieux
- Institut de Biologie de l'Ecole Normale Supérieure, UMR 8197 CNRS/INSERM, Paris 75005, France
| | - Vincent Colot
- Institut de Biologie de l'Ecole Normale Supérieure, UMR 8197 CNRS/INSERM, Paris 75005, France
| | - Yvon Jaillais
- Laboratoire de Reproduction et Développement des Plantes, UMR 5667 CNRS/INRA/ENS-Lyon/Université de Lyon, 46 allée d’Italie, 69364 Lyon Cedex 07, France
- For correspondence (, , or )
| | - François Roudier
- Institut de Biologie de l'Ecole Normale Supérieure, UMR 8197 CNRS/INSERM, Paris 75005, France
- For correspondence (, , or )
| | - Grégory Vert
- Institute for Integrative Biology of the Cell, UMR 9198 CNRS/CEA/University Paris-Sud, Avenue de la Terrasse, 91190 Gif-sur-Yvette, France
- For correspondence (, , or )
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10
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Ikeuchi M, Iwase A, Rymen B, Harashima H, Shibata M, Ohnuma M, Breuer C, Morao AK, de Lucas M, De Veylder L, Goodrich J, Brady SM, Roudier F, Sugimoto K. PRC2 represses dedifferentiation of mature somatic cells in Arabidopsis. Nat Plants 2015; 1:15089. [PMID: 27250255 DOI: 10.1038/nplants.2015.89] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 05/29/2015] [Indexed: 05/18/2023]
Abstract
Plant somatic cells are generally acknowledged to retain totipotency, the potential to develop into any cell type within an organism. This astonishing plasticity may contribute to a high regenerative capacity on severe damage, but how plants control this potential during normal post-embryonic development remains largely unknown(1,2). Here we show that POLYCOMB REPRESSIVE COMPLEX 2 (PRC2), a chromatin regulator that maintains gene repression through histone modification, prevents dedifferentiation of mature somatic cells in Arabidopsis thaliana roots. Loss-of-function mutants in PRC2 subunits initially develop unicellular root hairs indistinguishable from those in wild type but fail to retain the differentiated state, ultimately resulting in the generation of an unorganized cell mass and somatic embryos from a single root hair. Strikingly, mutant root hairs complete the normal endoreduplication programme, increasing their nuclear ploidy, but subsequently reinitiate mitotic division coupled with successive DNA replication. Our data show that the WOUND INDUCED DEDIFFERENTIATION3 (WIND3) and LEAFY COTYLEDON2 (LEC2) genes are among the PRC2 targets involved in this reprogramming, as their ectopic overexpression partly phenocopies the dedifferentiation phenotype of PRC2 mutants. These findings unveil the pivotal role of PRC2-mediated gene repression in preventing unscheduled reprogramming of fully differentiated plant cells.
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Affiliation(s)
- Momoko Ikeuchi
- RIKEN Centre for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Akira Iwase
- RIKEN Centre for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Bart Rymen
- RIKEN Centre for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Hirofumi Harashima
- RIKEN Centre for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Michitaro Shibata
- RIKEN Centre for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Mariko Ohnuma
- RIKEN Centre for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Christian Breuer
- RIKEN Centre for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Ana Karina Morao
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197, INSERM U1024, 46 rue d'Ulm, Paris Cedex 05 75230, France
| | - Miguel de Lucas
- Department of Plant Biology and Genome Center, University of California, Davis, 1002 Life Sciences, One Shields Avenue, Davis, California 95616, USA
| | - Lieven De Veylder
- Department of Plant Systems Biology, VIB, Gent B-9052, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent B-9052, Belgium
| | - Justin Goodrich
- Institute of Molecular Plant Sciences, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, 1002 Life Sciences, One Shields Avenue, Davis, California 95616, USA
| | - François Roudier
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197, INSERM U1024, 46 rue d'Ulm, Paris Cedex 05 75230, France
| | - Keiko Sugimoto
- RIKEN Centre for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
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