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Cai J, Zhang Y, He R, Jiang L, Qu Z, Gu J, Yang J, Legascue MF, Wang ZY, Ariel F, Adelson DL, Zhu Y, Wang D. LncRNA DANA1 promotes drought tolerance and histone deacetylation of drought responsive genes in Arabidopsis. EMBO Rep 2024; 25:796-812. [PMID: 38177920 PMCID: PMC10897447 DOI: 10.1038/s44319-023-00030-4] [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: 06/29/2023] [Revised: 11/29/2023] [Accepted: 12/04/2023] [Indexed: 01/06/2024] Open
Abstract
Although many long noncoding RNAs have been discovered in plants, little is known about their biological function and mode of action. Here we show that the drought-induced long intergenic noncoding RNA DANA1 interacts with the L1p/L10e family member protein DANA1-INTERACTING PROTEIN 1 (DIP1) in the cell nucleus of Arabidopsis, and both DANA1 and DIP1 promote plant drought resistance. DANA1 and DIP1 increase histone deacetylase HDA9 binding to the CYP707A1 and CYP707A2 loci. DIP1 further interacts with PWWP3, a member of the PEAT complex that associates with HDA9 and has histone deacetylase activity. Mutation of DANA1 enhances CYP707A1 and CYP707A2 acetylation and expression resulting in impaired drought tolerance, in agreement with dip1 and pwwp3 mutant phenotypes. Our results demonstrate that DANA1 is a positive regulator of drought response and that DANA1 works jointly with the novel chromatin-related factor DIP1 on epigenetic reprogramming of the plant transcriptome during the response to drought.
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Affiliation(s)
- Jingjing Cai
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, 330031, Jiangxi, China
| | - Yongdi Zhang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, 330031, Jiangxi, China
| | - Reqing He
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, 330031, Jiangxi, China
| | - Liyun Jiang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, 330031, Jiangxi, China
| | - Zhipeng Qu
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, 5005, SA, Australia
| | - Jinbao Gu
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, 510316, Guangdong, China
| | - Jun Yang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, 330031, Jiangxi, China
| | - María Florencia Legascue
- Instituto de Agrobiotecnología del Litoral, CONICET, FBCB, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, Santa Fe, 3000, Argentina
| | - Zhen-Yu Wang
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, 510316, Guangdong, China
| | - Federico Ariel
- Instituto de Agrobiotecnología del Litoral, CONICET, FBCB, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, Santa Fe, 3000, Argentina
| | - David L Adelson
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, 5005, SA, Australia
| | - Youlin Zhu
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, 330031, Jiangxi, China
| | - Dong Wang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, 330031, Jiangxi, China.
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Roulé T, Legascue MF, Barrios A, Gaggion N, Crespi M, Ariel F, Blein T. The long intergenic noncoding RNA ARES modulates root architecture in Arabidopsis. IUBMB Life 2023; 75:880-892. [PMID: 37409758 DOI: 10.1002/iub.2761] [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: 07/06/2022] [Accepted: 05/24/2023] [Indexed: 07/07/2023]
Abstract
Long noncoding RNAs (lncRNAs) have emerged as important regulators of gene expression in plants. They have been linked to a wide range of molecular mechanisms, including epigenetics, miRNA activity, RNA processing and translation, and protein localization or stability. In Arabidopsis, characterized lncRNAs have been implicated in several physiological contexts, including plant development and the response to the environment. Here we searched for lncRNA loci located nearby key genes involved in root development and identified the lncRNA ARES (AUXIN REGULATOR ELEMENT DOWNSTREAM SOLITARYROOT) downstream of the lateral root master gene IAA14/SOLITARYROOT (SLR). Although ARES and IAA14 are co-regulated during development, the knockdown and knockout of ARES did not affect IAA14 expression. However, in response to exogenous auxin, ARES knockdown impairs the induction of its other neighboring gene encoding the transcription factor NF-YB3. Furthermore, knockdown/out of ARES results in a root developmental phenotype in control conditions. Accordingly, a transcriptomic analysis revealed that a subset of ARF7-dependent genes is deregulated. Altogether, our results hint at the lncRNA ARES as a novel regulator of the auxin response governing lateral root development, likely by modulating gene expression in trans.
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Affiliation(s)
- Thomas Roulé
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Evry, Université Paris-Saclay, Gif-sur-Yvette, France
- Institute of Plant Sciences Paris-Saclay IPS2, Université de Paris, Gif-sur-Yvette, France
| | - María Florencia Legascue
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Andana Barrios
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Evry, Université Paris-Saclay, Gif-sur-Yvette, France
- Institute of Plant Sciences Paris-Saclay IPS2, Université de Paris, Gif-sur-Yvette, France
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Nicolás Gaggion
- Institute for Signals, Systems and Computational Intelligence, sinc(i) CONICET-Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Martin Crespi
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Evry, Université Paris-Saclay, Gif-sur-Yvette, France
- Institute of Plant Sciences Paris-Saclay IPS2, Université de Paris, Gif-sur-Yvette, France
| | - Federico Ariel
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Thomas Blein
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Evry, Université Paris-Saclay, Gif-sur-Yvette, France
- Institute of Plant Sciences Paris-Saclay IPS2, Université de Paris, Gif-sur-Yvette, France
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Fonouni-Farde C, Christ A, Blein T, Legascue MF, Ferrero L, Moison M, Lucero L, Ramírez-Prado JS, Latrasse D, Gonzalez D, Benhamed M, Quadrana L, Crespi M, Ariel F. The Arabidopsis APOLO and human UPAT sequence-unrelated long noncoding RNAs can modulate DNA and histone methylation machineries in plants. Genome Biol 2022; 23:181. [PMID: 36038910 PMCID: PMC9422110 DOI: 10.1186/s13059-022-02750-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 08/02/2021] [Accepted: 08/17/2022] [Indexed: 03/24/2023] Open
Abstract
BACKGROUND RNA-DNA hybrid (R-loop)-associated long noncoding RNAs (lncRNAs), including the Arabidopsis lncRNA AUXIN-REGULATED PROMOTER LOOP (APOLO), are emerging as important regulators of three-dimensional chromatin conformation and gene transcriptional activity. RESULTS Here, we show that in addition to the PRC1-component LIKE HETEROCHROMATIN PROTEIN 1 (LHP1), APOLO interacts with the methylcytosine-binding protein VARIANT IN METHYLATION 1 (VIM1), a conserved homolog of the mammalian DNA methylation regulator UBIQUITIN-LIKE CONTAINING PHD AND RING FINGER DOMAINS 1 (UHRF1). The APOLO-VIM1-LHP1 complex directly regulates the transcription of the auxin biosynthesis gene YUCCA2 by dynamically determining DNA methylation and H3K27me3 deposition over its promoter during the plant thermomorphogenic response. Strikingly, we demonstrate that the lncRNA UHRF1 Protein Associated Transcript (UPAT), a direct interactor of UHRF1 in humans, can be recognized by VIM1 and LHP1 in plant cells, despite the lack of sequence homology between UPAT and APOLO. In addition, we show that increased levels of APOLO or UPAT hamper VIM1 and LHP1 binding to YUCCA2 promoter and globally alter the Arabidopsis transcriptome in a similar manner. CONCLUSIONS Collectively, our results uncover a new mechanism in which a plant lncRNA coordinates Polycomb action and DNA methylation through the interaction with VIM1, and indicates that evolutionary unrelated lncRNAs with potentially conserved structures may exert similar functions by interacting with homolog partners.
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Affiliation(s)
- Camille Fonouni-Farde
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000, Santa Fe, Argentina
| | - Aurélie Christ
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405, Orsay, France.,Institute of Plant Sciences Paris-Saclay IPS2, Université de Paris, Bâtiment 630, 91405, Orsay, France
| | - Thomas Blein
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405, Orsay, France.,Institute of Plant Sciences Paris-Saclay IPS2, Université de Paris, Bâtiment 630, 91405, Orsay, France
| | - María Florencia Legascue
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000, Santa Fe, Argentina
| | - Lucía Ferrero
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000, Santa Fe, Argentina
| | - Michaël Moison
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000, Santa Fe, Argentina
| | - Leandro Lucero
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000, Santa Fe, Argentina
| | - Juan Sebastián Ramírez-Prado
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405, Orsay, France.,Institute of Plant Sciences Paris-Saclay IPS2, Université de Paris, Bâtiment 630, 91405, Orsay, France
| | - David Latrasse
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405, Orsay, France.,Institute of Plant Sciences Paris-Saclay IPS2, Université de Paris, Bâtiment 630, 91405, Orsay, France
| | - Daniel Gonzalez
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000, Santa Fe, Argentina
| | - Moussa Benhamed
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405, Orsay, France.,Institute of Plant Sciences Paris-Saclay IPS2, Université de Paris, Bâtiment 630, 91405, Orsay, France
| | - Leandro Quadrana
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405, Orsay, France.,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
| | - Martin Crespi
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405, Orsay, France.,Institute of Plant Sciences Paris-Saclay IPS2, Université de Paris, Bâtiment 630, 91405, Orsay, France
| | - Federico Ariel
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000, Santa Fe, Argentina.
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