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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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Pacheco JM, Mansilla N, Moison M, Lucero L, Gabarain VB, Ariel F, Estevez JM. The lncRNA APOLO and the transcription factor WRKY42 target common cell wall EXTENSIN encoding genes to trigger root hair cell elongation. Plant Signal Behav 2021; 16:1920191. [PMID: 33944666 PMCID: PMC8244768 DOI: 10.1080/15592324.2021.1920191] [Citation(s) in RCA: 3] [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] [Indexed: 05/17/2023]
Abstract
Plant long noncoding RNAs (lncRNAs) are key chromatin dynamics regulators, directing the transcriptional programs driving a wide variety of developmental outputs. Recently, we uncovered how the lncRNA AUXIN REGULATED PROMOTER LOOP (APOLO) directly recognizes the locus encoding the root hair (RH) master regulator ROOT HAIR DEFECTIVE 6 (RHD6) modulating its transcriptional activation and leading to low temperature-induced RH elongation. We further demonstrated that APOLO interacts with the transcription factor WRKY42 in a novel ribonucleoprotein complex shaping RHD6 epigenetic environment and integrating signals governing RH growth and development. In this work, we expand this model showing that APOLO is able to bind and positively control the expression of several cell wall EXTENSIN (EXT) encoding genes, including EXT3, a key regulator for RH growth. Interestingly, EXT3 emerged as a novel common target of APOLO and WRKY42. Furthermore, we showed that the ROS homeostasis-related gene NADPH OXIDASE C (NOXC) is deregulated upon APOLO overexpression, likely through the RHD6-RSL4 pathway, and that NOXC is required for low temperature-dependent enhancement of RH growth. Collectively, our results uncover an intricate regulatory network involving the APOLO/WRKY42 hub in the control of master and effector genes during RH development.
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Affiliation(s)
| | - Natanael Mansilla
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, FBCB/FHUC, Centro Científico Tecnológico CONICET Santa Fe, Paraje El Pozo, Santa Fe, Argentina
| | - Michaël Moison
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, FBCB/FHUC, Centro Científico Tecnológico CONICET Santa Fe, Paraje El Pozo, Santa Fe, Argentina
| | - Leandro Lucero
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, FBCB/FHUC, Centro Científico Tecnológico CONICET Santa Fe, Paraje El Pozo, Santa Fe, Argentina
| | | | - Federico Ariel
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, FBCB/FHUC, Centro Científico Tecnológico CONICET Santa Fe, Paraje El Pozo, Santa Fe, Argentina
- CONTACT Federico Ariel Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, FBCB/FHUC, Centro Científico Tecnológico CONICET Santa Fe, Colectora Ruta Nacional No 168km. 0, Paraje El Pozo, Santa Fe3000, Argentina
| | - José M. Estevez
- Fundación Instituto Leloir and IIBBA-CONICET, Buenos Aires, CP, Argentina
- Centro de Biotecnología Vegetal (CBV), Facultad de Ciencias de la Vida (Fcsv), Universidad Andres Bello and Millennium Institute for Integrative Biology (Ibio), Santiago, Chile
- José M. Estevez Fundación Instituto Leloir and IIBBA-CONICET, Av. Patricias Argentinas 435, Buenos Aires, CPC1405BWE, Argentina
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Moison M, Pacheco JM, Lucero L, Fonouni-Farde C, Rodríguez-Melo J, Mansilla N, Christ A, Bazin J, Benhamed M, Ibañez F, Crespi M, Estevez JM, Ariel F. The lncRNA APOLO interacts with the transcription factor WRKY42 to trigger root hair cell expansion in response to cold. Mol Plant 2021; 14:937-948. [PMID: 33689931 DOI: 10.1016/j.molp.2021.03.008] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 02/08/2021] [Accepted: 03/03/2021] [Indexed: 05/25/2023]
Abstract
Plant long noncoding RNAs (lncRNAs) have emerged as important regulators of chromatin dynamics, impacting on transcriptional programs leading to different developmental outputs. The lncRNA AUXIN-REGULATED PROMOTER LOOP (APOLO) directly recognizes multiple independent loci across the Arabidopsis genome and modulates their three-dimensional chromatin conformation, leading to transcriptional shifts. Here, we show that APOLO recognizes the locus encoding the root hair (RH) master regulator ROOT HAIR DEFECTIVE 6 (RHD6) and controls RHD6 transcriptional activity, leading to cold-enhanced RH elongation through the consequent activation of the transcription factor gene RHD6-like RSL4. Furthermore, we demonstrate that APOLO interacts with the transcription factor WRKY42 and modulates its binding to the RHD6 promoter. WRKY42 is required for the activation of RHD6 by low temperatures and WRKY42 deregulation impairs cold-induced RH expansion. Collectively, our results indicate that a novel ribonucleoprotein complex with APOLO and WRKY42 forms a regulatory hub to activate RHD6 by shaping its epigenetic environment and integrate signals governing RH growth and development.
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Affiliation(s)
- Michaël Moison
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, FBCB/FHUC, Centro Científico Tecnológico CONICET Santa Fe, Colectora Ruta Nacional No 168 km. 0, Paraje El Pozo, Santa Fe 3000, Argentina
| | - Javier Martínez Pacheco
- Fundación Instituto Leloir and IIBBA-CONICET, Av. Patricias Argentinas 435, Buenos Aires CP C1405BWE, Argentina
| | - Leandro Lucero
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, FBCB/FHUC, Centro Científico Tecnológico CONICET Santa Fe, Colectora Ruta Nacional No 168 km. 0, Paraje El Pozo, Santa Fe 3000, Argentina
| | - Camille Fonouni-Farde
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, FBCB/FHUC, Centro Científico Tecnológico CONICET Santa Fe, Colectora Ruta Nacional No 168 km. 0, Paraje El Pozo, Santa Fe 3000, Argentina
| | - Johan Rodríguez-Melo
- Instituto de Investigaciones Agrobiotecnológicas, CONICET, Universidad Nacional de Río Cuarto, Río Cuarto 5800, Argentina
| | - Natanael Mansilla
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, FBCB/FHUC, Centro Científico Tecnológico CONICET Santa Fe, Colectora Ruta Nacional No 168 km. 0, Paraje El Pozo, Santa Fe 3000, Argentina
| | - Aurélie Christ
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Saclay and University of Paris Bâtiment 630, 91192 Gif sur Yvette, France
| | - Jérémie Bazin
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Saclay and University of Paris Bâtiment 630, 91192 Gif sur Yvette, France
| | - Moussa Benhamed
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Saclay and University of Paris Bâtiment 630, 91192 Gif sur Yvette, France
| | - Fernando Ibañez
- Instituto de Investigaciones Agrobiotecnológicas, CONICET, Universidad Nacional de Río Cuarto, Río Cuarto 5800, Argentina
| | - Martin Crespi
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Saclay and University of Paris Bâtiment 630, 91192 Gif sur Yvette, France
| | - José M Estevez
- Fundación Instituto Leloir and IIBBA-CONICET, Av. Patricias Argentinas 435, Buenos Aires CP C1405BWE, Argentina; Centro de Biotecnología Vegetal (CBV), Facultad de Ciencias de la Vida (FCsV), Universidad Andres Bello, Santiago, Chile and Millennium Institute for Integrative Biology (iBio), Santiago, Chile.
| | - Federico Ariel
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, FBCB/FHUC, Centro Científico Tecnológico CONICET Santa Fe, Colectora Ruta Nacional No 168 km. 0, Paraje El Pozo, Santa Fe 3000, Argentina.
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