1
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Hsieh CH, Chang YTS, Yen MR, Hsieh JWA, Chen PY. Predicting protein synergistic effect in Arabidopsis using epigenome profiling. Nat Commun 2024; 15:9160. [PMID: 39448614 PMCID: PMC11502919 DOI: 10.1038/s41467-024-53565-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 10/15/2024] [Indexed: 10/26/2024] Open
Abstract
Histone modifications can regulate transcription epigenetically by marking specific genomic loci, which can be mapped using chromatin immunoprecipitation sequencing (ChIP-seq). Here we present QHistone, a predictive database of 1534 ChIP-seqs from 27 histone modifications in Arabidopsis, offering three key functionalities. Firstly, QHistone employs machine learning to predict the epigenomic profile of a query protein, characterized by its most associated histone modifications, and uses these modifications to infer the protein's role in transcriptional regulation. Secondly, it predicts synergistic regulatory activities between two proteins by comparing their profiles. Lastly, it detects previously unexplored co-regulating protein pairs by screening all known proteins. QHistone accurately identifies histone modifications associated with specific known proteins, and allows users to computationally validate their results using gene expression data from various plant tissues. These functions demonstrate an useful approach to utilizing epigenome data for gene regulation analysis, making QHistone a valuable resource for the scientific community ( https://qhistone.paoyang.ipmb.sinica.edu.tw ).
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Affiliation(s)
- Chih-Hung Hsieh
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115201, Taiwan
| | | | - Ming-Ren Yen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115201, Taiwan
| | - Jo-Wei Allison Hsieh
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115201, Taiwan
| | - Pao-Yang Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115201, Taiwan.
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2
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Cawood GL, Ton J. Decoding resilience: ecology, regulation, and evolution of biosynthetic gene clusters. TRENDS IN PLANT SCIENCE 2024:S1360-1385(24)00241-3. [PMID: 39393973 DOI: 10.1016/j.tplants.2024.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 08/28/2024] [Accepted: 09/13/2024] [Indexed: 10/13/2024]
Abstract
Secondary metabolism is crucial for plant survival and can generate chemistry with nutritional, therapeutic, and industrial value. Biosynthetic genes of selected secondary metabolites cluster within localised chromosomal regions. The arrangement of these biosynthetic gene clusters (BGCs) challenges the long-held model of random gene order in eukaryotes, raising questions about their regulation, ecological significance, and evolution. In this review, we address these questions by exploring the contribution of BGCs to ecologically relevant plant-biotic interactions, while also evaluating the molecular-(epi)genetic mechanisms controlling their coordinated stress- and tissue-specific expression. Based on evidence that BGCs have distinct chromatin signatures and are enriched with transposable elements (TEs), we integrate emerging hypotheses into an updated evolutionary model emphasising how stress-induced epigenetic processes have shaped BGC formation.
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Affiliation(s)
- George Lister Cawood
- Plants, Photosynthesis and Soil, School of Biosciences, The University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.
| | - Jurriaan Ton
- Plants, Photosynthesis and Soil, School of Biosciences, The University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.
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3
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Dias Lopes C, He X, Ariel F, Pereyra-Bistraín LI, Benhamed M. The MVPs (masterful versatile players): Chromatin factors as pivotal mediators between 3D genome organization and the response to environment. CURRENT OPINION IN PLANT BIOLOGY 2024; 81:102599. [PMID: 38991465 DOI: 10.1016/j.pbi.2024.102599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 06/05/2024] [Accepted: 06/17/2024] [Indexed: 07/13/2024]
Abstract
In recent years, the study of genome dynamics has become a prominent research field due to its influence on understanding the control of gene expression. The study of 3D genome organization has unveiled multiple mechanisms in orchestrating chromosome folding. Growing evidence reveals that these mechanisms are not only important for genome organization, but play a pivotal role in enabling plants to adapt to environmental stimuli. In this review, we provide an overview of the current knowledge concerning epigenetic factors and regulatory elements driving 3D genome dynamics and their responses to external stimuli. We discuss the most recent findings, previous evidence, and explore their implications for future research.
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Affiliation(s)
- Chloé Dias Lopes
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, 91405, France
| | - Xiaoning He
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, 91405, France
| | - Federico Ariel
- Universidad de Buenos Aires (UBA), Facultad de Ciencias Exactas y Naturales, and Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-UBA, Buenos Aires, Argentina
| | - Leonardo I Pereyra-Bistraín
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, 91405, France; Université de Paris Cité, Institute of Plant Sciences Paris-Saclay (IPS2), F-91190, Gif-sur-Yvette, France.
| | - Moussa Benhamed
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, 91405, France; Université de Paris Cité, Institute of Plant Sciences Paris-Saclay (IPS2), F-91190, Gif-sur-Yvette, France; Institut Universitaire de France (IUF), Orsay, 91405, France.
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4
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Chae J, Han SJ, Karthik S, Kim HJ, Kim JH, Yun HR, Chung YS, Sung S, Heo JB. LIKE HETEROCHROMATIN PROTEIN 1 (LHP1) partially inhibits the transcriptional activation of FT by MYB73 and regulates flowering in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 120:187-198. [PMID: 39133829 PMCID: PMC11424248 DOI: 10.1111/tpj.16980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 06/05/2024] [Accepted: 07/26/2024] [Indexed: 09/27/2024]
Abstract
Polycomb group (PcG) proteins are essential gene repressors in higher eukaryotes. However, how PcG proteins mediate transcriptional regulation of specific genes remains unknown. LIKE HETEROCHROMATIN PROTEIN 1 (LHP1), as a component of Polycomb Repression Complexes (PRC), epigenetically mediates several plant developmental processes together with PcG proteins. We observed physical interaction between MYB73 and LHP1 in vitro and in vivo. Genetic analysis indicated that myb73 mutants showed slightly late flowering, and the lhp1-3 myb73-2 double mutant exhibited delayed flowering and downregulated FT expression compared to lhp1-3. Chromatin immunoprecipitation and yeast one-hybrid assays revealed that MYB73 preferentially binds to the FT promoter. Additionally, our protoplast transient assays demonstrated that MYB73 activates to the FT promoter. Interestingly, the LHP1-MYB73 interaction is necessary to repress the FT promoter, suggesting that the LHP1-MYB73 interaction prevents FT activation by MYB73 in Arabidopsis. Our results show an example in which a chromatin regulator affects transcriptional regulation by negatively regulating a transcription factor through direct interaction.
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Affiliation(s)
- Jia Chae
- Department of Molecular Genetic Engineering, Dong-A University, Busan 49315, Republic of Korea
| | - Seong Ju Han
- Department of Molecular Genetic Engineering, Dong-A University, Busan 49315, Republic of Korea
| | - Sivabalan Karthik
- Department of Molecular Genetic Engineering, Dong-A University, Busan 49315, Republic of Korea
| | - Hye Jeong Kim
- Department of Molecular Genetic Engineering, Dong-A University, Busan 49315, Republic of Korea
| | - Jee Hye Kim
- Department of Molecular Genetic Engineering, Dong-A University, Busan 49315, Republic of Korea
| | - Hee Rang Yun
- Department of Molecular Genetic Engineering, Dong-A University, Busan 49315, Republic of Korea
| | - Young-Soo Chung
- Department of Molecular Genetic Engineering, Dong-A University, Busan 49315, Republic of Korea
| | - Sibum Sung
- Department of Molecular Biosciences, The University of Texas, Austin, TX, 78712, USA
| | - Jae Bok Heo
- Department of Molecular Genetic Engineering, Dong-A University, Busan 49315, Republic of Korea
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5
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Zanetti ME, Blanco F, Ferrari M, Ariel F, Benoit M, Niebel A, Crespi M. Epigenetic control during root development and symbiosis. PLANT PHYSIOLOGY 2024; 196:697-710. [PMID: 38865442 DOI: 10.1093/plphys/kiae333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 05/02/2024] [Accepted: 05/24/2024] [Indexed: 06/14/2024]
Abstract
The roots of plants play multiple functions that are essential for growth and development, including anchoring to the soil as well as water and nutrient acquisition. These underground organs exhibit the plasticity to modify their root system architecture in response to environmental cues, allowing adaptation to change in water and nutrient availability. In addition, roots enter in mutualistic interactions with soil microorganisms, for example, the root nodule symbiosis (RNS) established between a limited group of plants and nitrogen-fixing soil bacteria and the arbuscular mycorrhiza symbiosis involving most land plants and fungi of the Glomeromycetes phylum. In the past 20 years, genetic approaches allowed the identification and functional characterization of genes required for the specific programs of root development, root nodule, and arbuscular mycorrhiza symbioses. These genetic studies provided evidence that the program of the RNS recruited components of the arbuscular mycorrhiza symbiosis and the root developmental programs. The execution of these programs is strongly influenced by epigenetic changes-DNA methylation and histone post-translational modifications-that alter chromatin conformation modifying the expression of key genes. In this review, we summarize recent advances that highlight how DNA methylation and histone post-translational modifications, as well as chromatin remodeling factors and long noncoding RNAs, shape the root system architecture and allow the successful establishment of both root nodule and arbuscular mycorrhiza symbioses. We anticipate that the analysis of dynamic epigenetic changes and chromatin 3D structure in specific single cells or tissue types of root organs will illuminate our understanding of how root developmental and symbiotic programs are orchestrated, opening exciting questions and new perspectives to modulate agronomical and ecological traits linked to nutrient acquisition.
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Affiliation(s)
- María Eugenia Zanetti
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata and Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata 1900, Argentina
| | - Flavio Blanco
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata and Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata 1900, Argentina
| | - Milagros Ferrari
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata and Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata 1900, Argentina
| | - Federico Ariel
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Universidad de Buenos Aires (UBA), Facultad de Ciencias Exactas y Naturales, and Consejo Nacional de Investigaciones Científicas y Técnicas CONICET, Buenos Aires C1428EGA, Argentina
| | - Matthias Benoit
- Laboratoire des Interactions Plantes-Microorganismes (LIPME), INRAE, CNRS, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan 31326, France
| | - Andreas Niebel
- Laboratoire des Interactions Plantes-Microorganismes (LIPME), INRAE, CNRS, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan 31326, France
| | - Martin Crespi
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette 91190, France
- Université Paris Cité, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette 91190, France
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6
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Shao Z, Bai Y, Huq E, Qiao H. LHP1 and INO80 cooperate with ethylene signaling for warm ambient temperature response by activating specific bivalent genes. Cell Rep 2024; 43:114758. [PMID: 39269904 DOI: 10.1016/j.celrep.2024.114758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 08/09/2024] [Accepted: 08/29/2024] [Indexed: 09/15/2024] Open
Abstract
Ethylene signaling has been indicated as a potential positive regulator of plant warm ambient temperature response, but its underlying molecular mechanisms are largely unknown. Here, we show that LHP1 and INO80 cooperate with ethylene signaling for warm ambient temperature response by activating specific bivalent genes. We found that the presence of warm ambient temperature activates ethylene signaling through EIN2 and EIN3, leading to an interaction between LHP1 and accumulated EIN2-C to co-regulate a subset of LHP1-bound genes marked by H3K27me3 and H3K4me3 bivalency. Furthermore, we demonstrate that INO80 is recruited to bivalent genes by interacting with EIN2-C and EIN3, promoting H3K4me3 enrichment and facilitating transcriptional activation in response to a warm ambient temperature. Together, our findings illustrate a mechanism wherein ethylene signaling orchestrates LHP1 and INO80 to regulate warm ambient temperature response by activating specific bivalent genes in Arabidopsis.
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Affiliation(s)
- Zhengyao Shao
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA; Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Yanan Bai
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA; Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Enamul Huq
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA; Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Hong Qiao
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA; Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.
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7
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Liang Z, Zhu T, Yu Y, Wu C, Huang Y, Hao Y, Song X, Fu W, Yuan L, Cui Y, Huang S, Li C. PICKLE-mediated nucleosome condensing drives H3K27me3 spreading for the inheritance of Polycomb memory during differentiation. Mol Cell 2024; 84:3438-3454.e8. [PMID: 39232583 DOI: 10.1016/j.molcel.2024.08.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 06/19/2024] [Accepted: 08/12/2024] [Indexed: 09/06/2024]
Abstract
Spreading of H3K27me3 is crucial for the maintenance of mitotically inheritable Polycomb-mediated chromatin silencing in animals and plants. However, how Polycomb repressive complex 2 (PRC2) accesses unmodified nucleosomes in spreading regions for spreading H3K27me3 remains unclear. Here, we show in Arabidopsis thaliana that the chromatin remodeler PICKLE (PKL) plays a specialized role in H3K27me3 spreading to safeguard cell identity during differentiation. PKL specifically localizes to H3K27me3 spreading regions but not to nucleation sites and physically associates with PRC2. Loss of PKL disrupts the occupancy of the PRC2 catalytic subunit CLF in spreading regions and leads to aberrant dedifferentiation. Nucleosome density increase endowed by the ATPase function of PKL ensures that unmodified nucleosomes are accessible to PRC2 catalytic activity for H3K27me3 spreading. Our findings demonstrate that PKL-dependent nucleosome compaction is critical for PRC2-mediated H3K27me3 read-and-write function in H3K27me3 spreading, thus revealing a mechanism by which repressive chromatin domains are established and propagated.
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Affiliation(s)
- Zhenwei Liang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Tao Zhu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yaoguang Yu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Caihong Wu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yisui Huang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yuanhao Hao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Xin Song
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Wei Fu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Liangbing Yuan
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yuhai Cui
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON N5V 4T3, Canada
| | - Shangzhi Huang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Chenlong Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China.
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8
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Go D, Lu B, Alizadeh M, Gazzarrini S, Song L. Voice from both sides: a molecular dialogue between transcriptional activators and repressors in seed-to-seedling transition and crop adaptation. FRONTIERS IN PLANT SCIENCE 2024; 15:1416216. [PMID: 39166233 PMCID: PMC11333834 DOI: 10.3389/fpls.2024.1416216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 06/20/2024] [Indexed: 08/22/2024]
Abstract
High-quality seeds provide valuable nutrients to human society and ensure successful seedling establishment. During maturation, seeds accumulate storage compounds that are required to sustain seedling growth during germination. This review focuses on the epigenetic repression of the embryonic and seed maturation programs in seedlings. We begin with an extensive overview of mutants affecting these processes, illustrating the roles of core proteins and accessory components in the epigenetic machinery by comparing mutants at both phenotypic and molecular levels. We highlight how omics assays help uncover target-specific functional specialization and coordination among various epigenetic mechanisms. Furthermore, we provide an in-depth discussion on the Seed dormancy 4 (Sdr4) transcriptional corepressor family, comparing and contrasting their regulation of seed germination in the dicotyledonous species Arabidopsis and two monocotyledonous crops, rice and wheat. Finally, we compare the similarities in the activation and repression of the embryonic and seed maturation programs through a shared set of cis-regulatory elements and discuss the challenges in applying knowledge largely gained in model species to crops.
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Affiliation(s)
- Dongeun Go
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Bailan Lu
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Milad Alizadeh
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Sonia Gazzarrini
- Department of Biological Science, University of Toronto Scarborough, Toronto, ON, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Liang Song
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
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9
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Sureshkumar S, Bandaranayake C, Lv J, Dent CI, Bhagat PK, Mukherjee S, Sarwade R, Atri C, York HM, Tamizhselvan P, Shamaya N, Folini G, Bergey BG, Yadav AS, Kumar S, Grummisch OS, Saini P, Yadav RK, Arumugam S, Rosonina E, Sadanandom A, Liu H, Balasubramanian S. SUMO protease FUG1, histone reader AL3 and chromodomain protein LHP1 are integral to repeat expansion-induced gene silencing in Arabidopsis thaliana. NATURE PLANTS 2024; 10:749-759. [PMID: 38641663 DOI: 10.1038/s41477-024-01672-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 03/15/2024] [Indexed: 04/21/2024]
Abstract
Epigenetic gene silencing induced by expanded repeats can cause diverse phenotypes ranging from severe growth defects in plants to genetic diseases such as Friedreich's ataxia in humans. The molecular mechanisms underlying repeat expansion-induced epigenetic silencing remain largely unknown. Using a plant model with a temperature-sensitive phenotype, we have previously shown that expanded repeats can induce small RNAs, which in turn can lead to epigenetic silencing through the RNA-dependent DNA methylation pathway. Here, using a genetic suppressor screen and yeast two-hybrid assays, we identified novel components required for epigenetic silencing caused by expanded repeats. We show that FOURTH ULP GENE CLASS 1 (FUG1)-an uncharacterized SUMO protease with no known role in gene silencing-is required for epigenetic silencing caused by expanded repeats. In addition, we demonstrate that FUG1 physically interacts with ALFIN-LIKE 3 (AL3)-a histone reader that is known to bind to active histone mark H3K4me2/3. Loss of function of AL3 abolishes epigenetic silencing caused by expanded repeats. AL3 physically interacts with the chromodomain protein LIKE HETEROCHROMATIN 1 (LHP1)-known to be associated with the spread of the repressive histone mark H3K27me3 to cause repeat expansion-induced epigenetic silencing. Loss of any of these components suppresses repeat expansion-associated phenotypes coupled with an increase in IIL1 expression with the reversal of gene silencing and associated change in epigenetic marks. Our findings suggest that the FUG1-AL3-LHP1 module is essential to confer repeat expansion-associated epigenetic silencing and highlight the importance of post-translational modifiers and histone readers in epigenetic silencing.
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Affiliation(s)
- Sridevi Sureshkumar
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia.
| | - Champa Bandaranayake
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | - Junqing Lv
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Craig I Dent
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | | | - Sourav Mukherjee
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | - Rucha Sarwade
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | - Chhaya Atri
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | - Harrison M York
- Monash Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia
- European Molecular Biology Laboratory, Australia (EMBL Australia), Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | - Prashanth Tamizhselvan
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | - Nawar Shamaya
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | - Giulia Folini
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | | | - Avilash Singh Yadav
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | - Subhasree Kumar
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | - Oliver S Grummisch
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | - Prince Saini
- Department of Biological Sciences, Indian Institute of Science Education and Research, Mohali, India
| | - Ram K Yadav
- Department of Biological Sciences, Indian Institute of Science Education and Research, Mohali, India
| | - Senthil Arumugam
- Monash Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia
- European Molecular Biology Laboratory, Australia (EMBL Australia), Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | - Emanuel Rosonina
- Department of Biology, York University, Toronto, Ontario, Canada
| | - Ari Sadanandom
- Department of Biosciences, Durham University, Durham, UK
| | - Hongtao Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
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10
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Wang H, Yin C, Zhang G, Yang M, Zhu B, Jiang J, Zeng Z. Cold-induced deposition of bivalent H3K4me3-H3K27me3 modification and nucleosome depletion in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:549-564. [PMID: 38184780 DOI: 10.1111/tpj.16624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 12/19/2023] [Accepted: 12/26/2023] [Indexed: 01/08/2024]
Abstract
Epigenetic regulation of gene expression plays a crucial role in plant development and environmental adaptation. The H3K4me3 and H3K27me3 have not only been discovered in the regulation of gene expression in multiple biological processes but also in responses to abiotic stresses in plants. However, evidence for the presence of both H3K4me3 and H3K27me3 on the same nucleosome is sporadic. Cold-induced deposition of bivalent H3K4me3-H3K27me3 modifications and nucleosome depletion over a considerable number of active genes is documented in potato tubers and provides clues on an additional role of the bivalent modifications. Limited by the available information of genes encoding PcG/TrxG proteins as well as their corresponding mutants in potatoes, the molecular mechanism underlying the cold-induced deposition of the bivalent mark remains elusive. In this study, we found a similar deposition of the bivalent H3K4me3-H3K27me3 mark over 2129 active genes in cold-treated Arabidopsis Col-0 seedlings. The expression levels of the bivalent mark-associated genes tend to be independent of bivalent modification levels. However, these genes were associated with greater chromatin accessibility, presumably to provide a distinct chromatin environment for gene expression. In mutants clf28 and lhp1, failure to deposit H3K27me3 in active genes upon cold treatment implies that the CLF is potentially involved in cold-induced deposition of H3K27me3, with assistance from LHP1. Failure to deposit H3K4me3 during cold treatment in atx1-2 suggests a regulatory role of ATX1 in the deposition of H3K4me3. In addition, we observed a cold-induced global reduction in nucleosome occupancy, which is potentially mediated by LHP1 in an H3K27me3-dependent manner.
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Affiliation(s)
- Hao Wang
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, 610101, Sichuan, China
| | - Chang Yin
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, 610101, Sichuan, China
| | - Guoyan Zhang
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, 610101, Sichuan, China
| | - Miao Yang
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, 610101, Sichuan, China
| | - Bo Zhu
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, 610101, Sichuan, China
- Plant Functional Genomics and Bioinformatics Research Center, Sichuan Normal University, Chengdu, 610101, Sichuan, China
| | - Jiming Jiang
- Department of Plant Biology, Department of Horticulture, Michigan State University AgBioResearch, Michigan State University, East Lansing, Michigan, 48824, USA
| | - Zixian Zeng
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, 610101, Sichuan, China
- Plant Functional Genomics and Bioinformatics Research Center, Sichuan Normal University, Chengdu, 610101, Sichuan, China
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11
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Song Y, He J, Guo J, Xie Y, Ma Z, Liu Z, Niu C, Li X, Chu B, Tahir MM, Xu J, Ma F, Guan Q. The chromatin remodeller MdRAD5B enhances drought tolerance by coupling MdLHP1-mediated H3K27me3 in apple. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:617-634. [PMID: 37874929 PMCID: PMC10893944 DOI: 10.1111/pbi.14210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 09/25/2023] [Accepted: 10/06/2023] [Indexed: 10/26/2023]
Abstract
RAD5B belongs to the Rad5/16-like group of the SNF2 family, which often functions in chromatin remodelling. However, whether RAD5B is involved in chromatin remodelling, histone modification, and drought stress tolerance is largely unclear. We identified a drought-inducible chromatin remodeler, MdRAD5B, which positively regulates apple drought tolerance. Transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) analysis showed that MdRAD5B affects the expression of 466 drought-responsive genes through its chromatin remodelling function in response to drought stress. In addition, MdRAD5B interacts with and degrades MdLHP1, a crucial regulator of histone H3 trimethylation at K27 (H3K27me3), through the ubiquitin-independent 20S proteasome. Chromatin immunoprecipitation-sequencing (ChIP-seq) analysis revealed that MdRAD5B modulates the H3K27me3 deposition of 615 genes in response to drought stress. Genetic interaction analysis showed that MdRAD5B mediates the H3K27me3 deposition of drought-responsive genes through MdLHP1, which causes their expression changes under drought stress. Our results unravelled a dual function of MdRAD5B in gene expression modulation in apple in response to drought, that is, via the regulation of chromatin remodelling and H3K27me3.
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Affiliation(s)
- Yi Song
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of HorticultureNorthwest A&F UniversityYanglingChina
| | - Jieqiang He
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of HorticultureNorthwest A&F UniversityYanglingChina
| | - Junxing Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of HorticultureNorthwest A&F UniversityYanglingChina
| | - Yinpeng Xie
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of HorticultureNorthwest A&F UniversityYanglingChina
| | - Ziqing Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of HorticultureNorthwest A&F UniversityYanglingChina
| | - Zeyuan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of HorticultureNorthwest A&F UniversityYanglingChina
| | - Chundong Niu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of HorticultureNorthwest A&F UniversityYanglingChina
| | - Xuewei Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of HorticultureNorthwest A&F UniversityYanglingChina
| | - Baohua Chu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of HorticultureNorthwest A&F UniversityYanglingChina
| | - Muhammad Mobeen Tahir
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of HorticultureNorthwest A&F UniversityYanglingChina
| | - Jidi Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of HorticultureNorthwest A&F UniversityYanglingChina
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of HorticultureNorthwest A&F UniversityYanglingChina
| | - Qingmei Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of HorticultureNorthwest A&F UniversityYanglingChina
- Shenzhen Research InstituteNorthwest A&F UniversityShenzhenChina
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12
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Mammarella MF, Lucero L, Hussain N, Muñoz‐Lopez A, Huang Y, Ferrero L, Fernandez‐Milmanda GL, Manavella P, Benhamed M, Crespi M, Ballare CL, Gutiérrez Marcos J, Cubas P, Ariel F. Long noncoding RNA-mediated epigenetic regulation of auxin-related genes controls shade avoidance syndrome in Arabidopsis. EMBO J 2023; 42:e113941. [PMID: 38054357 PMCID: PMC10711646 DOI: 10.15252/embj.2023113941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 10/04/2023] [Accepted: 10/18/2023] [Indexed: 12/07/2023] Open
Abstract
The long noncoding RNA (lncRNA) AUXIN-REGULATED PROMOTER LOOP (APOLO) recognizes a subset of target loci across the Arabidopsis thaliana genome by forming RNA-DNA hybrids (R-loops) and modulating local three-dimensional chromatin conformation. Here, we show that APOLO regulates shade avoidance syndrome by dynamically modulating expression of key factors. In response to far-red (FR) light, expression of APOLO anti-correlates with that of its target BRANCHED1 (BRC1), a master regulator of shoot branching in Arabidopsis thaliana. APOLO deregulation results in BRC1 transcriptional repression and an increase in the number of branches. Accumulation of APOLO transcription fine-tunes the formation of a repressive chromatin loop encompassing the BRC1 promoter, which normally occurs only in leaves and in a late response to far-red light treatment in axillary buds. In addition, our data reveal that APOLO participates in leaf hyponasty, in agreement with its previously reported role in the control of auxin homeostasis through direct modulation of auxin synthesis gene YUCCA2, and auxin efflux genes PID and WAG2. We show that direct application of APOLO RNA to leaves results in a rapid increase in auxin signaling that is associated with changes in the plant response to far-red light. Collectively, our data support the view that lncRNAs coordinate shade avoidance syndrome in A. thaliana, and reveal their potential as exogenous bioactive molecules. Deploying exogenous RNAs that modulate plant-environment interactions may therefore become a new tool for sustainable agriculture.
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Affiliation(s)
| | - Leandro Lucero
- Instituto de Agrobiotecnología del Litoral, CONICETUniversidad Nacional del LitoralSanta FeArgentina
| | | | - Aitor Muñoz‐Lopez
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología‐CSICCampus Universidad Autónoma de MadridMadridSpain
| | - Ying Huang
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRAUniversité Evry, Université Paris‐SaclayOrsayFrance
- Institute of Plant Sciences Paris‐Saclay IPS2Université de ParisOrsayFrance
| | - Lucia Ferrero
- Instituto de Agrobiotecnología del Litoral, CONICETUniversidad Nacional del LitoralSanta FeArgentina
| | - Guadalupe L Fernandez‐Milmanda
- Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)Universidad de Buenos AiresBuenos AiresArgentina
| | - Pablo Manavella
- Instituto de Agrobiotecnología del Litoral, CONICETUniversidad Nacional del LitoralSanta FeArgentina
| | - Moussa Benhamed
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRAUniversité Evry, Université Paris‐SaclayOrsayFrance
- Institute of Plant Sciences Paris‐Saclay IPS2Université de ParisOrsayFrance
| | - Martin Crespi
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRAUniversité Evry, Université Paris‐SaclayOrsayFrance
- Institute of Plant Sciences Paris‐Saclay IPS2Université de ParisOrsayFrance
| | - Carlos L Ballare
- Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)Universidad de Buenos AiresBuenos AiresArgentina
- Instituto de Investigaciones Biotecnológicas (IIBIO), CONICETUniversidad Nacional de San MartínBuenos AiresArgentina
| | | | - Pilar Cubas
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología‐CSICCampus Universidad Autónoma de MadridMadridSpain
| | - Federico Ariel
- Instituto de Agrobiotecnología del Litoral, CONICETUniversidad Nacional del LitoralSanta FeArgentina
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13
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Li Z, Zhang Y, Ding CH, Chen Y, Wang H, Zhang J, Ying S, Wang M, Zhang R, Liu J, Xie Y, Tang T, Diao H, Ye L, Zhuang Y, Teng W, Zhang B, Huang L, Tong Y, Zhang W, Li G, Benhamed M, Dong Z, Gou JY, Zhang Y. LHP1-mediated epigenetic buffering of subgenome diversity and defense responses confers genome plasticity and adaptability in allopolyploid wheat. Nat Commun 2023; 14:7538. [PMID: 37985755 PMCID: PMC10661560 DOI: 10.1038/s41467-023-43178-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 10/25/2023] [Indexed: 11/22/2023] Open
Abstract
Polyploidization is a major driver of genome diversification and environmental adaptation. However, the merger of different genomes may result in genomic conflicts, raising a major question regarding how genetic diversity is interpreted and regulated to enable environmental plasticity. By analyzing the genome-wide binding of 191 trans-factors in allopolyploid wheat, we identified like heterochromatin protein 1 (LHP1) as a master regulator of subgenome-diversified genes. Transcriptomic and epigenomic analyses of LHP1 mutants reveal its role in buffering the expression of subgenome-diversified defense genes by controlling H3K27me3 homeostasis. Stripe rust infection releases latent subgenomic variations by eliminating H3K27me3-related repression. The simultaneous inactivation of LHP1 homoeologs by CRISPR-Cas9 confers robust stripe rust resistance in wheat seedlings. The conditional repression of subgenome-diversified defenses ensures developmental plasticity to external changes, while also promoting neutral-to-non-neutral selection transitions and adaptive evolution. These findings establish an LHP1-mediated buffering system at the intersection of genotypes, environments, and phenotypes in polyploid wheat. Manipulating the epigenetic buffering capacity offers a tool to harness cryptic subgenomic variations for crop improvement.
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Affiliation(s)
- Zijuan Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, 200032, Shanghai, China
- University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Yuyun Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, 200032, Shanghai, China
- University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Ci-Hang Ding
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, China
| | - Yan Chen
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, 510006, Guangzhou, China
| | - Haoyu Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, 200032, Shanghai, China
- Henan University, School of Life Science, 457000, Kaifeng, Henan, China
| | - Jinyu Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, 200032, Shanghai, China
- University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Songbei Ying
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Meiyue Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Rongzhi Zhang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
- Ministry of Agriculture, Key Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River Valley, Jinan, China
- National Engineering Research Center for Wheat and Maize, Jinan, Shandong, China
| | - Jinyi Liu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, 200032, Shanghai, China
- University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Yilin Xie
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, 200032, Shanghai, China
- University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Tengfei Tang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, 200032, Shanghai, China
- Henan University, School of Life Science, 457000, Kaifeng, Henan, China
| | - Huishan Diao
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Luhuan Ye
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, 200032, Shanghai, China
| | - Yili Zhuang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, 200032, Shanghai, China
| | - Wan Teng
- University of the Chinese Academy of Sciences, 100049, Beijing, China
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, 100101, Beijing, China
| | - Bo Zhang
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 810008, Xining, China
| | - Lin Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, 611130, Wenjiang, Chengdu, China
| | - Yiping Tong
- University of the Chinese Academy of Sciences, 100049, Beijing, China
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, 100101, Beijing, China
| | - Wenli Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No.1 Weigang, 210095, Nanjing, Jiangsu, China
| | - Genying Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
- Ministry of Agriculture, Key Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River Valley, Jinan, China
- National Engineering Research Center for Wheat and Maize, Jinan, Shandong, China
| | - Moussa Benhamed
- Université Paris Cité, Institute of Plant Sciences Paris-Saclay (IPS2), F-75006, Paris, France.
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France.
| | - Zhicheng Dong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, 510006, Guangzhou, China.
| | - Jin-Ying Gou
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, China.
| | - Yijing Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China.
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14
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Hamali B, Amine AAA, Al-Sady B. Regulation of the heterochromatin spreading reaction by trans-acting factors. Open Biol 2023; 13:230271. [PMID: 37935357 PMCID: PMC10645111 DOI: 10.1098/rsob.230271] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 10/03/2023] [Indexed: 11/09/2023] Open
Abstract
Heterochromatin is a gene-repressive protein-nucleic acid ultrastructure that is initially nucleated by DNA sequences. However, following nucleation, heterochromatin can then propagate along the chromatin template in a sequence-independent manner in a reaction termed spreading. At the heart of this process are enzymes that deposit chemical information on chromatin, which attracts the factors that execute chromatin compaction and transcriptional or co/post-transcriptional gene silencing. Given that these enzymes deposit guiding chemical information on chromatin they are commonly termed 'writers'. While the processes of nucleation and central actions of writers have been extensively studied and reviewed, less is understood about how the spreading process is regulated. We discuss how the chromatin substrate is prepared for heterochromatic spreading, and how trans-acting factors beyond writer enzymes regulate it. We examine mechanisms by which trans-acting factors in Suv39, PRC2, SETDB1 and SIR writer systems regulate spreading of the respective heterochromatic marks across chromatin. While these systems are in some cases evolutionarily and mechanistically quite distant, common mechanisms emerge which these trans-acting factors exploit to tune the spreading reaction.
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Affiliation(s)
- Bulut Hamali
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
- The G. W. Hooper Foundation, San Francisco, CA 94143, USA
- College of Dentistry, The Ohio State University, Columbus, OH, USA
| | - Ahmed A A Amine
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
- The G. W. Hooper Foundation, San Francisco, CA 94143, USA
| | - Bassem Al-Sady
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
- The G. W. Hooper Foundation, San Francisco, CA 94143, USA
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15
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Chorostecki U, Bologna NG, Ariel F. The plant noncoding transcriptome: a versatile environmental sensor. EMBO J 2023; 42:e114400. [PMID: 37735935 PMCID: PMC10577639 DOI: 10.15252/embj.2023114400] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 08/11/2023] [Accepted: 08/21/2023] [Indexed: 09/23/2023] Open
Abstract
Plant noncoding RNA transcripts have gained increasing attention in recent years due to growing evidence that they can regulate developmental plasticity. In this review article, we comprehensively analyze the relationship between noncoding RNA transcripts in plants and their response to environmental cues. We first provide an overview of the various noncoding transcript types, including long and small RNAs, and how the environment modulates their performance. We then highlight the importance of noncoding RNA secondary structure for their molecular and biological functions. Finally, we discuss recent studies that have unveiled the functional significance of specific long noncoding transcripts and their molecular partners within ribonucleoprotein complexes during development and in response to biotic and abiotic stress. Overall, this review sheds light on the fascinating and complex relationship between dynamic noncoding transcription and plant environmental responses, and highlights the need for further research to uncover the underlying molecular mechanisms and exploit the potential of noncoding transcripts for crop resilience in the context of global warming.
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Affiliation(s)
- Uciel Chorostecki
- Faculty of Medicine and Health SciencesUniversitat Internacional de CatalunyaBarcelonaSpain
| | - Nicolas G. Bologna
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBBarcelonaSpain
| | - Federico Ariel
- Instituto de Agrobiotecnologia del Litoral, CONICET, FBCBUniversidad Nacional del LitoralSanta FeArgentina
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16
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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] [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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17
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Sun L, Cao Y, Li Z, Liu Y, Yin X, Deng XW, He H, Qian W. Conserved H3K27me3-associated chromatin looping mediates physical interactions of gene clusters in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:1966-1982. [PMID: 37154484 DOI: 10.1111/jipb.13502] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/26/2023] [Accepted: 05/06/2023] [Indexed: 05/10/2023]
Abstract
Higher-order chromatin organization is essential for transcriptional regulation, genome stability maintenance, and other genome functions. Increasing evidence has revealed significant differences in 3D chromatin organization between plants and animals. However, the extent, pattern, and rules of chromatin organization in plants are still unclear. In this study, we systematically identified and characterized long-range chromatin loops in the Arabidopsis 3D genome. We identified hundreds of long-range cis chromatin loops and found their anchor regions are closely associated with H3K27me3 epigenetic modifications. Furthermore, we demonstrated that these chromatin loops are dependent on Polycomb group (PcG) proteins, suggesting that the Polycomb repressive complex 2 (PRC2) complex is essential for establishing and maintaining these novel loops. Although most of these PcG-medicated chromatin loops are stable, many of these loops are tissue-specific or dynamically regulated by different treatments. Interestingly, tandemly arrayed gene clusters and metabolic gene clusters are enriched in anchor regions. Long-range H3K27me3-marked chromatin interactions are associated with the coregulation of specific gene clusters. Finally, we also identified H3K27me3-associated chromatin loops associated with gene clusters in Oryza sativa and Glycine max, indicating that these long-range chromatin loops are conserved in plants. Our results provide novel insights into genome evolution and transcriptional coregulation in plants.
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Affiliation(s)
- Linhua Sun
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
| | - Yuxin Cao
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
| | - Zhu Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China
- School of Plant Science and Food Security, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Yi Liu
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
| | - Xiaochang Yin
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
| | - Xing Wang Deng
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
| | - Hang He
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
| | - Weiqiang Qian
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
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18
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Nugroho ABD, Kim S, Lee SW, Kim DH. Transcriptomic and epigenomic analyses revealed that polycomb repressive complex 2 regulates not only developmental but also stress responsive metabolism in Brassica rapa. FRONTIERS IN PLANT SCIENCE 2023; 14:1079218. [PMID: 36890886 PMCID: PMC9986605 DOI: 10.3389/fpls.2023.1079218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Polycomb group proteins (PcG) play a crucial role in developmental programs in eukaryotic organisms, including plants. PcG-mediated gene repression is achieved by epigenetic histone modification on target chromatins. Loss of PcG components leads to severe developmental defects. CURLY LEAF (CLF), a PcG component in Arabidopsis, catalyzes the trimethylation of histone H3 on lysine 27 (H3K27me3), a repressive histone mark in numerous genes in Arabidopsis. In this study, we isolated a single homolog of Arabidopsis CLF, namely, BrCLF, in Brassica rapa ssp. trilocularis. Transcriptomic analysis revealed that BrCLF participated in B. rapa developmental processes, such as seed dormancy, leaf and flower organ development, and floral transition. BrCLF was also involved in stress signaling and stress-responsive metabolism, such as aliphatic and indolic glucosinolate metabolism in B. rapa. Epigenome analysis showed that H3K27me3 was substantially enriched in genes related to these developmental and stress-responsive processes. Thus, this study provided a basis for elucidating the molecular mechanism of the PcG-mediated regulation of development and stress responses in B. rapa.
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19
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Velay F, Méteignier LV, Laloi C. You shall not pass! A Chromatin barrier story in plants. FRONTIERS IN PLANT SCIENCE 2022; 13:888102. [PMID: 36212303 PMCID: PMC9540200 DOI: 10.3389/fpls.2022.888102] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 08/15/2022] [Indexed: 06/16/2023]
Abstract
As in other eukaryotes, the plant genome is functionally organized in two mutually exclusive chromatin fractions, a gene-rich and transcriptionally active euchromatin, and a gene-poor, repeat-rich, and transcriptionally silent heterochromatin. In Drosophila and humans, the molecular mechanisms by which euchromatin is preserved from heterochromatin spreading have been extensively studied, leading to the identification of insulator DNA elements and associated chromatin factors (insulator proteins), which form boundaries between chromatin domains with antagonistic features. In contrast, the identity of factors assuring such a barrier function remains largely elusive in plants. Nevertheless, several genomic elements and associated protein factors have recently been shown to regulate the spreading of chromatin marks across their natural boundaries in plants. In this minireview, we focus on recent findings that describe the spreading of chromatin and propose avenues to improve the understanding of how plant chromatin architecture and transitions between different chromatin domains are defined.
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Affiliation(s)
- Florent Velay
- Aix Marseille Université, CEA, CNRS, Biosciences and Biotechnologies Institute of Aix-Marseille (BIAM), Equipe de Luminy de Génétique et Biophysique des Plantes, Marseille, F-13009, France
| | - Louis-Valentin Méteignier
- Aix Marseille Université, CEA, CNRS, Biosciences and Biotechnologies Institute of Aix-Marseille (BIAM), Equipe de Luminy de Génétique et Biophysique des Plantes, Marseille, F-13009, France
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France
| | - Christophe Laloi
- Aix Marseille Université, CEA, CNRS, Biosciences and Biotechnologies Institute of Aix-Marseille (BIAM), Equipe de Luminy de Génétique et Biophysique des Plantes, Marseille, F-13009, France
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20
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Séré D, Cassan O, Bellegarde F, Fizames C, Boucherez J, Schivre G, Azevedo J, Lagrange T, Gojon A, Martin A. Loss of Polycomb proteins CLF and LHP1 leads to excessive RNA degradation in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:5400-5413. [PMID: 35595271 DOI: 10.1093/jxb/erac216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Polycomb-group (PcG) proteins are major chromatin complexes that regulate gene expression, mainly described as repressors keeping genes in a transcriptionally silent state during development. Recent studies have nonetheless suggested that PcG proteins might have additional functions, including targeting active genes or acting independently of gene expression regulation. However, the reasons for the implication of PcG proteins and their associated chromatin marks on active genes are still largely unknown. Here, we report that combining mutations for CURLY LEAF (CLF) and LIKE HETEROCHROMATIN PROTEIN1 (LHP1), two Arabidopsis PcG proteins, results in deregulation of expression of active genes that are targeted by PcG proteins or enriched in associated chromatin marks. We show that this deregulation is associated with accumulation of small RNAs corresponding to massive degradation of active gene transcripts. We demonstrate that transcriptionally active genes and especially those targeted by PcG proteins are prone to RNA degradation, even though deregulation of RNA degradation following the loss of function of PcG proteins is not likely to be mediated by a PcG protein-mediated chromatin environment. Therefore, we conclude that PcG protein function is essential to maintain an accurate level of RNA degradation to ensure accurate gene expression.
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Affiliation(s)
- David Séré
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Océane Cassan
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Fanny Bellegarde
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Cécile Fizames
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Jossia Boucherez
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Geoffrey Schivre
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Jacinthe Azevedo
- CNRS, LGDP UMR5096, Université de Perpignan, 66860 Perpignan, France
| | - Thierry Lagrange
- CNRS, LGDP UMR5096, Université de Perpignan, 66860 Perpignan, France
| | - Alain Gojon
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Antoine Martin
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
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21
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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: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [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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22
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Oya S, Takahashi M, Takashima K, Kakutani T, Inagaki S. Transcription-coupled and epigenome-encoded mechanisms direct H3K4 methylation. Nat Commun 2022; 13:4521. [PMID: 35953471 PMCID: PMC9372134 DOI: 10.1038/s41467-022-32165-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
Mono-, di-, and trimethylation of histone H3 lysine 4 (H3K4me1/2/3) are associated with transcription, yet it remains controversial whether H3K4me1/2/3 promote or result from transcription. Our previous characterizations of Arabidopsis H3K4 demethylases suggest roles for H3K4me1 in transcription. However, the control of H3K4me1 remains unexplored in Arabidopsis, in which no methyltransferase for H3K4me1 has been identified. Here, we identify three Arabidopsis methyltransferases that direct H3K4me1. Analyses of their genome-wide localization using ChIP-seq and machine learning reveal that one of the enzymes cooperates with the transcription machinery, while the other two are associated with specific histone modifications and DNA sequences. Importantly, these two types of localization patterns are also found for the other H3K4 methyltransferases in Arabidopsis and mice. These results suggest that H3K4me1/2/3 are established and maintained via interplay with transcription as well as inputs from other chromatin features, presumably enabling elaborate gene control.
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Affiliation(s)
- Satoyo Oya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
| | | | | | - Tetsuji Kakutani
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
- National Institute of Genetics, Mishima, Japan.
| | - Soichi Inagaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan.
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23
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Topoisomerase VI participates in an insulator-like function that prevents H3K9me2 spreading. Proc Natl Acad Sci U S A 2022; 119:e2001290119. [PMID: 35759655 PMCID: PMC9271158 DOI: 10.1073/pnas.2001290119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [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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24
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Roulé T, Christ A, Hussain N, Huang Y, Hartmann C, Benhamed M, Gutierrez-Marcos J, Ariel F, Crespi M, Blein T. The lncRNA MARS modulates the epigenetic reprogramming of the marneral cluster in response to ABA. MOLECULAR PLANT 2022; 15:840-856. [PMID: 35150931 DOI: 10.1016/j.molp.2022.02.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 11/05/2021] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
Clustered organization of biosynthetic non-homologous genes is emerging as a characteristic feature of plant genomes. The co-regulation of clustered genes seems to largely depend on epigenetic reprogramming and three-dimensional chromatin conformation. In this study, we identified the long non-coding RNA (lncRNA) MARneral Silencing (MARS), localized inside the Arabidopsis marneral cluster, which controls the local epigenetic activation of its surrounding region in response to abscisic acid (ABA). MARS modulates the POLYCOMB REPRESSIVE COMPLEX 1 (PRC1) component LIKE HETEROCHROMATIN PROTEIN 1 (LHP1) binding throughout the cluster in a dose-dependent manner, determining H3K27me3 deposition and chromatin condensation. In response to ABA, MARS decoys LHP1 away from the cluster and promotes the formation of a chromatin loop bringing together the MARNERAL SYNTHASE 1 (MRN1) locus and a distal ABA-responsive enhancer. The enrichment of co-regulated lncRNAs in clustered metabolic genes in Arabidopsis suggests that the acquisition of novel non-coding transcriptional units may constitute an additional regulatory layer driving the evolution of biosynthetic pathways.
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Affiliation(s)
- Thomas Roulé
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France; Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
| | - Aurelie Christ
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France; Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
| | - Nosheen Hussain
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Ying Huang
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France; Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
| | - Caroline Hartmann
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France; Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
| | - Moussa Benhamed
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France; Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
| | | | - Federico Ariel
- Instituto de Agrobiotecnología del Litoral, CONICET, FBCB, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000 Santa Fe, Argentina
| | - Martin Crespi
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France; Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France.
| | - Thomas Blein
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France; Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France.
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25
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Godwin J, Farrona S. The Importance of Networking: Plant Polycomb Repressive Complex 2 and Its Interactors. EPIGENOMES 2022; 6:epigenomes6010008. [PMID: 35323212 PMCID: PMC8948837 DOI: 10.3390/epigenomes6010008] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 12/13/2022] Open
Abstract
Polycomb Repressive Complex 2 (PRC2) is arguably the best-known plant complex of the Polycomb Group (PcG) pathway, formed by a group of proteins that epigenetically represses gene expression. PRC2-mediated deposition of H3K27me3 has amply been studied in Arabidopsis and, more recently, data from other plant model species has also been published, allowing for an increasing knowledge of PRC2 activities and target genes. How PRC2 molecular functions are regulated and how PRC2 is recruited to discrete chromatin regions are questions that have brought more attention in recent years. A mechanism to modulate PRC2-mediated activity is through its interaction with other protein partners or accessory proteins. Current evidence for PRC2 interactors has demonstrated the complexity of its protein network and how far we are from fully understanding the impact of these interactions on the activities of PRC2 core subunits and on the formation of new PRC2 versions. This review presents a list of PRC2 interactors, emphasizing their mechanistic action upon PRC2 functions and their effects on transcriptional regulation.
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26
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Rodriguez-Granados NY, Ramirez-Prado JS, Brik-Chaouche R, An J, Manza-Mianza D, Sircar S, Troadec C, Hanique M, Soulard C, Costa R, Dogimont C, Latrasse D, Raynaud C, Boualem A, Benhamed M, Bendahmane A. CmLHP1 proteins play a key role in plant development and sex determination in melon (Cucumis melo). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:1213-1228. [PMID: 34897855 DOI: 10.1111/tpj.15627] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 11/26/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
In monoecious melon (Cucumis melo), sex is determined by the differential expression of sex determination genes (SDGs) and adoption of sex-specific transcriptional programs. Histone modifications such as H3K27me3 have been previously shown to be a hallmark associated to unisexual flower development in melon; yet, no genetic approaches have been conducted for elucidating the roles of H3K27me3 writers, readers, and erasers in this process. Here we show that melon homologs to Arabidopsis LHP1, CmLHP1A and B, redundantly control several aspects of plant development, including sex expression. Cmlhp1ab double mutants displayed an overall loss and redistribution of H3K27me3, leading to a deregulation of genes involved in hormone responses, plant architecture, and flower development. Consequently, double mutants display pleiotropic phenotypes and, interestingly, a general increase of the male:female ratio. We associated this phenomenon with a general deregulation of some hormonal response genes and a local activation of male-promoting SDGs and MADS-box transcription factors. Altogether, these results reveal a novel function for CmLHP1 proteins in maintenance of monoecy and provide novel insights into the polycomb-mediated epigenomic regulation of sex lability in plants.
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Affiliation(s)
- Natalia Yaneth Rodriguez-Granados
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Juan Sebastian Ramirez-Prado
- Centre of Microbial and Plant Genetics, KU Leuven, 3001, Leuven, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
| | - Rim Brik-Chaouche
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Jing An
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Deborah Manza-Mianza
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Sanchari Sircar
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Christelle Troadec
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Melissa Hanique
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Camille Soulard
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Rafael Costa
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Catherine Dogimont
- INRA, UR 1052, Unité de Génétique et d'Amélioration des Fruits et Légumes, BP 94, F-84143, Montfavet, France
| | - David Latrasse
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Cécile Raynaud
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Adnane Boualem
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Moussa Benhamed
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Abdelhafid Bendahmane
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
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Liu Y, Yang X, Zhou M, Yang Y, Li F, Yan X, Zhang M, Wei Z, Qin S, Min J. Structural basis for the recognition of methylated histone H3 by the Arabidopsis LHP1 chromodomain. J Biol Chem 2022; 298:101623. [PMID: 35074427 PMCID: PMC8861120 DOI: 10.1016/j.jbc.2022.101623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 12/02/2022] Open
Abstract
Arabidopsis LHP1 (LIKE HETEROCHROMATIN PROTEIN 1), a unique homolog of HP1 in Drosophila, plays important roles in plant development, growth, and architecture. In contrast to specific binding of the HP1 chromodomain to methylated H3K9 histone tails, the chromodomain of LHP1 has been shown to bind to both methylated H3K9 and H3K27 histone tails, and LHP1 carries out its function mainly via its interaction with these two epigenetic marks. However, the molecular mechanism for the recognition of methylated histone H3K9/27 by the LHP1 chromodomain is still unknown. In this study, we characterized the binding ability of LHP1 to histone H3K9 and H3K27 peptides and found that the chromodomain of LHP1 binds to histone H3K9me2/3 and H3K27me2/3 peptides with comparable affinities, although it exhibited no binding or weak binding to unmodified or monomethylated H3K9/K27 peptides. Our crystal structures of the LHP1 chromodomain in peptide-free and peptide-bound forms coupled with mutagenesis studies reveal that the chromodomain of LHP1 bears a slightly different chromodomain architecture and recognizes methylated H3K9 and H3K27 peptides via a hydrophobic clasp, similar to the chromodomains of human Polycomb proteins, which could not be explained only based on primary structure analysis. Our binding and structural studies of the LHP1 chromodomain illuminate a conserved ligand interaction mode between chromodomains of both animals and plants, and shed light on further functional study of the LHP1 protein.
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Affiliation(s)
- Yanli Liu
- College of Pharmaceutical Sciences, Soochow University, Su Zhou, Jiangsu 215021, PR China.
| | - Xiajie Yang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei 430079, PR China
| | - Mengqi Zhou
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei 430079, PR China
| | - Yinxue Yang
- College of Pharmaceutical Sciences, Soochow University, Su Zhou, Jiangsu 215021, PR China
| | - Fangzhou Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei 430079, PR China
| | - Xuemei Yan
- College of Pharmaceutical Sciences, Soochow University, Su Zhou, Jiangsu 215021, PR China
| | | | - Zhengguo Wei
- School of Biology and Basic Medical Science, Soochow University, Su Zhou, Jiangsu 215021, PR China
| | - Su Qin
- Life Science Research Center, Southern University of Science and Technology, Shenzhen, Guangdong 518055, PR China
| | - Jinrong Min
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei 430079, PR China.
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28
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Nugroho ABD, Lee SW, Pervitasari AN, Moon H, Choi D, Kim J, Kim DH. Transcriptomic and metabolic analyses revealed the modulatory effect of vernalization on glucosinolate metabolism in radish (Raphanus sativus L.). Sci Rep 2021; 11:24023. [PMID: 34912010 PMCID: PMC8674254 DOI: 10.1038/s41598-021-03557-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 12/01/2021] [Indexed: 12/13/2022] Open
Abstract
Vernalization is the process by which long-term cold like winter triggers transition to flowering in plants. Many biennial and perennial plants including Brassicaceae family plants require vernalization for floral transition. Not only floral transition, but dynamic physiological and metabolic changes might also take place during vernalization. However, vernalization-mediated metabolic change is merely investigated so far. One of secondary metabolites found in Brassiceceae family plants is glucosinolates (GSLs). GSLs provides defense against pathogens and herbivores attack in plants and also exhibits inhibitory activity against human cancer cell. Profiles of GSLs are highly modulated by different environmental stresses in Brassciaceae family plants. To grasp the effect of vernalization on GSLs metabolic dynamics in radish (Raphanus sativus L.), we performed transcriptomic and metabolic analysis during vernalization in radish. Through transcriptome analysis, we found many GSLs metabolic genes were significantly down-regulated by vernalization in radish plants. Ultra-High Performance Liquid Chromatography analysis also revealed that GSLs compounds were substantially reduced in vernalized radish samples compared to non-vernalized radish samples. Furthermore, we found that repressive histone modification (i.e. H3K27me3) is involved in the modulation of GSLs metabolism via epigenetic suppression of Glucoraphasatin Synthase 1 (GRS1) during vernalization in radish. This study revealed that GSLs metabolism is modulated by vernalization, suggestive of a newly identified target of vernalization in radish.
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Affiliation(s)
- Adji Baskoro Dwi Nugroho
- Department of Plant Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Sang Woo Lee
- Department of Plant Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | | | - Heewon Moon
- Department of Plant Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Dasom Choi
- Department of Plant Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Jongkee Kim
- Department of Plant Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Dong-Hwan Kim
- Department of Plant Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea. .,Research Center for Plant Plasticity, Seoul National University, Seoul, 08826, Republic of Korea.
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29
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Di Stefano M, Nützmann HW. Modeling the 3D genome of plants. Nucleus 2021; 12:65-81. [PMID: 34057011 PMCID: PMC8168717 DOI: 10.1080/19491034.2021.1927503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 04/29/2021] [Accepted: 05/05/2021] [Indexed: 12/11/2022] Open
Abstract
Chromosomes are the carriers of inheritable traits and define cell function and development. This is not only based on the linear DNA sequence of chromosomes but also on the additional molecular information they are associated with, including the transcription machinery, histone modifications, and their three-dimensional folding. The synergistic application of experimental approaches and computer simulations has helped to unveil how these organizational layers of the genome interplay in various organisms. However, such multidisciplinary approaches are still rarely explored in the plant kingdom. Here, we provide an overview of our current knowledge on plant 3D genome organization and review recent efforts to integrate cutting-edge experiments from microscopy and next-generation sequencing approaches with theoretical models. Building on these recent approaches, we propose possible avenues to extend the application of theoretical modeling in the characterization of the 3D genome organization in plants.
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Affiliation(s)
- Marco Di Stefano
- Institute of Human Genetics, Centre National de la Recherche Scientifique, University of Montpellier, Montpellier, France
| | - Hans-Wilhelm Nützmann
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
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30
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Shim S, Park CM, Seo PJ. iRegNet: an integrative Regulatory Network analysis tool for Arabidopsis thaliana. PLANT PHYSIOLOGY 2021; 187:1292-1309. [PMID: 34618085 PMCID: PMC8566287 DOI: 10.1093/plphys/kiab389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/09/2021] [Indexed: 05/24/2023]
Abstract
Gene expression is delicately controlled via multilayered genetic and/or epigenetic regulatory mechanisms. Rapid development of the high-throughput sequencing (HTS) technology and its derivative methods including chromatin immunoprecipitation sequencing (ChIP-seq) and DNA affinity purification sequencing (DAP-seq) have generated a large volume of data on DNA-protein interactions (DPIs) and histone modifications on a genome-wide scale. However, the ability to comprehensively retrieve empirically validated upstream regulatory networks of genes of interest (GOIs) and genomic regions of interest (ROIs) remains limited. Here, we present integrative Regulatory Network (iRegNet), a web application that analyzes the upstream regulatory network for user-queried GOIs or ROIs in the Arabidopsis (Arabidopsis thaliana) genome. iRegNet covers the largest empirically proven DNA-binding profiles of Arabidopsis transcription factors (TFs) and non-TF proteins, and histone modifications obtained from all currently available Arabidopsis ChIP-seq and DAP-seq data. iRegNet not only catalogs upstream regulomes and epigenetic chromatin states for single-query gene/genomic region but also suggests significantly overrepresented upstream genetic regulators and epigenetic chromatin states of user-submitted multiple query genes/genomic regions. Furthermore, gene-to-gene coexpression index and protein-protein interaction information were also integrated into iRegNet for a more reliable identification of upstream regulators and realistic regulatory networks. Thus, iRegNet will help discover upstream regulators as well as molecular regulatory networks of GOI(s) and/or ROI(s), and is freely available at http://chromatindynamics.snu.ac.kr:8082/iRegNet_main.
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Affiliation(s)
- Sangrea Shim
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea
| | - Chung-Mo Park
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea
- Research Institute of Basic Sciences, Seoul National University, Seoul 08826, Korea
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea
- Research Institute of Basic Sciences, Seoul National University, Seoul 08826, Korea
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31
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Bieluszewski T, Xiao J, Yang Y, Wagner D. PRC2 activity, recruitment, and silencing: a comparative perspective. TRENDS IN PLANT SCIENCE 2021; 26:1186-1198. [PMID: 34294542 DOI: 10.1016/j.tplants.2021.06.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 06/08/2021] [Accepted: 06/16/2021] [Indexed: 05/22/2023]
Abstract
Polycomb repressive complex (PRC)-mediated gene silencing is vital for cell identity and development in both the plant and the animal kingdoms. It also modulates responses to stress. Two major protein complexes, PRC1 and PRC2, execute conserved nuclear functions in metazoans and plants through covalent modification of histones and by compacting chromatin. While a general requirement for Polycomb complexes in mitotically heritable gene repression in the context of chromatin is well established, recent studies have brought new insights into the regulation of Polycomb complex activity and recruitment. Here, we discuss these recent advances with emphasis on PRC2.
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Affiliation(s)
- Tomasz Bieluszewski
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19103, USA
| | - Jun Xiao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; Centre of Excellence for Plant and Microbial Science (CEPAMS), the John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Yiman Yang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19103, USA.
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32
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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 SIGNALING & BEHAVIOR 2021; 16:1920191. [PMID: 33944666 PMCID: PMC8244768 DOI: 10.1080/15592324.2021.1920191] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [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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33
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Plant long non-coding RNAs in the regulation of transcription. Essays Biochem 2021; 65:751-760. [PMID: 34296250 DOI: 10.1042/ebc20200090] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/19/2021] [Accepted: 06/17/2021] [Indexed: 01/22/2023]
Abstract
Eukaryotic genomes are pervasively transcribed, producing large numbers of non-coding RNAs (ncRNAs), including tens of thousands of long ncRNAs (lncRNAs), defined as ncRNAs longer than 200 nucleotides. Recent studies have revealed the important roles lncRNAs play in the regulation of gene expression at various levels in all eukaryotes; moreover, emerging research in plants has identified roles for lncRNAs in key processes such as flowering time control, root organogenesis, reproduction, and adaptation to environmental changes. LncRNAs participate in regulating most steps of gene expression, including reshaping nuclear organization and chromatin structure; governing multiple steps of transcription, splicing, mRNA stability, and translation; and affecting post-translational protein modifications. In this review, I present the latest progress on the lncRNA-mediated regulatory mechanisms modulating transcription in Arabidopsis thaliana, focusing on their functions in regulation of gene expression via chromatin structure and interactions with the transcriptional machinery.
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34
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Post-Embryonic Phase Transitions Mediated by Polycomb Repressive Complexes in Plants. Int J Mol Sci 2021; 22:ijms22147533. [PMID: 34299153 PMCID: PMC8305008 DOI: 10.3390/ijms22147533] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/05/2021] [Accepted: 07/09/2021] [Indexed: 12/20/2022] Open
Abstract
Correct timing of developmental phase transitions is critical for the survival and fitness of plants. Developmental phase transitions in plants are partially promoted by controlling relevant genes into active or repressive status. Polycomb Repressive Complex1 (PRC1) and PRC2, originally identified in Drosophila, are essential in initiating and/or maintaining genes in repressive status to mediate developmental phase transitions. Our review summarizes mechanisms in which the embryo-to-seedling transition, the juvenile-to-adult transition, and vegetative-to-reproductive transition in plants are mediated by PRC1 and PRC2, and suggests that PRC1 could act either before or after PRC2, or that they could function independently of each other. Details of the exact components of PRC1 and PRC2 in each developmental phase transitions and how they are recruited or removed will need to be addressed in the future.
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35
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Huang Y, Sicar S, Ramirez-Prado JS, Manza-Mianza D, Antunez-Sanchez J, Brik-Chaouche R, Rodriguez-Granados NY, An J, Bergounioux C, Mahfouz MM, Hirt H, Crespi M, Concia L, Barneche F, Amiard S, Probst AV, Gutierrez-Marcos J, Ariel F, Raynaud C, Latrasse D, Benhamed M. Polycomb-dependent differential chromatin compartmentalization determines gene coregulation in Arabidopsis. Genome Res 2021; 31:1230-1244. [PMID: 34083408 PMCID: PMC8256866 DOI: 10.1101/gr.273771.120] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 05/20/2021] [Indexed: 11/24/2022]
Abstract
In animals, distant H3K27me3-marked Polycomb targets can establish physical interactions forming repressive chromatin hubs. In plants, growing evidence suggests that H3K27me3 acts directly or indirectly to regulate chromatin interactions, although how this histone modification modulates 3D chromatin architecture remains elusive. To decipher the impact of the dynamic deposition of H3K27me3 on the Arabidopsis thaliana nuclear interactome, we combined genetics, transcriptomics, and several 3D epigenomic approaches. By analyzing mutants defective for histone H3K27 methylation or demethylation, we uncovered the crucial role of this chromatin mark in short- and previously unnoticed long-range chromatin loop formation. We found that a reduction in H3K27me3 levels led to a decrease in the interactions within Polycomb-associated repressive domains. Regions with lower H3K27me3 levels in the H3K27 methyltransferase clf mutant established new interactions with regions marked with H3K9ac, a histone modification associated with active transcription, indicating that a reduction in H3K27me3 levels induces a global reconfiguration of chromatin architecture. Altogether, our results reveal that the 3D genome organization is tightly linked to reversible histone modifications that govern chromatin interactions. Consequently, nuclear organization dynamics shapes the transcriptional reprogramming during plant development and places H3K27me3 as a key feature in the coregulation of distant genes.
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Affiliation(s)
- Ying Huang
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
| | - Sanchari Sicar
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
| | - Juan S Ramirez-Prado
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
| | - Deborah Manza-Mianza
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
| | | | - Rim Brik-Chaouche
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
| | - Natalia Y Rodriguez-Granados
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
| | - Jing An
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
| | - Catherine Bergounioux
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
| | - Magdy M Mahfouz
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Heribert Hirt
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Martin Crespi
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
| | - Lorenzo Concia
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), ENS, CNRS UMR8197, INSERM U1024, PSL Research University, 75005, Paris, France
| | - Fredy Barneche
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), ENS, CNRS UMR8197, INSERM U1024, PSL Research University, 75005, Paris, France
| | - Simon Amiard
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001, Clermont-Ferrand, France
| | - Aline V Probst
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001, Clermont-Ferrand, France
| | | | - Federico Ariel
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - Cécile Raynaud
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
| | - David Latrasse
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
| | - Moussa Benhamed
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
- Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), F-75006 Paris, France
- Institut Universitaire de France (IUF)
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36
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Honaas L, Hargarten H, Hadish J, Ficklin SP, Serra S, Musacchi S, Wafula E, Mattheis J, dePamphilis CW, Rudell D. Transcriptomics of Differential Ripening in 'd'Anjou' Pear ( Pyrus communis L.). FRONTIERS IN PLANT SCIENCE 2021; 12:609684. [PMID: 34220875 PMCID: PMC8243007 DOI: 10.3389/fpls.2021.609684] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 04/06/2021] [Indexed: 06/13/2023]
Abstract
Estimating maturity in pome fruits is a critical task that directs virtually all postharvest supply chain decisions. This is especially important for European pear (Pyrus communis) cultivars because losses due to spoilage and senescence must be minimized while ensuring proper ripening capacity is achieved (in part by satisfying a fruit chilling requirement). Reliable methods are lacking for accurate estimation of pear fruit maturity, and because ripening is maturity dependent it makes predicting ripening capacity a challenge. In this study of the European pear cultivar 'd'Anjou', we sorted fruit at harvest based upon on-tree fruit position to build contrasts of maturity. Our sorting scheme showed clear contrasts of maturity between canopy positions, yet there was substantial overlap in the distribution of values for the index of absorbance difference (I AD ), a non-destructive spectroscopic measurement that has been used as a proxy for pome fruit maturity. This presented an opportunity to explore a contrast of maturity that was more subtle than I AD could differentiate, and thus guided our subsequent transcriptome analysis of tissue samples taken at harvest and during storage. Using a novel approach that tests for condition-specific differences of co-expressed genes, we discovered genes with a phased character that mirrored our sorting scheme. The expression patterns of these genes are associated with fruit quality and ripening differences across the experiment. Functional profiles of these co-expressed genes are concordant with previous findings, and also offer new clues, and thus hypotheses, about genes involved in pear fruit quality, maturity, and ripening. This work may lead to new tools for enhanced postharvest management based on activity of gene co-expression modules, rather than individual genes. Further, our results indicate that modules may have utility within specific windows of time during postharvest management of 'd'Anjou' pear.
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Affiliation(s)
- Loren Honaas
- USDA, ARS, Tree Fruit Research Laboratory, Wenatchee, WA, United States
| | - Heidi Hargarten
- USDA, ARS, Tree Fruit Research Laboratory, Wenatchee, WA, United States
| | - John Hadish
- Molecular Plant Sciences, Washington State University, Pullman, WA, United States
| | - Stephen P. Ficklin
- Molecular Plant Sciences, Washington State University, Pullman, WA, United States
- Department of Horticulture, Washington State University, Pullman, WA, United States
| | - Sara Serra
- Department of Horticulture, Washington State University, Pullman, WA, United States
- Tree Fruit Research and Extension Center, Washington State University, Wenatchee, WA, United States
| | - Stefano Musacchi
- Department of Horticulture, Washington State University, Pullman, WA, United States
- Tree Fruit Research and Extension Center, Washington State University, Wenatchee, WA, United States
| | - Eric Wafula
- Department of Biology, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States
| | - James Mattheis
- USDA, ARS, Tree Fruit Research Laboratory, Wenatchee, WA, United States
| | - Claude W. dePamphilis
- Department of Biology, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States
| | - David Rudell
- USDA, ARS, Tree Fruit Research Laboratory, Wenatchee, WA, United States
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37
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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. MOLECULAR PLANT 2021; 14:937-948. [PMID: 33689931 DOI: 10.1016/j.molp.2021.03.008] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [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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38
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Zhao B, Xi Y, Kim J, Sung S. Chromatin architectural proteins regulate flowering time by precluding gene looping. SCIENCE ADVANCES 2021; 7:eabg3097. [PMID: 34117065 PMCID: PMC8195489 DOI: 10.1126/sciadv.abg3097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 04/28/2021] [Indexed: 05/03/2023]
Abstract
Chromatin structure is critical for gene expression and many other cellular processes. In Arabidopsis thaliana, the floral repressor FLC adopts a self-loop chromatin structure via bridging of its flanking regions. This local gene loop is necessary for active FLC expression. However, the molecular mechanism underlying the formation of this class of gene loops is unknown. Here, we report the characterization of a group of linker histone-like proteins, named the GH1-HMGA family in Arabidopsis, which act as chromatin architecture modulators. We demonstrate that these family members redundantly promote the floral transition through the repression of FLC A genome-wide study revealed that this family preferentially binds to the 5' and 3' ends of gene bodies. The loss of this binding increases FLC expression by stabilizing the FLC 5' to 3' gene looping. Our study provides mechanistic insights into how a family of evolutionarily conserved proteins regulates the formation of local gene loops.
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Affiliation(s)
- Bo Zhao
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Yanpeng Xi
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Junghyun Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Sibum Sung
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.
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39
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Kim J, Lee H, Lee HG, Seo PJ. Get closer and make hotspots: liquid-liquid phase separation in plants. EMBO Rep 2021; 22:e51656. [PMID: 33913240 DOI: 10.15252/embr.202051656] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 01/14/2021] [Accepted: 03/30/2021] [Indexed: 12/18/2022] Open
Abstract
Liquid-liquid phase separation (LLPS) facilitates the formation of membraneless compartments in a cell and allows the spatiotemporal organization of biochemical reactions by concentrating macromolecules locally. In plants, LLPS defines cellular reaction hotspots, and stimulus-responsive LLPS is tightly linked to a variety of cellular and biological functions triggered by exposure to various internal and external stimuli, such as stress responses, hormone signaling, and temperature sensing. Here, we provide an overview of the current understanding of physicochemical forces and molecular factors that drive LLPS in plant cells. We illustrate how the biochemical features of cellular condensates contribute to their biological functions. Additionally, we highlight major challenges for the comprehensive understanding of biological LLPS, especially in view of the dynamic and robust organization of biochemical reactions underlying plastic responses to environmental fluctuations in plants.
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Affiliation(s)
- Jiwoo Kim
- Department of Chemistry, Seoul National University, Seoul, Korea
| | - Hongwoo Lee
- Department of Chemistry, Seoul National University, Seoul, Korea
| | - Hong Gil Lee
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul, Korea.,Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea
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40
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Zhang C, Cheng Q, Wang H, Gao H, Fang X, Chen X, Zhao M, Wei W, Song B, Liu S, Wu J, Zhang S, Xu P. GmBTB/POZ promotes the ubiquitination and degradation of LHP1 to regulate the response of soybean to Phytophthora sojae. Commun Biol 2021; 4:372. [PMID: 33742112 PMCID: PMC7979691 DOI: 10.1038/s42003-021-01907-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 02/24/2021] [Indexed: 01/07/2023] Open
Abstract
Phytophthora sojae is a pathogen that causes stem and root rot in soybean (Glycine max [L.] Merr.). We previously demonstrated that GmBTB/POZ, a BTB/POZ domain-containing nuclear protein, enhances resistance to P. sojae in soybean, via a process that depends on salicylic acid (SA). Here, we demonstrate that GmBTB/POZ associates directly with soybean LIKE HETEROCHROMATIN PROTEIN1 (GmLHP1) in vitro and in vivo and promotes its ubiquitination and degradation. Both overexpression and RNA interference analysis of transgenic lines demonstrate that GmLHP1 negatively regulates the response of soybean to P. sojae by reducing SA levels and repressing GmPR1 expression. The WRKY transcription factor gene, GmWRKY40, a SA-induced gene in the SA signaling pathway, is targeted by GmLHP1, which represses its expression via at least two mechanisms (directly binding to its promoter and impairing SA accumulation). Furthermore, the nuclear localization of GmLHP1 is required for the GmLHP1-mediated negative regulation of immunity, SA levels and the suppression of GmWRKY40 expression. Finally, GmBTB/POZ releases GmLHP1-regulated GmWRKY40 suppression and increases resistance to P. sojae in GmLHP1-OE hairy roots. These findings uncover a regulatory mechanism by which GmBTB/POZ-GmLHP1 modulates resistance to P. sojae in soybean, likely by regulating the expression of downstream target gene GmWRKY40.
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Affiliation(s)
- Chuanzhong Zhang
- Soybean Research Institute, Northeast Agricultural University, Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin, China
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Qun Cheng
- Soybean Research Institute, Northeast Agricultural University, Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin, China
| | - Huiyu Wang
- Soybean Research Institute, Northeast Agricultural University, Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin, China
| | - Hong Gao
- Soybean Research Institute, Northeast Agricultural University, Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin, China
| | - Xin Fang
- Soybean Research Institute, Northeast Agricultural University, Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin, China
| | - Xi Chen
- Soybean Research Institute, Northeast Agricultural University, Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin, China
| | - Ming Zhao
- Soybean Research Institute, Northeast Agricultural University, Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin, China
| | - Wanling Wei
- Soybean Research Institute, Northeast Agricultural University, Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin, China
| | - Bo Song
- Soybean Research Institute, Northeast Agricultural University, Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin, China
| | - Shanshan Liu
- Soybean Research Institute, Northeast Agricultural University, Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin, China
| | - Junjiang Wu
- Soybean Research Institute of Heilongjiang Academy of Agricultural Sciences, Key Laboratory of Soybean Cultivation of Ministry of Agriculture, Harbin, China
| | - Shuzhen Zhang
- Soybean Research Institute, Northeast Agricultural University, Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin, China.
| | - Pengfei Xu
- Soybean Research Institute, Northeast Agricultural University, Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin, China.
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41
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Inagaki S, Takahashi M, Takashima K, Oya S, Kakutani T. Chromatin-based mechanisms to coordinate convergent overlapping transcription. NATURE PLANTS 2021; 7:295-302. [PMID: 33649596 DOI: 10.1038/s41477-021-00868-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
In eukaryotic genomes, the transcription units of genes often overlap with other protein-coding and/or noncoding transcription units1,2. In such intertwined genomes, the coordinated transcription of nearby or overlapping genes would be important to ensure the integrity of genome function3-6; however, the mechanisms underlying this coordination are largely unknown. Here, we show in Arabidopsis thaliana that genes with convergent orientation of transcription are major sources of antisense transcripts and that these genes transcribed on both strands are regulated by a putative Lysine-Specific Demethylase 1 family histone demethylase, FLOWERING LOCUS D (FLD)7,8. Our genome-wide chromatin profiling revealed that FLD, as well as its associating factor LUMINIDEPENDENS9, downregulates histone H3K4me1 in regions with convergent overlapping transcription. FLD localizes to actively transcribed genes, where it colocalizes with elongating RNA polymerase II phosphorylated at the Ser2 or Ser5 sites. Genome-wide transcription analyses suggest that FLD-mediated H3K4me1 removal negatively regulates the transcription of genes with high levels of antisense transcription. Furthermore, the effect of FLD on transcription dynamics is antagonized by DNA topoisomerase I. Our study reveals chromatin-based mechanisms to cope with overlapping transcription, which may occur by modulating DNA topology. This global mechanism to cope with overlapping transcription could be co-opted for specific epigenetic processes, such as cellular memory of responses to the environment10.
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Affiliation(s)
- Soichi Inagaki
- Department of Biological Sciences, Faculty of Science, The University of Tokyo, Tokyo, Japan.
- National Institute of Genetics, Mishima, Japan.
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Shonankokusaimura, Hayama, Japan.
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan.
| | | | | | - Satoyo Oya
- Department of Biological Sciences, Faculty of Science, The University of Tokyo, Tokyo, Japan
| | - Tetsuji Kakutani
- Department of Biological Sciences, Faculty of Science, The University of Tokyo, Tokyo, Japan
- National Institute of Genetics, Mishima, Japan
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Shonankokusaimura, Hayama, Japan
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42
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Di Stefano M, Nützmann HW, Marti-Renom M, Jost D. Polymer modelling unveils the roles of heterochromatin and nucleolar organizing regions in shaping 3D genome organization in Arabidopsis thaliana. Nucleic Acids Res 2021; 49:1840-1858. [PMID: 33444439 PMCID: PMC7913674 DOI: 10.1093/nar/gkaa1275] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 11/16/2020] [Accepted: 01/13/2021] [Indexed: 01/10/2023] Open
Abstract
The 3D genome is characterized by a complex organization made of genomic and epigenomic layers with profound implications on gene regulation and cell function. However, the understanding of the fundamental mechanisms driving the crosstalk between nuclear architecture and (epi)genomic information is still lacking. The plant Arabidopsis thaliana is a powerful model organism to address these questions owing to its compact genome for which we have a rich collection of microscopy, chromosome conformation capture (Hi-C) and ChIP-seq experiments. Using polymer modelling, we investigate the roles of nucleolus formation and epigenomics-driven interactions in shaping the 3D genome of A. thaliana. By validation of several predictions with published data, we demonstrate that self-attracting nucleolar organizing regions and repulsive constitutive heterochromatin are major mechanisms to regulate the organization of chromosomes. Simulations also suggest that interphase chromosomes maintain a partial structural memory of the V-shapes, typical of (sub)metacentric chromosomes in anaphase. Additionally, self-attraction between facultative heterochromatin regions facilitates the formation of Polycomb bodies hosting H3K27me3-enriched gene-clusters. Since nucleolus and heterochromatin are highly-conserved in eukaryotic cells, our findings pave the way for a comprehensive characterization of the generic principles that are likely to shape and regulate the 3D genome in many species.
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Affiliation(s)
- Marco Di Stefano
- CNAG-CRG, The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Hans-Wilhelm Nützmann
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
| | - Marc A Marti-Renom
- CNAG-CRG, The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- CRG, The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- ICREA, Barcelona, Spain
| | - Daniel Jost
- Université de Lyon, ENS de Lyon, Univ Claude Bernard, CNRS, Laboratoire de Biologie et Modélisation de la Cellule, Lyon, France
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43
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Fonouni-Farde C, Ariel F, Crespi M. Plant Long Noncoding RNAs: New Players in the Field of Post-Transcriptional Regulations. Noncoding RNA 2021; 7:12. [PMID: 33671131 PMCID: PMC8005961 DOI: 10.3390/ncrna7010012] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/12/2021] [Accepted: 02/14/2021] [Indexed: 02/08/2023] Open
Abstract
The first reference to the "C-value paradox" reported an apparent imbalance between organismal genome size and morphological complexity. Since then, next-generation sequencing has revolutionized genomic research and revealed that eukaryotic transcriptomes contain a large fraction of non-protein-coding components. Eukaryotic genomes are pervasively transcribed and noncoding regions give rise to a plethora of noncoding RNAs with undeniable biological functions. Among them, long noncoding RNAs (lncRNAs) seem to represent a new layer of gene expression regulation, participating in a wide range of molecular mechanisms at the transcriptional and post-transcriptional levels. In addition to their role in epigenetic regulation, plant lncRNAs have been associated with the degradation of complementary RNAs, the regulation of alternative splicing, protein sub-cellular localization, the promotion of translation and protein post-translational modifications. In this review, we report and integrate numerous and complex mechanisms through which long noncoding transcripts regulate post-transcriptional gene expression in plants.
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Affiliation(s)
- Camille Fonouni-Farde
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Bat 630, 91192 Gif sur Yvette, France;
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Bat 630, 91192 Gif sur Yvette, France
| | - Federico Ariel
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000 Santa Fe, Argentina;
| | - Martin Crespi
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Bat 630, 91192 Gif sur Yvette, France;
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Bat 630, 91192 Gif sur Yvette, France
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44
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Luján-Soto E, Dinkova TD. Time to Wake Up: Epigenetic and Small-RNA-Mediated Regulation during Seed Germination. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10020236. [PMID: 33530470 PMCID: PMC7911344 DOI: 10.3390/plants10020236] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/22/2021] [Accepted: 01/22/2021] [Indexed: 05/03/2023]
Abstract
Plants make decisions throughout their lifetime based on complex networks. Phase transitions during seed growth are not an exception. From embryo development through seedling growth, several molecular pathways control genome stability, environmental signal transduction and the transcriptional landscape. Particularly, epigenetic modifications and small non-coding RNAs (sRNAs) have been extensively studied as significant handlers of these processes in plants. Here, we review key epigenetic (histone modifications and methylation patterns) and sRNA-mediated regulatory networks involved in the progression from seed maturation to germination, their relationship with seed traits and crosstalk with environmental inputs.
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45
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Yuan L, Song X, Zhang L, Yu Y, Liang Z, Lei Y, Ruan J, Tan B, Liu J, Li C. The transcriptional repressors VAL1 and VAL2 recruit PRC2 for genome-wide Polycomb silencing in Arabidopsis. Nucleic Acids Res 2021; 49:98-113. [PMID: 33270882 PMCID: PMC7797069 DOI: 10.1093/nar/gkaa1129] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 10/19/2020] [Accepted: 11/07/2020] [Indexed: 12/11/2022] Open
Abstract
The Polycomb repressive complex 2 (PRC2) catalyzes histone H3 Lys27 trimethylation (H3K27me3) to repress gene transcription in multicellular eukaryotes. Despite its importance in gene silencing and cellular differentiation, how PRC2 is recruited to target loci is still not fully understood. Here, we report genome-wide evidence for the recruitment of PRC2 by the transcriptional repressors VIVIPAROUS1/ABI3-LIKE1 (VAL1) and VAL2 in Arabidopsis thaliana. We show that the val1 val2 double mutant possesses somatic embryonic phenotypes and a transcriptome strikingly similar to those of the swn clf double mutant, which lacks the PRC2 catalytic subunits SWINGER (SWN) and CURLY LEAF (CLF). We further show that VAL1 and VAL2 physically interact with SWN and CLF in vivo. Genome-wide binding profiling demonstrated that they colocalize with SWN and CLF at PRC2 target loci. Loss of VAL1/2 significantly reduces SWN and CLF enrichment at PRC2 target loci and leads to a genome-wide redistribution of H3K27me3 that strongly affects transcription. Finally, we provide evidence that the VAL1/VAL2-RY regulatory system is largely independent of previously identified modules for Polycomb silencing in plants. Together, our work demonstrates an extensive genome-wide interaction between VAL1/2 and PRC2 and provides mechanistic insights into the establishment of Polycomb silencing in plants.
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Affiliation(s)
- Liangbing Yuan
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Xin Song
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Lu Zhang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China.,Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou 571158, China
| | - Yaoguang Yu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Zhenwei Liang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yawen Lei
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Jiuxiao Ruan
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Bin Tan
- Guangdong Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510624, China
| | - Jun Liu
- Guangdong Provincial Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Chenlong Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
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46
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Tyagi V, Parihar V, Singh D, Kapoor S, Kapoor M. The DEAD-box RNA helicase eIF4A1 interacts with the SWI2/SNF2-related chromatin remodelling ATPase DDM1 in the moss Physcomitrella. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140592. [PMID: 33359411 DOI: 10.1016/j.bbapap.2020.140592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 12/27/2022]
Abstract
eIF4A is a DEAD box containing RNA helicase that plays crucial roles in regulating translation initiation, growth and abiotic stress tolerance in plants. It also functions as an ATP-dependent RNA binding protein to curb granule formation by limiting RNA-RNA interactions that promote RNA condensation and formation of ribonucleoprotein particles in vivo. Helicase activity of eIF4A is known to be dictated by its binding partners. Proteins interacting with eIF4A have been identified across land plants. In monocots a close link between eIF4A regulated processes and DNA methylation in epigenetic regulation of plant development is inferred from interaction between OseIF4A and the de novo methyltransferase OsDRM2 and loss-of-function studies of these genes in Oryza sativa and Brachypodium distachyon. In the moss Physcomitrella patens, eIF4A1 encoded by Pp3c6_1080V3.1 interacts with the heterogeneous nuclear ribonucleoprotein (hnRNP) PpLIF2L1, homolog of which in Arabidopsis regulates transcription of stress-responsive genes. In this study, using different protein-protein interaction methods, targeted gene knockout strategy and quantitative expression analysis we show genetic interaction between PpeIF4A1 and the putative nucleosome remodeler protein PpDDM1 and between PpDDM1 and PpLIF2L1 in vivo. Stress-induced co-expression of PpeIF4A1, PpDDM1 and PpLIF2L1, their roles in salt stress tolerance and differences in subnuclear distribution of PpLIF2L1 in ppeif4a1 cells in comparison to wild type suggest existence of a regulatory network comprising of RNA helicases, chromatin remodelling proteins and hnRNP active in stress-responsive biological processes in P. patens.
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Affiliation(s)
- Vidhi Tyagi
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi 110078, India
| | - Vimala Parihar
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi 110078, India
| | - Darshika Singh
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi 110078, India
| | - Sanjay Kapoor
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus Benito Juarez Road, New Delhi 110021, India
| | - Meenu Kapoor
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi 110078, India.
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47
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Cui Y, Cheng J, Ruan S, Qi P, Liu W, Bian H, Ye L, Zhang Y, Hu J, Dong G, Guo L, Zhang Y, Qian Q, Hu X. The heterochronic gene Oryza sativa LIKE HETEROCHROMATIN PROTEIN 1 modulates miR156b/c/i/e levels. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:1839-1852. [PMID: 32644250 DOI: 10.1111/jipb.12991] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 07/08/2020] [Indexed: 06/11/2023]
Abstract
The juvenile-to-adult transition in plants involves changes in vegetative growth and plant architecture; the timing of this transition has important implications for agriculture. The microRNA miR156 regulates this transition and shoot maturation in plants. In Arabidopsis thaliana, deposition of histone H3 trimethylation on lysine 27 (H3K27me3, a repressive mark) at the MIR156A/C loci is regulated by Polycomb Repressive Complex 1 (PRC1) or PRC2, depending on the developmental stage. The levels of miR156 progressively decline during shoot maturation. The amount of H3K27me3 at MIR156A/C loci affects miR156 levels; however, whether this epigenetic regulation is conserved remains unclear. Here, we found that in rice (Oryza sativa), the putative PRC1 subunit LIKE HETEROCHROMATIN PROTEIN 1 (OsLHP1), with the miR156-SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) module, affects developmental phase transitions. Loss of OsLHP1 function results in ectopic expression of MIR156B/C/I/E, phenocopy of miR156 overexpression, and reduced H3k27me3 levels at MIR156B/C/I/E. This indicates that OsLHP1 has functionally diverged from Arabidopsis LHP1. Genetic and transcriptome analyses of wild-type, miR156b/c-overexpression, and Oslhp1-2 mutant plants suggest that OsLHP1 acts upstream of miR156 and SPL during the juvenile-to-adult transition. Therefore, modifying the OsLHP1-miR156-SPL pathway may enable alteration of the vegetative period and plant architecture.
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Affiliation(s)
- Yongtao Cui
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Jingfei Cheng
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Shuang Ruan
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Peipei Qi
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Wei Liu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Hongwu Bian
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Luhuan Ye
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yuping Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Jiang Hu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Guojun Dong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Longbiao Guo
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Yijing Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Xingming Hu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
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48
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DasGupta A, Lee TL, Li C, Saltzman AL. Emerging Roles for Chromo Domain Proteins in Genome Organization and Cell Fate in C. elegans. Front Cell Dev Biol 2020; 8:590195. [PMID: 33195254 PMCID: PMC7649781 DOI: 10.3389/fcell.2020.590195] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 09/08/2020] [Indexed: 11/28/2022] Open
Abstract
In most eukaryotes, the genome is packaged with histones and other proteins to form chromatin. One of the major mechanisms for chromatin regulation is through post-translational modification of histone proteins. Recognition of these modifications by effector proteins, often dubbed histone “readers,” provides a link between the chromatin landscape and gene regulation. The diversity of histone reader proteins for each modification provides an added layer of regulatory complexity. In this review, we will focus on the roles of chromatin organization modifier (chromo) domain containing proteins in the model nematode, Caenorhabditis elegans. An amenability to genetic and cell biological approaches, well-studied development and a short life cycle make C. elegans a powerful system to investigate the diversity of chromo domain protein functions in metazoans. We will highlight recent insights into the roles of chromo domain proteins in the regulation of heterochromatin and the spatial conformation of the genome as well as their functions in cell fate, fertility, small RNA pathways and transgenerational epigenetic inheritance. The spectrum of different chromatin readers may represent a layer of regulation that integrates chromatin landscape, genome organization and gene expression.
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Affiliation(s)
- Abhimanyu DasGupta
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Tammy L Lee
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Chengyin Li
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Arneet L Saltzman
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada
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49
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Kim S, Piquerez SJM, Ramirez-Prado JS, Mastorakis E, Veluchamy A, Latrasse D, Manza-Mianza D, Brik-Chaouche R, Huang Y, Rodriguez-Granados NY, Concia L, Blein T, Citerne S, Bendahmane A, Bergounioux C, Crespi M, Mahfouz MM, Raynaud C, Hirt H, Ntoukakis V, Benhamed M. GCN5 modulates salicylic acid homeostasis by regulating H3K14ac levels at the 5' and 3' ends of its target genes. Nucleic Acids Res 2020; 48:5953-5966. [PMID: 32396165 PMCID: PMC7293002 DOI: 10.1093/nar/gkaa369] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 04/27/2020] [Accepted: 05/02/2020] [Indexed: 01/01/2023] Open
Abstract
The modification of histones by acetyl groups has a key role in the regulation of chromatin structure and transcription. The Arabidopsis thaliana histone acetyltransferase GCN5 regulates histone modifications as part of the Spt-Ada-Gcn5 Acetyltransferase (SAGA) transcriptional coactivator complex. GCN5 was previously shown to acetylate lysine 14 of histone 3 (H3K14ac) in the promoter regions of its target genes even though GCN5 binding did not systematically correlate with gene activation. Here, we explored the mechanism through which GCN5 controls transcription. First, we fine-mapped its GCN5 binding sites genome-wide and then used several global methodologies (ATAC-seq, ChIP-seq and RNA-seq) to assess the effect of GCN5 loss-of-function on the expression and epigenetic regulation of its target genes. These analyses provided evidence that GCN5 has a dual role in the regulation of H3K14ac levels in their 5′ and 3′ ends of its target genes. While the gcn5 mutation led to a genome-wide decrease of H3K14ac in the 5′ end of the GCN5 down-regulated targets, it also led to an increase of H3K14ac in the 3′ ends of GCN5 up-regulated targets. Furthermore, genome-wide changes in H3K14ac levels in the gcn5 mutant correlated with changes in H3K9ac at both 5′ and 3′ ends, providing evidence for a molecular link between the depositions of these two histone modifications. To understand the biological relevance of these regulations, we showed that GCN5 participates in the responses to biotic stress by repressing salicylic acid (SA) accumulation and SA-mediated immunity, highlighting the role of this protein in the regulation of the crosstalk between diverse developmental and stress-responsive physiological programs. Hence, our results demonstrate that GCN5, through the modulation of H3K14ac levels on its targets, controls the balance between biotic and abiotic stress responses and is a master regulator of plant-environmental interactions.
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Affiliation(s)
- Soonkap Kim
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France.,Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Sophie J M Piquerez
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France.,School of Life Sciences and Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, UK
| | - Juan S Ramirez-Prado
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Emmanouil Mastorakis
- School of Life Sciences and Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, UK
| | - Alaguraj Veluchamy
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - David Latrasse
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Deborah Manza-Mianza
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Rim Brik-Chaouche
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Ying Huang
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Natalia Y Rodriguez-Granados
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Lorenzo Concia
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Thomas Blein
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Sylvie Citerne
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles 78000, France
| | - Abdelhafid Bendahmane
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Catherine Bergounioux
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Martin Crespi
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Magdy M Mahfouz
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Cécile Raynaud
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Heribert Hirt
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France.,Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Vardis Ntoukakis
- School of Life Sciences and Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, UK
| | - Moussa Benhamed
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France.,Institut Universitaire de France (IUF)
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50
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Huang Y, Rodriguez-Granados NY, Latrasse D, Raynaud C, Benhamed M, Ramirez-Prado JS. The matrix revolutions: towards the decoding of the plant chromatin three-dimensional reality. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5129-5147. [PMID: 32639553 DOI: 10.1093/jxb/eraa322] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 07/05/2020] [Indexed: 06/11/2023]
Abstract
In recent years, we have witnessed a significant increase in studies addressing the three-dimensional (3D) chromatin organization of the plant nucleus. Important advances in chromatin conformation capture (3C)-derived and related techniques have allowed the exploration of the nuclear topology of plants with large and complex genomes, including various crops. In addition, the increase in their resolution has permitted the depiction of chromatin compartmentalization and interactions at the gene scale. These studies have revealed the highly complex mechanisms governing plant nuclear architecture and the remarkable knowledge gaps in this field. Here we discuss the state-of-the-art in plant chromosome architecture, including our knowledge of the hierarchical organization of the genome in 3D space and regarding other nuclear components. Furthermore, we highlight the existence in plants of topologically associated domain (TAD)-like structures that display striking differences from their mammalian counterparts, proposing the concept of ICONS-intergenic condensed spacers. Similarly, we explore recent advances in the study of chromatin loops and R-loops, and their implication in the regulation of gene activity. Finally, we address the impact that polyploidization has had on the chromatin topology of modern crops, and how this is related to phenomena such as subgenome dominance and biased gene retention in these organisms.
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Affiliation(s)
- Ying Huang
- Institute of Plant Sciences Paris of Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Orsay, France
| | - Natalia Yaneth Rodriguez-Granados
- Institute of Plant Sciences Paris of Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Orsay, France
| | - David Latrasse
- Institute of Plant Sciences Paris of Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Orsay, France
| | - Cecile Raynaud
- Institute of Plant Sciences Paris of Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Orsay, France
| | - Moussa Benhamed
- Institute of Plant Sciences Paris of Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Orsay, France
- Institut Universitaire de France (IUF), France
| | - Juan Sebastian Ramirez-Prado
- Institute of Plant Sciences Paris of Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Orsay, France
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