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Wang W, Sung S. Chromatin sensing: integration of environmental signals to reprogram plant development through chromatin regulators. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4332-4345. [PMID: 38436409 PMCID: PMC11263488 DOI: 10.1093/jxb/erae086] [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: 12/19/2023] [Accepted: 02/29/2024] [Indexed: 03/05/2024]
Abstract
Chromatin regulation in eukaryotes plays pivotal roles in controlling the developmental regulatory gene network. This review explores the intricate interplay between chromatin regulators and environmental signals, elucidating their roles in shaping plant development. As sessile organisms, plants have evolved sophisticated mechanisms to perceive and respond to environmental cues, orchestrating developmental programs that ensure adaptability and survival. A central aspect of this dynamic response lies in the modulation of versatile gene regulatory networks, mediated in part by various chromatin regulators. Here, we summarized current understanding of the molecular mechanisms through which chromatin regulators integrate environmental signals, influencing key aspects of plant development.
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Affiliation(s)
- Wenli Wang
- Department of Molecular Biosciences, The University of Texas at Austin, TX 78712, USA
| | - Sibum Sung
- Department of Molecular Biosciences, The University of Texas at Austin, TX 78712, USA
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Xin X, Li P, Zhao X, Yu Y, Wang W, Jin G, Wang J, Sun L, Zhang D, Zhang F, Yu S, Su T. Temperature-dependent jumonji demethylase modulates flowering time by targeting H3K36me2/3 in Brassica rapa. Nat Commun 2024; 15:5470. [PMID: 38937441 PMCID: PMC11211497 DOI: 10.1038/s41467-024-49721-z] [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: 01/02/2023] [Accepted: 06/12/2024] [Indexed: 06/29/2024] Open
Abstract
Global warming has a severe impact on the flowering time and yield of crops. Histone modifications have been well-documented for their roles in enabling plant plasticity in ambient temperature. However, the factor modulating histone modifications and their involvement in habitat adaptation have remained elusive. In this study, through genome-wide pattern analysis and quantitative-trait-locus (QTL) mapping, we reveal that BrJMJ18 is a candidate gene for a QTL regulating thermotolerance in thermotolerant B. rapa subsp. chinensis var. parachinensis (or Caixin, abbreviated to Par). BrJMJ18 encodes an H3K36me2/3 Jumonji demethylase that remodels H3K36 methylation across the genome. We demonstrate that the BrJMJ18 allele from Par (BrJMJ18Par) influences flowering time and plant growth in a temperature-dependent manner via characterizing overexpression and CRISPR/Cas9 mutant plants. We further show that overexpression of BrJMJ18Par can modulate the expression of BrFLC3, one of the five BrFLC orthologs. Furthermore, ChIP-seq and transcriptome data reveal that BrJMJ18Par can regulate chlorophyll biosynthesis under high temperatures. We also demonstrate that three amino acid mutations may account for function differences in BrJMJ18 between subspecies. Based on these findings, we propose a working model in which an H3K36me2/3 demethylase, while not affecting agronomic traits under normal conditions, can enhance resilience under heat stress in Brassica rapa.
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Affiliation(s)
- Xiaoyun Xin
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, China
- Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing, China
| | - Peirong Li
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, China
- Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing, China
| | - Xiuyun Zhao
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, China
- Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing, China
| | - Yangjun Yu
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, China
- Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing, China
| | - Weihong Wang
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, China
- Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing, China
| | - Guihua Jin
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
| | - Jiao Wang
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
| | - Liling Sun
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
| | - Deshuang Zhang
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, China
- Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing, China
| | - Fenglan Zhang
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China.
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China.
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, China.
- Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing, China.
| | - Shuancang Yu
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China.
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China.
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, China.
- Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing, China.
| | - Tongbing Su
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China.
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China.
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, China.
- Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing, China.
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Poza-Viejo L, Payá-Milans M, Wilkinson MD, Piñeiro M, Jarillo JA, Crevillén P. Brassica rapa CURLY LEAF is a major H3K27 methyltransferase regulating flowering time. PLANTA 2024; 260:27. [PMID: 38865018 PMCID: PMC11169032 DOI: 10.1007/s00425-024-04454-7] [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: 01/15/2024] [Accepted: 06/02/2024] [Indexed: 06/13/2024]
Abstract
MAIN CONCLUSION In Brassica rapa, the epigenetic modifier BraA.CLF orchestrates flowering by modulating H3K27me3 levels at the floral integrator genes FT, SOC1, and SEP3, thereby influencing their expression. CURLY LEAF (CLF) is the catalytic subunit of the plant Polycomb Repressive Complex 2 that mediates the trimethylation of histone H3 lysine 27 (H3K27me3), an epigenetic modification that leads to gene silencing. While the function of CURLY LEAF (CLF) has been extensively studied in Arabidopsis thaliana, its role in Brassica crops is barely known. In this study, we focused on the Brassica rapa homolog of CLF and found that the loss-of-function mutant braA.clf-1 exhibits an accelerated flowering together with pleiotropic phenotypic alterations compared to wild-type plants. In addition, we carried out transcriptomic and H3K27me3 genome-wide analyses to identify the genes regulated by BraA.CLF. Interestingly, we observed that several floral regulatory genes, including the B. rapa homologs of FT, SOC1 and SEP3, show reduced H3K27me3 levels and increased transcript levels compared to wild-type plants, suggesting that they are direct targets of BraA.CLF and key players in regulating flowering time in this crop. In addition, the results obtained will enhance our understanding of the epigenetic mechanisms regulating key developmental traits and will aid to increase crop yield by engineering new Brassica varieties with different flowering time requirements.
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Affiliation(s)
- Laura Poza-Viejo
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Pozuelo de Alarcón, Madrid, Spain
| | - Miriam Payá-Milans
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Pozuelo de Alarcón, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocío, Seville, Spain
| | - Mark D Wilkinson
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Pozuelo de Alarcón, Madrid, Spain
| | - Manuel Piñeiro
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Pozuelo de Alarcón, Madrid, Spain
| | - José A Jarillo
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Pozuelo de Alarcón, Madrid, Spain
| | - Pedro Crevillén
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Pozuelo de Alarcón, Madrid, Spain.
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Akter A, Kakizaki T, Itabashi E, Kunita K, Shimizu M, Akter MA, Mehraj H, Okazaki K, Dennis ES, Fujimoto R. Characterization of FLOWERING LOCUS C 5 in Brassica rapa L. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:58. [PMID: 37484542 PMCID: PMC10356691 DOI: 10.1007/s11032-023-01405-0] [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: 01/18/2023] [Accepted: 07/08/2023] [Indexed: 07/25/2023]
Abstract
Brassica rapa L., which includes Chinese cabbage, turnip, and pak choi, has more complex flowering time regulation than does Arabidopsis thaliana due to the presence of multiple paralogous flowering time genes. FLOWERING LOCUS C (FLC) is one of the key genes regulating the flowering time, and B. rapa has four FLC paralogs. BrFLC5 on the reference genome is deemed a pseudogene because of a mutation (from G to A) in the splice site of the third intron, but there are some accessions with a G nucleotide in the splice site. In this study, we genotyped 310 B. rapa accessions and found that 19 had homozygous and 81 had heterozygous putative functional BrFLC5 alleles. Accessions of turnip showed the highest proportion with a functional BrFLC5 allele. BrFLC5 acts as a floral repressor when overexpressed in A. thaliana. The BrFLC5 expression level varied in pre-vernalized plants, and this transcriptional variation was not associated with the G/A polymorphism in the third intron. Three accessions having a higher BrFLC5 expression in pre-vernalized plants had a 584-bp insertion in the promoter region. Many regions homologous to this 584-bp sequence are present in the B. rapa genome, and this 584-bp inserted region has tandem duplications of an AT-rich sequence in its central region. The possibility that a high expression of a functional BrFLC5 could contribute to producing premature bolting-resistant lines in B. rapa vegetables is discussed. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01405-0.
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Affiliation(s)
- Ayasha Akter
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe, 657-8501 Japan
- Department of Horticulture, Bangladesh Agricultural University, Mymensingh, 2202 Bangladesh
| | - Tomohiro Kakizaki
- Institute of Vegetable and Floriculture Science, NARO, Kusawa, Ano, Tsu, Mie 514-2392 Japan
| | - Etsuko Itabashi
- Institute of Vegetable and Floriculture Science, NARO, Kusawa, Ano, Tsu, Mie 514-2392 Japan
| | - Kohei Kunita
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe, 657-8501 Japan
| | - Motoki Shimizu
- Iwate Biotechnology Research Center, Narita, Kitakami, Iwate, 024-0003 Japan
| | - Mst. Arjina Akter
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe, 657-8501 Japan
- Department of Plant Pathology, Bangladesh Agricultural University, Mymensingh, 2202 Bangladesh
| | - Hasan Mehraj
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe, 657-8501 Japan
| | - Keiichi Okazaki
- Graduate School of Science and Technology, Niigata University, Niigata, 950-2181 Japan
| | - Elizabeth S. Dennis
- CSIRO Agriculture and Food, ACT, Canberra, 2601 Australia
- Faculty of Science, School of Life Science, University of Technology Sydney, Broadway, Sydney, NSW 2007 Australia
| | - Ryo Fujimoto
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe, 657-8501 Japan
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Wu J, Liang J, Lin R, Cai X, Zhang L, Guo X, Wang T, Chen H, Wang X. Investigation of Brassica and its relative genomes in the post-genomics era. HORTICULTURE RESEARCH 2022; 9:uhac182. [PMID: 36338847 PMCID: PMC9627752 DOI: 10.1093/hr/uhac182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 08/07/2022] [Indexed: 06/16/2023]
Abstract
The Brassicaceae family includes many economically important crop species, as well as cosmopolitan agricultural weed species. In addition, Arabidopsis thaliana, a member of this family, is used as a molecular model plant species. The genus Brassica is mesopolyploid, and the genus comprises comparatively recently originated tetrapolyploid species. With these characteristics, Brassicas have achieved the commonly accepted status of model organisms for genomic studies. This paper reviews the rapid research progress in the Brassicaceae family from diverse omics studies, including genomics, transcriptomics, epigenomics, and three-dimensional (3D) genomics, with a focus on cultivated crops. The morphological plasticity of Brassicaceae crops is largely due to their highly variable genomes. The origin of several important Brassicaceae crops has been established. Genes or loci domesticated or contributing to important traits are summarized. Epigenetic alterations and 3D structures have been found to play roles in subgenome dominance, either in tetraploid Brassica species or their diploid ancestors. Based on this progress, we propose future directions and prospects for the genomic investigation of Brassicaceae crops.
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Affiliation(s)
| | | | | | - Xu Cai
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Lei Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Xinlei Guo
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Tianpeng Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Haixu Chen
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
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Transcriptional Association between mRNAs and Their Paired Natural Antisense Transcripts Following Fusarium oxysporum Inoculation in Brassica rapa L. HORTICULTURAE 2021. [DOI: 10.3390/horticulturae8010017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Long noncoding RNAs (lncRNAs) play important roles in abiotic and biotic stress responses; however, studies on the mechanism of regulation of lncRNA expression are limited in plants. The present study examined the relationship between lncRNA expression level and two active histone modifications (H3K4me3 and H3K36me3) in Brassica rapa. Both histone marks were enriched in the chromatin regions encoding lncRNAs, especially around the transcription start site. The transcription level of long intergenic noncoding RNAs was positively associated with the level of H3K4me3 and H3K36me3, while this association was not observed in natural antisense RNAs (NATs) and intronic noncoding RNAs. As coordinate expression of mRNAs and paired NATs under biotic stress treatment has been identified, the transcriptional relationship between mRNAs and their paired NATs following Fusarium oxysporum f. sp. conglutinans (Foc) inoculation was examined. A positive association of expression levels between mRNAs and their paired NATs following Foc inoculation was observed. This association held for several defense-response-related genes and their NAT pairs. These results suggest that coordinate expression of mRNAs and paired NATs plays a role in the defense response against Foc.
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The Dynamism of Transposon Methylation for Plant Development and Stress Adaptation. Int J Mol Sci 2021; 22:ijms222111387. [PMID: 34768817 PMCID: PMC8583499 DOI: 10.3390/ijms222111387] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/13/2021] [Accepted: 10/19/2021] [Indexed: 02/06/2023] Open
Abstract
Plant development processes are regulated by epigenetic alterations that shape nuclear structure, gene expression, and phenotypic plasticity; these alterations can provide the plant with protection from environmental stresses. During plant growth and development, these processes play a significant role in regulating gene expression to remodel chromatin structure. These epigenetic alterations are mainly regulated by transposable elements (TEs) whose abundance in plant genomes results in their interaction with genomes. Thus, TEs are the main source of epigenetic changes and form a substantial part of the plant genome. Furthermore, TEs can be activated under stress conditions, and activated elements cause mutagenic effects and substantial genetic variability. This introduces novel gene functions and structural variation in the insertion sites and primarily contributes to epigenetic modifications. Altogether, these modifications indirectly or directly provide the ability to withstand environmental stresses. In recent years, many studies have shown that TE methylation plays a major role in the evolution of the plant genome through epigenetic process that regulate gene imprinting, thereby upholding genome stability. The induced genetic rearrangements and insertions of mobile genetic elements in regions of active euchromatin contribute to genome alteration, leading to genomic stress. These TE-mediated epigenetic modifications lead to phenotypic diversity, genetic variation, and environmental stress tolerance. Thus, TE methylation is essential for plant evolution and stress adaptation, and TEs hold a relevant military position in the plant genome. High-throughput techniques have greatly advanced the understanding of TE-mediated gene expression and its associations with genome methylation and suggest that controlled mobilization of TEs could be used for crop breeding. However, development application in this area has been limited, and an integrated view of TE function and subsequent processes is lacking. In this review, we explore the enormous diversity and likely functions of the TE repertoire in adaptive evolution and discuss some recent examples of how TEs impact gene expression in plant development and stress adaptation.
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