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Lin M, Liu H, Liu B, Li X, Qian W, Zhou D, Jiang J, Zhang Y. Transcriptome-wide m 6A methylation profile reveals tissue specific regulatory networks in switchgrass (Panicum virgatum L.) under cadmium stress. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:134904. [PMID: 38996680 DOI: 10.1016/j.jhazmat.2024.134904] [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: 03/14/2024] [Revised: 05/20/2024] [Accepted: 06/12/2024] [Indexed: 07/14/2024]
Abstract
The heavy metal cadmium (Cd), known for its high toxicity, poses a grave threat to human health through the food chain. N6-methyladenosine (m6A), the most abundant internal modification, regulates plant adaptation to various adversities, yet the panorama of m6A modifications in switchgrass under cadmium stress remains elusive. This study examines the physiological responses of switchgrass roots and shoots exposed to 50 μM CdCl2, alongside an overview of transcriptome-wide m6A methylation patterns. After cadmium treatment, methylation modifications are primarily enriched near stop codons and the 3'UTR region, with a negative correlation between m6A modification and gene expression levels. In shoots, approximately 58 % of DEGs with m6A modifications show upregulation in expression and decrease in m6A peaks, including zinc transporter 4-like (ZIP4). In roots, about 43 % of DEGs with m6A modifications exhibit downregulation in expression and increase in m6A peaks, such as the ABC transporter family member (ABCG25). We further validate the m6A enrichment, gene expression and mRNA stability of ZIP4 in response to Cd treatment. The results suggest that the negative correlation of m6A enrichment and gene expression is due to altered mRNA stability. Our study establishes an m6A regulatory network governing cadmium transport in switchgrass roots and shoots, offering new avenues for candidate gene manipulation in phytoremediation applications of heavy metal pollution.
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Affiliation(s)
- Mengzhuo Lin
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China
| | - Huayue Liu
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China
| | - Bowen Liu
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xue Li
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China
| | - Wenwu Qian
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China
| | - Die Zhou
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China
| | - Jishan Jiang
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Yunwei Zhang
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China.
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2
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Tang J, Lei D, Yang J, Chen S, Wang X, Huang X, Zhang S, Cai Z, Zhu S, Wan J, Jia G. OsALKBH9-mediated m 6A demethylation regulates tapetal PCD and pollen exine accumulation in rice. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:2410-2423. [PMID: 38634166 PMCID: PMC11332222 DOI: 10.1111/pbi.14354] [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: 10/06/2023] [Revised: 02/24/2024] [Accepted: 03/30/2024] [Indexed: 04/19/2024]
Abstract
The N6-methyladenosine (m6A) mRNA modification is crucial for plant development and stress responses. In rice, the male sterility resulting from the deficiency of OsFIP37, a core component of m6A methyltransferase complex, emphasizes the significant role of m6A in male fertility. m6A is reversible and can be removed by m6A demethylases. However, whether mRNA m6A demethylase regulates male fertility in rice has remained unknown. Here, we identify the mRNA m6A demethylase OsALKBH9 and demonstrate its involvement in male fertility regulation. Knockout of OsALKBH9 causes male sterility, dependent on its m6A demethylation activity. Cytological analysis reveals defective tapetal programmed cell death (PCD) and excessive accumulation of microspores exine in Osalkbh9-1. Transcriptome analysis of anthers shows up-regulation of genes involved in tapetum development, sporopollenin synthesis, and transport pathways in Osalkbh9-1. Additionally, we demonstrate that OsALKBH9 demethylates the m6A modification in TDR and GAMYB transcripts, which affects the stability of these mRNAs and ultimately leads to excessive accumulation of pollen exine. Our findings highlight the precise control of mRNA m6A modification and reveal the pivotal roles played by OsALKBH9-mediated m6A demethylation in tapetal PCD and pollen exine accumulation in rice.
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Affiliation(s)
- Jun Tang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular EngineeringPeking UniversityBeijingChina
- Institute of Animal SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Dekun Lei
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop Sciences, Chinese Academy of Agricultural SciencesBeijingChina
| | - Junbo Yang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular EngineeringPeking UniversityBeijingChina
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenGuangdongChina
| | - Shuyan Chen
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular EngineeringPeking UniversityBeijingChina
| | - Xueping Wang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular EngineeringPeking UniversityBeijingChina
| | - Xiaoxin Huang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular EngineeringPeking UniversityBeijingChina
| | - Shasha Zhang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular EngineeringPeking UniversityBeijingChina
| | - Zhihe Cai
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular EngineeringPeking UniversityBeijingChina
| | - Shanshan Zhu
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop Sciences, Chinese Academy of Agricultural SciencesBeijingChina
| | - Jianmin Wan
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop Sciences, Chinese Academy of Agricultural SciencesBeijingChina
| | - Guifang Jia
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular EngineeringPeking UniversityBeijingChina
- Peking‐Tsinghua Center for Life Sciences, Peking UniversityBeijingChina
- Beijing Advanced Center of RNA BiologyPeking UniversityBeijingChina
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3
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Su D, Shu P, Hu N, Chen Y, Wu Y, Deng H, Du X, Zhang X, Wang R, Li H, Zeng Y, Li D, Xie Y, Li M, Hong Y, Liu K, Liu M. Dynamic m6A mRNA methylation reveals the involvement of AcALKBH10 in ripening-related quality regulation in kiwifruit. THE NEW PHYTOLOGIST 2024; 243:2265-2278. [PMID: 39056285 DOI: 10.1111/nph.20008] [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: 06/18/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024]
Abstract
Kiwifruit ripening is a complex and highly coordinated process that occurs in conjunction with the formation of fruit edible quality. The significance of epigenetic changes, particularly the impact of N6-methyladenosine (m6A) RNA modification on fruit ripening and quality formation, has been largely overlooked. We monitored m6A levels and gene expression changes in kiwifruit at four different stages using LC-MS/MS, MeRIP, RNA-seq, and validated the function of AcALKBH10 through heterologous transgenic expression in tomato. Notable m6A modifications occurred predominantly at the stop codons and the 3' UTRs and exhibited a gradual reduction in m6A levels during the fruit ripening process. Moreover, these m6A modifications in the aforementioned sites demonstrated a discernible inverse relationship with the levels of mRNA abundance throughout the ripening process, suggesting a repression effect of m6A modification in the modulation of kiwifruit ripening. We further demonstrated that AcALKBH10 rather than AcECT9 predominantly regulates m6A levels in ripening-related genes, thereby exerting the regulatory control over the ripening process and the accumulation of soluble sugars and organic acids, ultimately influencing fruit ripening and quality formation. In conclusion, our findings illuminate the epi-regulatory mechanism involving m6A in kiwifruit ripening, offering a fresh perspective for cultivating high-quality kiwifruit with enhanced nutritional attributes.
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Affiliation(s)
- Dan Su
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Peng Shu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
- Clinical Medical Research Center, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Nan Hu
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, 455000, Henan, China
| | - Yuan Chen
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Yi Wu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Heng Deng
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Xiaofei Du
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Xumeng Zhang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Ruochen Wang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Huajia Li
- Institute of Agro-Products Processing Science and Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Yunliu Zeng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dawei Li
- Wuhan Botanical Garden, Chinese Academy of Sciences, Jiufeng 1 Road, Wuhan, 430074, Hubei, China
| | - Yue Xie
- China-New Zealand the Belt and Road Joint Laboratory on Kiwifruit, Kiwifruit Breeding and Utilization Key Laboratory of Sichuan Province, Sichuan Academy of Natural Resource Sciences, Chengdu, 610041, China
| | - Mingzhang Li
- China-New Zealand the Belt and Road Joint Laboratory on Kiwifruit, Kiwifruit Breeding and Utilization Key Laboratory of Sichuan Province, Sichuan Academy of Natural Resource Sciences, Chengdu, 610041, China
| | - Yiguo Hong
- School of Science and the Environment, University of Worcester, Worcester, WR2 6AJ, UK
- State Key Laboratory of North China Crop Improvement and Regulation, College of Horticulture, Hebei Agricultural University, Baoding, 071000, China
| | - Kaidong Liu
- Life Science and Technology School, Lingnan Normal University, Zhanjiang, 524048, China
| | - Mingchun Liu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
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4
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Chen S, Han J, Wu S, Guo S, Tang Y, Zheng Y, Hu L, Zhang X, Zhang P, Zhang H, Ren G, Gao S. From non-coding RNAs to histone modification: The epigenetic mechanisms in tomato fruit ripening and quality regulation. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 215:109070. [PMID: 39191041 DOI: 10.1016/j.plaphy.2024.109070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 07/28/2024] [Accepted: 08/22/2024] [Indexed: 08/29/2024]
Abstract
Ripening is one of the most important stages of fruit development and determines the fruit quality. Various factors play a role in this process, with epigenetic mechanisms emerging as important players. Epigenetic regulation encompasses DNA methylation, histone modifications and variants, chromatin remodeling, RNA modifications, and non-coding RNAs. Over the past decade, studies using tomato as a model have made considerable progress in understanding the impact of epigenetic regulation on fleshy fruit ripening and quality. In this paper, we provide an overview of recent advancements in the epigenetic regulation of tomato fruit ripening and quality regulation, focusing on three main mechanisms: DNA/RNA modifications, non-coding RNAs, and histone modifications. Furthermore, we highlight the unresolved issues and challenges within this research field, offering perspectives for future investigations to drive agricultural innovation.
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Affiliation(s)
- Shengbo Chen
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou, 311300, China
| | - Jiazhen Han
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou, 311300, China
| | - Shu Wu
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou, 311300, China
| | - Shangjing Guo
- Qingdao Agricultural University, Qingdao, 266109, China
| | - Yufei Tang
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou, 311300, China
| | - Yujing Zheng
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou, 311300, China
| | - Lei Hu
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou, 311300, China
| | - Xingxing Zhang
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou, 311300, China
| | - Peng Zhang
- Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | | | - Guodong Ren
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China.
| | - Shuai Gao
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou, 311300, China.
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5
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Zhang J, Wu L, Mu L, Wang Y, Zhao M, Wang H, Li X, Zhao L, Lin C, Zhang H, Gu L. Evolution and post-transcriptional regulation insights of m 6A writers, erasers, and readers in plant epitranscriptome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39167634 DOI: 10.1111/tpj.16996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 06/30/2024] [Accepted: 08/09/2024] [Indexed: 08/23/2024]
Abstract
As a dynamic and reversible post-transcriptional marker, N6-methyladenosine (m6A) plays an important role in the regulation of biological functions, which are mediated by m6A pathway components including writers (MT-A70, FIP37, VIR and HAKAI family), erasers (ALKBH family) and readers (YTH family). There is an urgent need for a comprehensive analysis of m6A pathway components across species at evolutionary levels. In this study, we identified 4062 m6A pathway components from 154 plant species including green algae, utilizing large-scale phylogenetic to explore their origin and evolution. We discovered that the copy number of writers was conserved among different plant lineages, with notable expansions in the ALKBH and YTH families. Synteny network analysis revealed conserved genomic contexts and lineage-specific transpositions. Furthermore, we used Direct RNA Sequencing (DRS) to reveal the Poly(A) length (PAL) and m6A ratio profiles in six angiosperms species, with a particular focus on the m6A pathway components. The ECT1/2-Poeaece4 sub-branches (YTH family) with unique genomic contexts exhibited significantly higher expression level than genes of other ECT1/2 poeaece sub-branches (ECT1/2-Poeaece1-3), accompanied by lower m6A modification and PAL. Besides, conserved m6A sites distributed in CDS and 3'UTR were detected in the ECT1/2-Poaceae4, and the dual-luciferase assay further demonstrated that these conserved m6A sites in the 3'UTR negatively regulated the expression of Firefly luciferase (LUC) gene. Finally, we developed transcription factor regulatory networks for m6A pathway components, using yeast one-hybrid assay demonstrated that PheBPC1 could interact with the PheECT1/2-5 promoter. Overall, this study presents a comprehensive evolutionary and functional analysis of m6A pathway components and their modifications in plants, providing a valuable resource for future functional analysis in this field.
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Affiliation(s)
- Jun Zhang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lin Wu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lele Mu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yuhua Wang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Mengna Zhao
- Basic Forestry and Proteomics Research Center, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Huiyuan Wang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiangrong Li
- Basic Forestry and Proteomics Research Center, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liangzhen Zhao
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chentao Lin
- Basic Forestry and Proteomics Research Center, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hangxiao Zhang
- Basic Forestry and Proteomics Research Center, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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6
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Santo Domingo M, Orduña L, Navarro D, Mayobre C, Santiago A, Valverde L, Alexiou KG, Matus JT, Pujol M, Garcia-Mas J. The ethylene-responsive transcription factor ERF024 is a novel regulator of climacteric fruit ripening in melon. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:1844-1858. [PMID: 38900073 DOI: 10.1111/tpj.16889] [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: 02/22/2024] [Revised: 05/21/2024] [Accepted: 06/06/2024] [Indexed: 06/21/2024]
Abstract
Fruit ripening is an essential developmental stage in Angiosperms triggered by hormonal signals such as ethylene, a major player in climacteric ripening. Melon is a unique crop showing both climacteric and non-climacteric cultivars, offering an ideal model for dissecting the genetic mechanisms underpinning this process. The major quantitative trait locus ETHQV8.1 was previously identified as a key regulator of melon fruit ripening. Here, we narrowed down ETHQV8.1 to a precise genomic region containing a single gene, the transcription factor CmERF024. Functional validation using CRISPR/Cas9 knock-out plants unequivocally identified CmERF024 as the causal gene governing ETHQV8.1. The erf024 mutants exhibited suppression of ethylene production, leading to a significant delay and attenuation of fruit ripening. Integrative multi-omic analyses encompassing RNA-seq, DAP-seq, and DNase-seq revealed the association of CmERF024 with chromatin accessibility and gene expression dynamics throughout fruit ripening. Our data suggest CmERF024 as a novel regulator of climacteric fruit ripening in melon.
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Affiliation(s)
- Miguel Santo Domingo
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Bellaterra, Barcelona, 08193, Spain
| | - Luis Orduña
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
| | - David Navarro
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
| | - Carlos Mayobre
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Bellaterra, Barcelona, 08193, Spain
| | - Antonio Santiago
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
| | - Laura Valverde
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Bellaterra, Barcelona, 08193, Spain
| | - Konstantinos G Alexiou
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Bellaterra, Barcelona, 08193, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Edifici CRAG, Campus UAB, Bellaterra, Barcelona, 08193, Spain
| | - José Tomás Matus
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
| | - Marta Pujol
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Bellaterra, Barcelona, 08193, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Edifici CRAG, Campus UAB, Bellaterra, Barcelona, 08193, Spain
| | - Jordi Garcia-Mas
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Bellaterra, Barcelona, 08193, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Edifici CRAG, Campus UAB, Bellaterra, Barcelona, 08193, Spain
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7
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Li Z, Zeng J, Zhou Y, Ding X, Jiang G, Wu K, Jiang Y, Duan X. Histone H3K27 demethylase SlJMJ3 modulates fruit ripening in tomato. PLANT PHYSIOLOGY 2024; 195:2727-2742. [PMID: 38669310 DOI: 10.1093/plphys/kiae233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 02/12/2024] [Accepted: 03/14/2024] [Indexed: 04/28/2024]
Abstract
The histone lysine (K) demethylase 4 (KDM4/JHDM3) subfamily of jumonji domain-containing demethylases (JMJs) has been implicated in various aspects of plant development. However, their involvement in regulating the ripening of fleshy fruits remains unclear. In this study, we identified SlJMJ3, a member of the KDM4/JHDM3 family, as an H3K27me3 demethylase in tomato (Solanum lycopersicum) that plays an important role in fruit ripening regulation. Overexpression of SlJMJ3 leads to accelerated fruit ripening, whereas loss of function of SlJMJ3 delays this process. Furthermore, we determined that SlJMJ3 exerts its regulatory function by modulating the expression of multiple ripening-related genes involved in ethylene biosynthesis and response, carotenoid metabolism, cell wall modification, transcriptional control, and DNA methylation modification. SlJMJ3 binds directly to the promoters of ripening-related genes harboring the CTCTGYTY motif and activates their expression. Additionally, SlJMJ3 reduces the levels of H3K27me3 at its target genes, thereby upregulating their expression. In summary, our findings highlight the role of SlJMJ3 in the regulation of fruit ripening in tomato. By removing the methyl group from trimethylated histone H3 lysine 27 at ripening-related genes, SlJMJ3 acts as an epigenetic regulator that orchestrates the complex molecular processes underlying fruit ripening.
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Affiliation(s)
- Zhiwei Li
- State Key Laboratory of Plant Diversity and Specialty Crops and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Zeng
- State Key Laboratory of Plant Diversity and Specialty Crops and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yijie Zhou
- State Key Laboratory of Plant Diversity and Specialty Crops and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Guangdong AIB Polytechnic, Guangzhou 510507, China
| | - Xiaochun Ding
- State Key Laboratory of Plant Diversity and Specialty Crops and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
| | - Guoxiang Jiang
- State Key Laboratory of Plant Diversity and Specialty Crops and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Keqiang Wu
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
| | - Yueming Jiang
- State Key Laboratory of Plant Diversity and Specialty Crops and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
| | - Xuewu Duan
- State Key Laboratory of Plant Diversity and Specialty Crops and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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8
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Pan Y, Jia Y, Liu W, Zhao Q, Pan W, Jia Y, Lv S, Liu X, Nie X. Transcriptome-wide m6A methylation profile reveals its potential role underlying drought response in wheat (Triticum aestivum L.). PLANTA 2024; 260:65. [PMID: 39073585 DOI: 10.1007/s00425-024-04491-2] [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: 01/26/2024] [Accepted: 07/18/2024] [Indexed: 07/30/2024]
Abstract
MAIN CONCLUSION This study revealed the transcriptome-wide m6A methylation profile under drought stress and found that TaETC9 might regulate drought tolerance through mediating RNA methylation in wheat. Drought is one of the most destructive environmental constraints limiting crop growth and development. N6-methyladenosine (m6A) is a prevalent and important post-transcriptional modification in various eukaryotic RNA molecules, playing the crucial role in regulating drought response in plants. However, the significance of m6A in wheat (Triticum aestivum L.), particularly its involvment in drought response, remains underexplored. In this study, we investigated the transcriptome-wide m6A profile under drought stress using parallel m6A immunoprecipitation sequencing (MeRIP-seq). Totally, 4221 m6A peaks in 3733 m6A-modified genes were obtained, of which 373 methylated peaks exhibited differential expression between the control (CK) and drought-stressed treatments. These m6A loci were significantly enriched in proximity to stop codons and within the 3'-untranslated region. Integration of MeRIP-seq and RNA-seq revealed a positive correlation between m6A methylation and mRNA abundance and the genes displaying both differential methylation and expression were obtained. Finally, qRT-PCR analyses were further performed and the results found that the m6A-binding protein (TaETC9) showed significant up-regulation, while the m6A demethylase (TaALKBH10B) was significantly down-regulated under drought stress, contributing to increased m6A levels. Furthermore, the loss-of-function mutant of TaECT9 displayed significantly higher drought sensitivity compared to the wild type, highlighting its role in regulating drought tolerance. This study reported the first wheat m6A profile associated with drought stress, laying the groundwork for unraveling the potential role of RNA methylation in drought responses and enhancing stress tolerance in wheat through epigenetic approaches.
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Affiliation(s)
- Yan Pan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Northwest, A&F University, Yangling, 712100, Shaanxi, China
| | - Yanzhe Jia
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Northwest, A&F University, Yangling, 712100, Shaanxi, China
| | - Wenxin Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Northwest, A&F University, Yangling, 712100, Shaanxi, China
| | - Qinlong Zhao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Northwest, A&F University, Yangling, 712100, Shaanxi, China
| | - Wenqiu Pan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Northwest, A&F University, Yangling, 712100, Shaanxi, China
| | - Yongpeng Jia
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, Nanyang Institute of Technology, Nanyang, 743004, Henan, China
| | - Shuzuo Lv
- Luoyang Academy of Agricultural and Forestry Sciences, 471027, Luoyang, Henan, China
| | - Xiaoqin Liu
- Peking University Institute of Advanced Agricultural Science, 261325, Weifang, Shandong, China.
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Northwest, A&F University, Yangling, 712100, Shaanxi, China.
- State Key Laboratory of Crop Stress Biology for Arid Areas, Pioneering Innovation Center for Wheat Stress Tolerance Improvement, Yangling, 712100, Shaanxi, China.
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9
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Xue F, Zhang J, Wu D, Sun S, Fu M, Wang J, Searle I, Gao H, Liang W. m 6A demethylase OsALKBH5 is required for double-strand break formation and repair by affecting mRNA stability in rice meiosis. THE NEW PHYTOLOGIST 2024. [PMID: 39044689 DOI: 10.1111/nph.19976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 06/13/2024] [Indexed: 07/25/2024]
Abstract
N6-methyladenosine (m6A) RNA modification is the most prevalent messenger RNA (mRNA) modification in eukaryotes and plays critical roles in the regulation of gene expression. m6A is a reversible RNA modification that is deposited by methyltransferases (writers) and removed by demethylases (erasers). The function of m6A erasers in plants is highly diversified and their roles in cereal crops, especially in reproductive development essential for crop yield, are largely unknown. Here, we demonstrate that rice OsALKBH5 acts as an m6A demethylase required for the normal progression of male meiosis. OsALKBH5 is a nucleo-cytoplasmic protein, highly enriched in rice anthers during meiosis, that associates with P-bodies and exon junction complexes, suggesting that it is involved in regulating mRNA processing and abundance. Mutations of OsALKBH5 cause reduced double-strand break (DSB) formation, severe defects in DSB repair, and delayed meiotic progression, leading to complete male sterility. Transcriptome analysis and m6A profiling indicate that OsALKBH5-mediated m6A demethylation stabilizes the mRNA level of multiple meiotic genes directly or indirectly, including several genes that regulate DSB formation and repair. Our study reveals the indispensable role of m6A metabolism in post-transcriptional regulation of meiotic progression in rice.
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Affiliation(s)
- Feiyang Xue
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jie Zhang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Di Wu
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shiyu Sun
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ming Fu
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jie Wang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Iain Searle
- Department of Molecular and Biomedical Sciences, School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Hongbo Gao
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wanqi Liang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, 572024, China
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10
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Ambrosino L, Riccardi A, Welling MS, Lauritano C. Comparative Transcriptomics to Identify RNA Writers and Erasers in Microalgae. Int J Mol Sci 2024; 25:8005. [PMID: 39125576 PMCID: PMC11312118 DOI: 10.3390/ijms25158005] [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: 05/03/2024] [Revised: 07/16/2024] [Accepted: 07/17/2024] [Indexed: 08/12/2024] Open
Abstract
Epitranscriptomics is considered as a new regulatory step in eukaryotes for developmental processes and stress responses. The aim of this study was, for the first time, to identify RNA methyltransferase (writers) and demethylase (erasers) in four investigated species, i.e., the dinoflagellates Alexandrium tamutum and Amphidinium carterae, the diatom Cylindrotheca closterium, and the green alga Tetraselmis suecica. As query sequences for the enzymatic classes of interest, we selected those ones that were previously detected in marine plants, evaluating their expression upon nutrient starvation stress exposure. The hypothesis was that upon stress exposure, the activation/deactivation of specific writers and erasers may occur. In microalgae, we found almost all plant writers and erasers (ALKBH9B, ALKBH10B, MTB, and FIP37), except for three writers (MTA, VIRILIZER, and HAKAI). A sequence similarity search by scanning the corresponding genomes confirmed their presence. Thus, we concluded that the three writer sequences were lacking from the studied transcriptomes probably because they were not expressed in those experimental conditions, rather than a real lack of these genes from their genomes. This study showed that some of them were expressed only in specific culturing conditions. We also investigated their expression in other culturing conditions (i.e., nitrogen depletion, phosphate depletion, and Zinc addition at two different concentrations) in A. carterae, giving new insights into their possible roles in regulating gene expression upon stress.
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Affiliation(s)
- Luca Ambrosino
- Research Infrastructure for Marine Biological Resources Department, Stazione Zoologica Anton Dohrn, Via Acton 55, 80133 Napoli, Italy;
| | - Alessia Riccardi
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy;
| | - Melina S. Welling
- Marine Biology Research Group, Ghent University, Krijgslaan 281, B-9000 Gent, Belgium;
| | - Chiara Lauritano
- Ecosustainable Marine Biotechnology Department, Stazione Zoologica Anton Dohrn, Via Acton 55, 80133 Napoli, Italy
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11
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Yao S, Song Y, Cheng X, Wang D, Li Q, Zhang J, Chen Q, Yu Q, Ji K. Transcriptome-Wide Identification of m 6A Writers, Erasers and Readers and Their Expression Profiles under Various Biotic and Abiotic Stresses in Pinus massoniana Lamb. Int J Mol Sci 2024; 25:7987. [PMID: 39063230 PMCID: PMC11277107 DOI: 10.3390/ijms25147987] [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: 06/29/2024] [Revised: 07/17/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024] Open
Abstract
N6-methyladenosine (m6A) RNA modification is the most prevalent form of RNA methylation and plays a crucial role in plant development. However, our understanding of m6A modification in Masson pine (Pinus massoniana Lamb.) remains limited. In this study, a complete analysis of m6A writers, erasers, and readers in Masson pine was performed, and 22 m6A regulatory genes were identified in total, including 7 m6A writers, 7 m6A erases, and 8 readers. Phylogenetic analysis revealed that all m6A regulators involved in Masson pine could be classified into three distinct groups based on their domains and motifs. The tissue expression analysis revealed that the m6A regulatory gene may exert a significant influence on the development of reproductive organs and leaves in Masson pine. Moreover, the results from stress and hormone expression analysis indicated that the m6A regulatory gene in Masson pine might be involved in drought stress response, ABA-signaling-pathway activation, as well as resistance to Monochamus alternatus. This study provided valuable and anticipated insights into the regulatory genes of m6A modification and their potential epigenetic regulatory mechanisms in Masson pine.
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Affiliation(s)
- Sheng Yao
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; (S.Y.); (Y.S.); (X.C.); (D.W.); (Q.L.); (J.Z.); (Q.C.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland Administration, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Yidan Song
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; (S.Y.); (Y.S.); (X.C.); (D.W.); (Q.L.); (J.Z.); (Q.C.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland Administration, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Xiang Cheng
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; (S.Y.); (Y.S.); (X.C.); (D.W.); (Q.L.); (J.Z.); (Q.C.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland Administration, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Dengbao Wang
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; (S.Y.); (Y.S.); (X.C.); (D.W.); (Q.L.); (J.Z.); (Q.C.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland Administration, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Qianzi Li
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; (S.Y.); (Y.S.); (X.C.); (D.W.); (Q.L.); (J.Z.); (Q.C.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland Administration, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Jingjing Zhang
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; (S.Y.); (Y.S.); (X.C.); (D.W.); (Q.L.); (J.Z.); (Q.C.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland Administration, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Qingyang Chen
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; (S.Y.); (Y.S.); (X.C.); (D.W.); (Q.L.); (J.Z.); (Q.C.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland Administration, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Qiong Yu
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; (S.Y.); (Y.S.); (X.C.); (D.W.); (Q.L.); (J.Z.); (Q.C.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland Administration, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
| | - Kongshu Ji
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; (S.Y.); (Y.S.); (X.C.); (D.W.); (Q.L.); (J.Z.); (Q.C.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland Administration, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
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12
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Xiang Y, Zhang D, Li L, Xue YX, Zhang CY, Meng QF, Wang J, Tan XL, Li YL. Detection, distribution, and functions of RNA N 6-methyladenosine (m 6A) in plant development and environmental signal responses. FRONTIERS IN PLANT SCIENCE 2024; 15:1429011. [PMID: 39081522 PMCID: PMC11286456 DOI: 10.3389/fpls.2024.1429011] [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: 05/07/2024] [Accepted: 06/24/2024] [Indexed: 08/02/2024]
Abstract
The epitranscriptomic mark N 6-methyladenosine (m6A) is the most common type of messenger RNA (mRNA) post-transcriptional modification in eukaryotes. With the discovery of the demethylase FTO (FAT MASS AND OBESITY-ASSOCIATED PROTEIN) in Homo Sapiens, this modification has been proven to be dynamically reversible. With technological advances, research on m6A modification in plants also rapidly developed. m6A modification is widely distributed in plants, which is usually enriched near the stop codons and 3'-UTRs, and has conserved modification sequences. The related proteins of m6A modification mainly consist of three components: methyltransferases (writers), demethylases (erasers), and reading proteins (readers). m6A modification mainly regulates the growth and development of plants by modulating the RNA metabolic processes and playing an important role in their responses to environmental signals. In this review, we briefly outline the development of m6A modification detection techniques; comparatively analyze the distribution characteristics of m6A in plants; summarize the methyltransferases, demethylases, and binding proteins related to m6A; elaborate on how m6A modification functions in plant growth, development, and response to environmental signals; and provide a summary and outlook on the research of m6A in plants.
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13
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Bian H, Song P, Gao Y, Deng Z, Huang C, Yu L, Wang H, Ye B, Cai Z, Pan Y, Wang F, Liu J, Gao X, Chen K, Jia G, Klee HJ, Zhang B. The m 6A reader SlYTH2 negatively regulates tomato fruit aroma by impeding the translation process. Proc Natl Acad Sci U S A 2024; 121:e2405100121. [PMID: 38950372 PMCID: PMC11253005 DOI: 10.1073/pnas.2405100121] [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: 03/20/2024] [Accepted: 05/29/2024] [Indexed: 07/03/2024] Open
Abstract
N6-methyladenosine (m6A) is a fundamentally important RNA modification for gene regulation, whose function is achieved through m6A readers. However, whether and how m6A readers play regulatory roles during fruit ripening and quality formation remains unclear. Here, we characterized SlYTH2 as a tomato m6A reader protein and profiled the binding sites of SlYTH2 at the transcriptome-wide level. SlYTH2 undergoes liquid-liquid phase separation and promotes RNA-protein condensate formation. The target mRNAs of SlYTH2, namely m6A-modified SlHPL and SlCCD1B associated with volatile synthesis, are enriched in SlYTH2-induced condensates. Through polysome profiling assays and proteomic analysis, we demonstrate that knockout of SlYTH2 expedites the translation process of SlHPL and SlCCD1B, resulting in augmented production of aroma-associated volatiles. This aroma enrichment significantly increased consumer preferences for CRISPR-edited fruit over wild type. These findings shed light on the underlying mechanisms of m6A in plant RNA metabolism and provided a promising strategy to generate fruits that are more attractive to consumers.
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Affiliation(s)
- Hanxiao Bian
- Zhejiang Key Laboratory of Horticultural Crop Quality Improvement, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou310058, China
| | - Peizhe Song
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing100871, China
| | - Ying Gao
- Zhejiang Key Laboratory of Horticultural Crop Quality Improvement, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou310058, China
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing401331, China
| | - Zhiping Deng
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou310021, China
| | - Chenyang Huang
- Key Laboratory of Macromolecular Synthesis and Functionalization of Ministry of Education, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou310058, China
| | - Lei Yu
- School of Public Health, Zhejiang University School of Medicine, Hangzhou310058, China
| | - Hanqing Wang
- Zhejiang Key Laboratory of Horticultural Crop Quality Improvement, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou310058, China
| | - Bingbing Ye
- Zhejiang Key Laboratory of Horticultural Crop Quality Improvement, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou310058, China
| | - Zhihe Cai
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing100871, China
| | - Yu Pan
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, Southwest University, Chongqing400715, China
| | - Fengqin Wang
- College of Animal Sciences, Key Laboratory of Animal Nutrition and Feed Sciences, Ministry of Agriculture, Zhejiang University, Hangzhou310058, China
| | - Jianzhao Liu
- Key Laboratory of Macromolecular Synthesis and Functionalization of Ministry of Education, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou310058, China
| | - Xiangwei Gao
- School of Public Health, Zhejiang University School of Medicine, Hangzhou310058, China
| | - Kunsong Chen
- Zhejiang Key Laboratory of Horticultural Crop Quality Improvement, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou310058, China
| | - Guifang Jia
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing100871, China
- Beijing Advanced Center of RNA Biology, Peking University, Beijing100871, China
| | - Harry J. Klee
- Zhejiang Key Laboratory of Horticultural Crop Quality Improvement, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou310058, China
| | - Bo Zhang
- Zhejiang Key Laboratory of Horticultural Crop Quality Improvement, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou310058, China
- Hainan Institute of Zhejiang University, Sanya, Hainan572000, China
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14
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Hu J, Xu T, Kang H. Crosstalk between RNA m 6A modification and epigenetic factors in plant gene regulation. PLANT COMMUNICATIONS 2024:101037. [PMID: 38971972 DOI: 10.1016/j.xplc.2024.101037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 06/04/2024] [Accepted: 07/03/2024] [Indexed: 07/08/2024]
Abstract
N6-methyladenosine (m6A) is the most abundant modification observed in eukaryotic mRNAs. Advances in transcriptome-wide m6A mapping and sequencing technologies have enabled the identification of several conserved motifs in plants, including the RRACH (R = A/G and H = A/C/U) and UGUAW (W = U or A) motifs. However, the mechanisms underlying deposition of m6A marks at specific positions in the conserved motifs of individual transcripts remain to be clarified. Evidence from plant and animal studies suggests that m6A writer or eraser components are recruited to specific genomic loci through interactions with particular transcription factors, 5-methylcytosine DNA methylation marks, and histone marks. In addition, recent studies in animal cells have shown that microRNAs play a role in depositing m6A marks at specific sites in transcripts through a base-pairing mechanism. m6A also affects the biogenesis and function of chromatin-associated regulatory RNAs and long noncoding RNAs. Although we have less of an understanding of the link between m6A modification and epigenetic factors in plants than in animals, recent progress in identifying the proteins that interact with m6A writer or eraser components has provided insights into the crosstalk between m6A modification and epigenetic factors, which plays a crucial role in transcript-specific methylation and regulation of m6A in plants.
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Affiliation(s)
- Jianzhong Hu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Tao Xu
- Jiangsu Key Laboratory of Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu Province 221116, China.
| | - Hunseung Kang
- Jiangsu Key Laboratory of Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu Province 221116, China; Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea.
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15
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Hasan M, Nishat ZS, Hasan MS, Hossain T, Ghosh A. Identification of m 6A RNA methylation genes in Oryza sativa and expression profiling in response to different developmental and environmental stimuli. Biochem Biophys Rep 2024; 38:101677. [PMID: 38511186 PMCID: PMC10950732 DOI: 10.1016/j.bbrep.2024.101677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/27/2024] [Accepted: 02/27/2024] [Indexed: 03/22/2024] Open
Abstract
Eukaryotic messenger RNAs (mRNAs) transcend their predominant function of protein encoding by incorporating auxiliary components that ultimately contribute to their processing, transportation, translation, and decay. In doing so, additional layers of modifications are incorporated in mRNAs at post-transcriptional stage. Among them, N6-methyladenosine (m6A) is the most frequently found mRNA modification that plays crucial roles in plant development and stress response. In the overall mechanism of m6A methylation, key proteins classified based on their functions such as writers, readers, and erasers dynamically add, read, and subtract methyl groups respectively to deliver relevant functions in response to external stimuli. In this study, we identified 30 m6A regulatory genes (9 writers, 5 erasers, and 16 readers) in rice that encode 53 proteins (13 writers, 7 erasers, and 33 readers) where segmental duplication was found in one writer and four reader gene pairs. Reproductive cells such as sperm, anther and panicle showed high levels of expression for most of the m6A regulatory genes. Notably, writers like OsMTA, OsMTD, and OsMTC showed varied responses in different stress and infection contexts, with initial upregulation in response to early exposure followed by downregulation later. OsALKBH9A, a noteworthy eraser, displayed varied expression in response to different stresses at different time intervals, but upregulation in certain infections. Reader genes like OsECT5, OsCPSF30-L3, and OsECT8 showed continuous upregulation in exertion of all kinds of stress relevant here. Conversely, other reader genes along with OsECT11 and OsCPSF30-L2 were observed to be consistently downregulated. The apparent correlation between the expression patterns of m6A regulatory genes and stress modulation pathways in this study underscores the need for additional research to unravel their intricate regulatory mechanisms that could ultimately contribute to the substantial development of enhanced stress tolerance in rice through mRNA modification.
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Affiliation(s)
| | | | - Md. Soyib Hasan
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Tanvir Hossain
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Ajit Ghosh
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
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16
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Liu H, Lin M, Zhou D, Liu B, Li X, Wang H, Bi X. Characterization of the m 6A gene family in switchgrass and functional analysis of PvALKBH10 during flowering. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 212:108781. [PMID: 38820914 DOI: 10.1016/j.plaphy.2024.108781] [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: 02/18/2024] [Revised: 04/30/2024] [Accepted: 05/27/2024] [Indexed: 06/02/2024]
Abstract
N6-methyladenosine (m6A), a nucleotide modification that is frequently seen in RNA, plays a crucial role in plant growth, development and stress resistance. However, the m6A regulatory machinery in switchgrass (Panicum virgatum L.), a model plant for cellulose-to-ethanol conversion, remains largely unknown. In this study, we identified 57 candidate genes involved in m6A-regulation in the switchgrass genome, and analyzed their chromosomal distribution, evolutionary relationships, and functions. Notably, we observed distinct gene expression patterns under salt and drought stress, with salt stress inducing writer and eraser genes, alongside drought stress predominantly affecting reader genes. Additionally, we knocked out PvALKBH10, an m6A demethylase gene, via CRISPR/Cas9 and found its potential function in controlling flowering time. This study provides insight into the genomic organization and evolutionary features of m6A-associated putative genes in switchgrass, and therefore serves as the basis for further functional studies.
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Affiliation(s)
- Huayue Liu
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Mengzhuo Lin
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Die Zhou
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Bowen Liu
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xue Li
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Hui Wang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xiaojing Bi
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China.
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17
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Zhou J, Zhou S, Chen B, Sangsoy K, Luengwilai K, Albornoz K, Beckles DM. Integrative analysis of the methylome and transcriptome of tomato fruit ( Solanum lycopersicum L.) induced by postharvest handling. HORTICULTURE RESEARCH 2024; 11:uhae095. [PMID: 38840937 PMCID: PMC11151332 DOI: 10.1093/hr/uhae095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 04/11/2024] [Indexed: 06/07/2024]
Abstract
Tomato fruit ripening is triggered by the demethylation of key genes, which alters their transcriptional levels thereby initiating and propagating a cascade of physiological events. What is unknown is how these processes are altered when fruit are ripened using postharvest practices to extend shelf-life, as these practices often reduce fruit quality. To address this, postharvest handling-induced changes in the fruit DNA methylome and transcriptome, and how they correlate with ripening speed, and ripening indicators such as ethylene, abscisic acid, and carotenoids, were assessed. This study comprehensively connected changes in physiological events with dynamic molecular changes. Ripening fruit that reached 'Turning' (T) after dark storage at 20°C, 12.5°C, or 5°C chilling (followed by 20°C rewarming) were compared to fresh-harvest fruit 'FHT'. Fruit stored at 12.5°C had the biggest epigenetic marks and alterations in gene expression, exceeding changes induced by postharvest chilling. Fruit physiological and chronological age were uncoupled at 12.5°C, as the time-to-ripening was the longest. Fruit ripening to Turning at 12.5°C was not climacteric; there was no respiratory or ethylene burst, rather, fruit were high in abscisic acid. Clear differentiation between postharvest-ripened and 'FHT' was evident in the methylome and transcriptome. Higher expression of photosynthetic genes and chlorophyll levels in 'FHT' fruit pointed to light as influencing the molecular changes in fruit ripening. Finally, correlative analyses of the -omics data putatively identified genes regulated by DNA methylation. Collectively, these data improve our interpretation of how tomato fruit ripening patterns are altered by postharvest practices, and long-term are expected to help improve fruit quality.
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Affiliation(s)
- Jiaqi Zhou
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, CA, USA
| | - Sitian Zhou
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, CA, USA
- Department of Biostatistics, School of Public Health, Columbia University, 722 West 168th Street, New York, NY 10032, USA
| | - Bixuan Chen
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, CA, USA
- Germains Seed Technology, 8333 Swanston Lane, Gilroy, CA 95020, USA
| | - Kamonwan Sangsoy
- Department of Horticulture, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand
| | - Kietsuda Luengwilai
- Department of Horticulture, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand
| | - Karin Albornoz
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, CA, USA
- Department of Food, Nutrition, and Packaging Sciences, Coastal Research and Education Center, Clemson University, 2700 Savannah Highway, Charleston, SC 29414 USA
| | - Diane M Beckles
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, CA, USA
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18
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Zhao Y, Han KJ, Tian YT, Jia KH, El-Kassaby YA, Wu Y, Liu J, Si HY, Sun YH, Li Y. N 6-methyladenosine mRNA methylation positively regulated the response of poplar to salt stress. PLANT, CELL & ENVIRONMENT 2024; 47:1797-1812. [PMID: 38314665 DOI: 10.1111/pce.14844] [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: 09/28/2023] [Revised: 01/18/2024] [Accepted: 01/23/2024] [Indexed: 02/06/2024]
Abstract
As the most abundant form of methylation modification in messenger RNA (mRNA), the distribution of N6-methyladenosine (m6A) has been preliminarily revealed in herbaceous plants under salt stress, but its function and mechanism in woody plants were still unknown. Here, we showed that global m6A levels increased during poplar response to salt stress. Methylated RNA immunoprecipitation sequencing (MeRIP-seq) revealed that m6A significantly enriched in the coding sequence region and 3'-untranslated regions in poplar, by recognising the conserved motifs, AGACU, GGACA and UGUAG. A large number of differential m6A transcripts have been identified, and some have been proved involving in salt response and plant growth and development. Further combined analysis of MeRIP-seq and RNA-seq revealed that the m6A hypermethylated and enrich in the CDS region preferred to positively regulate expression abundance. Writer inhibitor, 3-deazaneplanocin A treatment increased the sensitivity of poplar to salt stress by reducing mRNA stability to regulate the expression of salt-responsive transcripts PagMYB48, PagGT2, PagNAC2, PagGPX8 and PagARF2. Furthermore, we verified that the methyltransferase PagFIP37 plays a positively role in the response of poplar to salt stress, overexpressed lines have stronger salt tolerance, while RNAi lines were more sensitive to salt, which relied on regulating mRNA stability in an m6A manner of salt-responsive transcripts PagMYB48, PagGT2, PagNAC2, PagGPX8 and PagARF2. Collectively, these results revealed the regulatory role of m6A methylation in poplar response to salt stress, and revealed the importance and mechanism of m6A methylation in the response of woody plants to salt stress for the first time.
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Affiliation(s)
- Ye Zhao
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Kun-Jin Han
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yan-Ting Tian
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Kai-Hua Jia
- Key Laboratory of Crop Genetic Improvement & Ecology and Physiology, Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, Shandong Province, China
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences Faculty of Forestry, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Yue Wu
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Jie Liu
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Hua-Yu Si
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yu-Han Sun
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yun Li
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
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19
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Song P, Cai Z, Jia G. Principles, functions, and biological implications of m 6A in plants. RNA (NEW YORK, N.Y.) 2024; 30:491-499. [PMID: 38531642 PMCID: PMC11019739 DOI: 10.1261/rna.079951.124] [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: 01/14/2024] [Accepted: 02/09/2024] [Indexed: 03/28/2024]
Abstract
Over the past decade, N 6-methyladenosine (m6A) has emerged as a prevalent and dynamically regulated modification across the transcriptome; it has been reversibly installed, removed, and interpreted by specific binding proteins, and has played crucial roles in molecular and biological processes. Within this scope, we consolidate recent advancements of m6A research in plants regarding gene expression regulation, diverse physiologic and pathogenic processes, as well as crop trial implications, to guide discussions on challenges associated with and leveraging epitranscriptome editing for crop improvement.
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Affiliation(s)
- Peizhe Song
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Zhihe Cai
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Guifang Jia
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- PKU-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- Beijing Advanced Center of RNA Biology, Peking University, Beijing 100871, China
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20
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Yu H, Bi X, Li Z, Fu X, Li Y, Li Y, Yang Y, Liu D, Li G, Dong W, Hu F. Transcriptomic Analysis of Alternative Splicing Events during Different Fruit Ripening Stages of Coffea arabica L. Genes (Basel) 2024; 15:459. [PMID: 38674393 PMCID: PMC11050144 DOI: 10.3390/genes15040459] [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: 03/15/2024] [Revised: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 04/28/2024] Open
Abstract
To date, genomic and transcriptomic data on Coffea arabica L. in public databases are very limited, and there has been no comprehensive integrated investigation conducted on alternative splicing (AS). Previously, we have constructed and sequenced eighteen RNA-seq libraries of C. arabica at different ripening stages of fruit development. From this dataset, a total of 3824, 2445, 2564, 2990, and 3162 DSGs were identified in a comparison of different fruit ripening stages. The largest proportion of DSGs, approximately 65%, were of the skipped exon (SE) type. Biologically, 9 and 29 differentially expressed DSGs in the spliceosome pathway and carbon metabolism pathway, respectively, were identified. These DSGs exhibited significant variations, primarily in S1 vs. S2 and S5 vs. S6, and they involve many aspects of organ development, hormone transduction, and the synthesis of flavor components. Through the examination of research findings regarding the biological functions and biochemical pathways associated with DSGs and DEGs, it was observed that six DSGs significantly enriched in ABC transporters, namely, LOC113712394, LOC113726618, LOC113739972, LOC113725240, LOC113730214, and LOC113707447, were continually down-regulated at the fruit ripening stage. In contrast, a total of four genes, which were LOC113732777, LOC113727880, LOC113690566, and LOC113711936, including those enriched in the cysteine and methionine metabolism, were continually up-regulated. Collectively, our findings may contribute to the exploration of alternative splicing mechanisms for focused investigations of potential genes associated with the ripening of fruits in C. arabica.
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Affiliation(s)
- Haohao Yu
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, China; (H.Y.); (X.B.)
| | - Xiaofei Bi
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, China; (H.Y.); (X.B.)
| | - Zhongxian Li
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, China; (H.Y.); (X.B.)
| | - Xingfei Fu
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, China; (H.Y.); (X.B.)
| | - Yanan Li
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, China; (H.Y.); (X.B.)
| | - Yaqi Li
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, China; (H.Y.); (X.B.)
| | - Yang Yang
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, China; (H.Y.); (X.B.)
| | - Dexin Liu
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, China; (H.Y.); (X.B.)
| | - Guiping Li
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, China; (H.Y.); (X.B.)
| | - Wenjiang Dong
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China
| | - Faguang Hu
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, China; (H.Y.); (X.B.)
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21
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Zhao K, Li Z, Ke Y, Ren R, Cao Z, Li Z, Wang K, Wang X, Wang J, Ma Q, Cao D, Zhao K, Li Y, Hu S, Qiu D, Gong F, Ma X, Zhang X, Fan G, Liang Z, Yin D. Dynamic N 6 -methyladenosine RNA modification regulates peanut resistance to bacterial wilt. THE NEW PHYTOLOGIST 2024; 242:231-246. [PMID: 38326943 DOI: 10.1111/nph.19568] [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: 08/27/2023] [Accepted: 01/17/2024] [Indexed: 02/09/2024]
Abstract
N6 -methyladenosine (m6 A) is the most abundant mRNA modification in eukaryotes and is an important regulator of gene expression as well as many other critical biological processes. However, the characteristics and functions of m6 A in peanut (Arachis hypogea L.) resistance to bacterial wilt (BW) remain unknown. Here, we analyzed the dynamic of m6 A during infection of resistant (H108) and susceptible (H107) peanut accessions with Ralstonia solanacearum (R. solanacearum), the causative agent of BW. Throughout the transcriptome, we identified 'URUAY' as a highly conserved motif for m6 A in peanut. The majority of differential m6 A located within the 3' untranslated region (UTR) of the transcript, with fewer in the exons. Integrative analysis of RNA-Seq and m6 A methylomes suggests the correlation between m6 A and gene expression in peanut R. solanacearum infection, and functional analysis reveals that m6 A-associated genes were related to plant-pathogen interaction. Our experimental analysis suggests that AhALKBH15 is an m6 A demethylase in peanut, leading to decreased m6 A levels and upregulation of the resistance gene AhCQ2G6Y. The upregulation of AhCQ2G6Y expression appears to promote BW resistance in the H108 accession.
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Affiliation(s)
- Kai Zhao
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural University, Zhengzhou, 450046, China
| | - Zhongfeng Li
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yunzhuo Ke
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Rui Ren
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural University, Zhengzhou, 450046, China
| | - Zenghui Cao
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural University, Zhengzhou, 450046, China
| | - Zhan Li
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural University, Zhengzhou, 450046, China
| | - Kuopeng Wang
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xiaoxuan Wang
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural University, Zhengzhou, 450046, China
| | - Jinzhi Wang
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural University, Zhengzhou, 450046, China
| | - Qian Ma
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural University, Zhengzhou, 450046, China
| | - Di Cao
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural University, Zhengzhou, 450046, China
| | - Kunkun Zhao
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yaoyao Li
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural University, Zhengzhou, 450046, China
| | - Sasa Hu
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural University, Zhengzhou, 450046, China
| | - Ding Qiu
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural University, Zhengzhou, 450046, China
| | - Fangping Gong
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xingli Ma
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xingguo Zhang
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural University, Zhengzhou, 450046, China
| | - Guoqiang Fan
- College of Forestry, Henan Agricultural University, Zhengzhou, 450046, China
| | - Zhe Liang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Dongmei Yin
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural University, Zhengzhou, 450046, China
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22
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Xiong J, Liu Y, Wu P, Bian Z, Li B, Zhang Y, Zhu B. Identification and virus-induced gene silencing (VIGS) analysis of methyltransferase affecting tomato (Solanum lycopersicum) fruit ripening. PLANTA 2024; 259:109. [PMID: 38558186 DOI: 10.1007/s00425-024-04384-4] [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: 11/09/2023] [Accepted: 03/09/2024] [Indexed: 04/04/2024]
Abstract
MAIN CONCLUSION Six methyltransferase genes affecting tomato fruit ripening were identified through genome-wide screening, VIGS assay, and expression pattern analysis. The data provide the basis for understanding new mechanisms of methyltransferases. Fruit ripening is a critical stage for the formation of edible quality and seed maturation, which is finely modulated by kinds of factors, including genetic regulators, hormones, external signals, etc. Methyltransferases (MTases), important genetic regulators, play vital roles in plant development through epigenetic regulation, post-translational modification, or other mechanisms. However, the regulatory functions of numerous MTases except DNA methylation in fruit ripening remain limited so far. Here, six MTases, which act on different types of substrates, were identified to affect tomato fruit ripening. First, 35 MTase genes with relatively high expression at breaker (Br) stage of tomato fruit were screened from the tomato MTase gene database encompassing 421 genes totally. Thereafter, six MTase genes were identified as potential regulators of fruit ripening via virus-induced gene silencing (VIGS), including four genes with a positive regulatory role and two genes with a negative regulatory role, respectively. The expression of these six MTase genes exhibited diverse patterns during the fruit ripening process, and responded to various external ripening-related factors, including ethylene, 1-methylcyclopropene (1-MCP), temperature, and light exposure. These results help to further elaborate the biological mechanisms of MTase genes in tomato fruit ripening and enrich the understanding of the regulatory mechanisms of fruit ripening involving MTases, despite of DNA MTases.
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Affiliation(s)
- Jiaxin Xiong
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, People's Republic of China
| | - Ye Liu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, People's Republic of China
| | - Peiwen Wu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, People's Republic of China
| | - Zheng Bian
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, People's Republic of China
| | - Bowen Li
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, People's Republic of China
| | - Yifan Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, People's Republic of China
| | - Benzhong Zhu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, People's Republic of China.
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23
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Luo JH, Guo T, Wang M, Liu JH, Zheng LM, He Y. RNA m6A modification facilitates DNA methylation during maize kernel development. PLANT PHYSIOLOGY 2024; 194:2165-2182. [PMID: 37995374 DOI: 10.1093/plphys/kiad625] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/27/2023] [Accepted: 10/02/2023] [Indexed: 11/25/2023]
Abstract
N6-methyladenosine (m6A) in mRNA and 5-methylcytosine (5mC) in DNA have critical functions for regulating gene expression and modulating plant growth and development. However, the interplay between m6A and 5mC is an elusive territory and remains unclear mechanistically in plants. We reported an occurrence of crosstalk between m6A and 5mC in maize (Zea mays) via the interaction between mRNA adenosine methylase (ZmMTA), the core component of the m6A methyltransferase complex, and decrease in DNA methylation 1 (ZmDDM1), a key chromatin-remodeling factor that regulates DNA methylation. Genes with m6A modification were coordinated with a much higher level of DNA methylation than genes without m6A modification. Dysfunction of ZmMTA caused severe arrest during maize embryogenesis and endosperm development, leading to a significant decrease in CHH methylation in the 5' region of m6A-modified genes. Instead, loss of function of ZmDDM1 had no noteworthy effects on ZmMTA-related activity. This study establishes a direct link between m6A and 5mC during maize kernel development and provides insights into the interplay between RNA modification and DNA methylation.
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Affiliation(s)
- Jin-Hong Luo
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ting Guo
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Min Wang
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Jing-Han Liu
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Lei-Ming Zheng
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Yan He
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
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24
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Liu Q, Ton J, Manavella PA, Komiya R, Zhai J. Focus on epigenetics. PLANT PHYSIOLOGY 2024; 194:1925-1928. [PMID: 38401162 PMCID: PMC10980384 DOI: 10.1093/plphys/kiae104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 02/21/2024] [Accepted: 02/21/2024] [Indexed: 02/26/2024]
Affiliation(s)
- Qikun Liu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Jurriaan Ton
- The University of Sheffield, School of Biosciences, Sheffield S10 2TN, UK
| | - Pablo Andrés Manavella
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora” (IHSM “La Mayora”), Universidad de Málaga-Consejo Superior de Investigaciones Cientificas (UMA-CSIC), Campus Teatinos, 29010 Málaga, Spain
| | - Reina Komiya
- Science and Technology Group, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
| | - Jixian Zhai
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
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25
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Sheikh AH, Tabassum N, Rawat A, Almeida Trapp M, Nawaz K, Hirt H. m6A RNA methylation counteracts dark-induced leaf senescence in Arabidopsis. PLANT PHYSIOLOGY 2024; 194:2663-2678. [PMID: 38084897 PMCID: PMC10980409 DOI: 10.1093/plphys/kiad660] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 11/16/2023] [Indexed: 04/01/2024]
Abstract
Senescence is an important physiological process which directly affects many agronomic traits in plants. Senescence induces chlorophyll degradation, phytohormone changes, cellular structure damage, and altered gene regulation. Although these physiological outputs are well defined, the molecular mechanisms employed are not known. Using dark-induced leaf senescence (DILS) as the experimental system, we investigated the role of N6-methyladenosine (m6A) mRNA methylation during senescence in Arabidopsis (Arabidopsis thaliana). Plants compromised in m6A machinery components like METHYLTRANSFERASE A (mta mutant) and VIRILIZER1 (vir-1 mutant) showed an enhanced DILS phenotype. This was accompanied by compromised chloroplast and photosynthesis performance in mta as well as accumulation of senescence-promoting camalexin and phytohormone jasmonic acid after dark treatment. m6A levels increased during DILS and destabilized senescence-related transcripts thereby preventing premature aging. Due to inefficient decay, senescence-related transcripts like ORESARA1 (ORE1), SENESCENCE-ASSOCIATED GENE 21 (SAG21), NAC-like, activated by AP3/PI (NAP), and NONYELLOWING 1 (NYE1) over-accumulated in mta thereby causing accelerated senescence during DILS. Overall, our data propose that m6A modification is involved in regulating the biological response to senescence in plants, providing targets for engineering stress tolerance of crops.
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Affiliation(s)
- Arsheed H Sheikh
- Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Naheed Tabassum
- Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Anamika Rawat
- Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Marilia Almeida Trapp
- Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Kashif Nawaz
- Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Heribert Hirt
- Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
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Fang X, Chen J, Meng F, Chen F, Chen X, Wang Y, Fang X, Zhang C, Song C. Linc-smad7 is involved in the regulation of lipid synthesis in mouse mammary epithelial cells. Int J Biol Macromol 2024; 262:129875. [PMID: 38320638 DOI: 10.1016/j.ijbiomac.2024.129875] [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: 11/01/2023] [Revised: 01/13/2024] [Accepted: 01/23/2024] [Indexed: 02/08/2024]
Abstract
Long intergenic non-coding RNA(lincRNA) is transcribed from the intermediate regions of coding genes and plays a pivotal role in the regulation of lipid synthesis. N6-methyladenosine (m6A) modification is widely prevalent in eukaryotic mRNAs and serves as a regulatory factor in diverse biological processes. This study aims to delineate the mechanism by which Linc-smad7 mediates m6A methylation to regulate milk fat synthesis. Tissue expression analysis in this study revealed a high expression of Linc-smad7 in breast tissue during pregnancy. Cell proliferation assays, including CCK8 and EdU assays, demonstrated that Linc-smad7 had no significant impact on the proliferation of mammary epithelial cells. However, during mammary epithelial cell differentiation, the overexpression of Linc-smad7 led to reduced lipid formation, whereas interference with Linc-smad7 promoted lipogenesis. Mechanistically, Linc-smad7 was found to modulate RNA m6A levels, as evidenced by dot blot assays and methylated RNA immunoprecipitation sequencing (MeRIP-Seq). Subsequent validation through RT-qPCR corroborated these findings, aligning with the m6A sequencing outcomes. Furthermore, co-transfection experiments elucidated that Linc-smad7 regulates lipid synthesis in mammary epithelial cells by influencing the expression of METTL14. In summary, these findings underscore the regulatory role of Linc-smad7 in controlling METTL14 gene expression, thereby mediating m6A modifications to regulate lipid synthesis in mammary epithelial cells.
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Affiliation(s)
- Xue Fang
- Institute of Cellular and Molecular Biology, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Junhao Chen
- Institute of Cellular and Molecular Biology, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Fantong Meng
- Institute of Cellular and Molecular Biology, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Fang Chen
- Institute of Cellular and Molecular Biology, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Xi Chen
- Institute of Cellular and Molecular Biology, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Yanhong Wang
- Institute of Cellular and Molecular Biology, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Xingtang Fang
- Institute of Cellular and Molecular Biology, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Chunlei Zhang
- Institute of Cellular and Molecular Biology, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China.
| | - Chengchuang Song
- Institute of Cellular and Molecular Biology, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China.
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27
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Su H, Meng L, Qu Z, Zhang W, Liu N, Cao P, Jin J. Genome-wide identification of the N 6-methyladenosine regulatory genes reveals NtFIP37B increases drought resistance of tobacco (Nicotiana tabacum L.). BMC PLANT BIOLOGY 2024; 24:134. [PMID: 38403644 PMCID: PMC10895791 DOI: 10.1186/s12870-024-04813-2] [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: 07/10/2023] [Accepted: 02/09/2024] [Indexed: 02/27/2024]
Abstract
BACKGROUND N6-methyladenosine (m6A) is one of the common internal RNA modifications found in eukaryotes. The m6A modification can regulate various biological processes in organisms through the modulation of alternative splicing, alternative polyadenylation, folding, translation, localization, transport, and decay of multiple types of RNA, without altering the nucleotide sequence. The three components involved in m6A modification, namely writer, eraser, and reader, mediate the abundance of RNA m6A modification through complex collaborative actions. Currently, research on m6A regulatory genes in plants is still in its infancy. RESULTS In this study, we identified 52 candidate m6A regulatory genes in common tobacco (Nicotiana tabacum L.). Gene structure, conserved domains, and motif analysis showed structural and functional diversity among different subgroups of tobacco m6A regulatory genes. The amplification of m6A regulatory genes were mainly driven by polyploidization and dispersed duplication, and duplicated genes evolved through purified selection. Based on the potential regulatory network and expression pattern analysis of m6A regulatory genes, a significant number of m6A regulatory genes might play important roles in growth, development, and stress response processes. Furthermore, we have confirmed the critical role of NtFIP37B, an m6A writer gene in tobacco, in enhancing drought resistance. CONCLUSIONS This study provides useful information for better understanding the evolution of m6A regulatory genes and the role of m6A modification in tobacco stress response, and lays the foundation for further elucidating the function of m6A regulatory genes in tobacco.
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Affiliation(s)
- Huan Su
- Beijing Life Science Academy, Beijing, 102200, China
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Lijun Meng
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Zechao Qu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Wei Zhang
- China National Tobacco Quality Supervision & Test Center, Zhengzhou, 450003, China
| | - Nan Liu
- China National Tobacco Quality Supervision & Test Center, Zhengzhou, 450003, China
| | - Peijian Cao
- Beijing Life Science Academy, Beijing, 102200, China.
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China.
| | - Jingjing Jin
- Beijing Life Science Academy, Beijing, 102200, China.
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China.
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28
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Zhang D, Gan Y, Le L, Pu L. Epigenetic variation in maize agronomical traits for breeding and trait improvement. J Genet Genomics 2024:S1673-8527(24)00028-6. [PMID: 38310944 DOI: 10.1016/j.jgg.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/28/2024] [Accepted: 01/29/2024] [Indexed: 02/06/2024]
Abstract
Epigenetics-mediated breeding (Epibreeding) involves engineering crop traits and stress responses through the targeted manipulation of key epigenetic features to enhance agricultural productivity. While conventional breeding methods raise concerns about reduced genetic diversity, epibreeding propels crop improvement through epigenetic variations that regulate gene expression, ultimately impacting crop yield. Epigenetic regulation in crops encompasses various modes, including histone modification, DNA modification, RNA modification, non-coding RNA, and chromatin remodeling. This review summarizes the epigenetic mechanisms underlying major agronomic traits in maize and identifies candidate epigenetic landmarks in the maize breeding process. We propose a valuable strategy for improving maize yield through epibreeding, combining CRISPR/Cas-based epigenome editing technology and Synthetic Epigenetics (SynEpi). Finally, we discuss the challenges and opportunities associated with maize trait improvement through epibreeding.
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Affiliation(s)
- Daolei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; School of Life Science, Inner Mongolia University, Hohhot, Inner Mongolia 010021, China
| | - Yujun Gan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Liang Le
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Li Pu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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29
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Wu M, Liu K, Li H, Li Y, Zhu Y, Su D, Zhang Y, Deng H, Wang Y, Liu M. Gibberellins involved in fruit ripening and softening by mediating multiple hormonal signals in tomato. HORTICULTURE RESEARCH 2024; 11:uhad275. [PMID: 38344652 PMCID: PMC10857933 DOI: 10.1093/hr/uhad275] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 12/06/2023] [Indexed: 04/10/2024]
Abstract
The phytohormone ethylene is well known for its important role in the ripening of climacteric fruit, such as tomato (Solanum lycopersicum). However, the role and mode of action of other plant hormones in climacteric fruit ripening regulation are not fully understood. Here, we showed that exogenous GA treatment or increasing endogenous gibberellin content by overexpressing the gibberellin synthesis gene SlGA3ox2 specifically in fruit tissues delayed tomato fruit ripening, whereas treatment with the GA biosynthesis inhibitor paclobutrazol (PAC) accelerated fruit ripening. Moreover, exogenous ethylene treatment cannot completely reverse the delayed fruit ripening phenotype. Furthermore, exogenous GA treatment of ethylene signalling mutant Never ripe (Nr) or SlEBF3-overexpressing lines still delayed fruit ripening, suggesting that GA involved in fruit ripening partially depends on ethylene. Transcriptome profiling showed that gibberellin affect the ripening of fruits by modulating the metabolism and signal transduction of multiple plant hormones, such as auxin and abscisic acid, in addition to ethylene. Overall, the results of this study provide new insight into the regulation of gibberellin in fruit ripening through mediating multiple hormone signals.
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Affiliation(s)
- Mengbo Wu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Kaidong Liu
- Life Science and Technology School, Lingnan Normal University, Zhanjiang, 524048, China
| | - Honghai Li
- Sichuan Academy of Forestry, Chengdu, 610081, Sichuan, China
| | - Ying Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Yunqi Zhu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Dan Su
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Yaoxin Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Heng Deng
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Yikui Wang
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | - Mingchun Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
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Amara U, Hu J, Park SJ, Kang H. ECT12, an YTH-domain protein, is a potential mRNA m 6A reader that affects abiotic stress responses by modulating mRNA stability in Arabidopsis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108255. [PMID: 38071803 DOI: 10.1016/j.plaphy.2023.108255] [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: 08/14/2023] [Revised: 11/15/2023] [Accepted: 11/29/2023] [Indexed: 02/15/2024]
Abstract
N6-methyladenosine (m6A), the most abundant modification found in eukaryotic mRNAs, is interpreted by m6A "readers," thus playing a crucial role in regulating RNA metabolism. The YT521-B homology-domain (YTHD) proteins, also known as EVOLUTIONARILY CONSERVED C-TERMINAL REGION (ECT), are recognized as m6A reader proteins in plants and animals. Among the 13 potential YTHD family proteins in Arabidopsis thaliana, the functions of only a few members are known. In this study, we determined the function of ECT12 (YTH11) as a potential m6A reader that plays a crucial role in response to abiotic stresses. The loss-of-function ect12 mutants showed no noticeable developmental defects under normal conditions but displayed hypersensitivity to salt or dehydration stress. The salt- or dehydration-hypersensitive phenotypes were correlated with altered levels of several m6A-modified stress-responsive transcripts. Notably, the increased or decreased transcript levels were associated with each transcript's reduced or enhanced decay, respectively. Electrophoretic mobility shift and RNA-immunoprecipitation assays showed that ECT12 binds to m6A-modified RNAs both in vitro and in planta, suggesting its role as an m6A reader. Collectively, these results indicate that the potential m6A reader ECT12 regulates the stability of m6A-modified RNA transcripts, thereby facilitating the response of Arabidopsis to abiotic stresses.
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Affiliation(s)
- Umme Amara
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, South Korea
| | - Jianzhong Hu
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, South Korea
| | - Su Jung Park
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, South Korea
| | - Hunseung Kang
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, South Korea.
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Shen H, Zhou Y, Liao C, Xie Q, Chen G, Hu Z, Wu T. The AlkB Homolog SlALKBH10B Negatively Affects Drought and Salt Tolerance in Solanum lycopersicum. Int J Mol Sci 2023; 25:173. [PMID: 38203345 PMCID: PMC10778744 DOI: 10.3390/ijms25010173] [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: 10/26/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 01/12/2024] Open
Abstract
ALKBH proteins, the homologs of Escherichia coli AlkB dioxygenase, constitute a single-protein repair system that safeguards cellular DNA and RNA against the harmful effects of alkylating agents. ALKBH10B, the first discovered N6-methyladenosine (m6A) demethylase in Arabidopsis (Arabidopsis thaliana), has been shown to regulate plant growth, development, and stress responses. However, until now, the functional role of the plant ALKBH10B has solely been reported in arabidopsis, cotton, and poplar, leaving its functional implications in other plant species shrouded in mystery. In this study, we identified the AlkB homolog SlALKBH10B in tomato (Solanum lycopersicum) through phylogenetic and gene expression analyses. SlALKBH10B exhibited a wide range of expression patterns and was induced by exogenous abscisic acid (ABA) and abiotic stresses. By employing CRISPR/Cas9 gene editing techniques to knock out SlALKBH10B, we observed an increased sensitivity of mutants to ABA treatment and upregulation of gene expression related to ABA synthesis and response. Furthermore, the Slalkbh10b mutants displayed an enhanced tolerance to drought and salt stress, characterized by higher water retention, accumulation of photosynthetic products, proline accumulation, and lower levels of reactive oxygen species and cellular damage. Collectively, these findings provide insights into the negative impact of SlALKBH10B on drought and salt tolerance in tomato plant, expanding our understanding of the biological functionality of SlALKBH10B.
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Affiliation(s)
- Hui Shen
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400030, China; (H.S.); (Y.Z.); (C.L.); (Q.X.); (G.C.)
- Key Laboratory of Vegetable Biology of Yunnan Province, College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China
| | - Ying Zhou
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400030, China; (H.S.); (Y.Z.); (C.L.); (Q.X.); (G.C.)
| | - Changguang Liao
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400030, China; (H.S.); (Y.Z.); (C.L.); (Q.X.); (G.C.)
| | - Qiaoli Xie
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400030, China; (H.S.); (Y.Z.); (C.L.); (Q.X.); (G.C.)
| | - Guoping Chen
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400030, China; (H.S.); (Y.Z.); (C.L.); (Q.X.); (G.C.)
| | - Zongli Hu
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400030, China; (H.S.); (Y.Z.); (C.L.); (Q.X.); (G.C.)
| | - Ting Wu
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400030, China; (H.S.); (Y.Z.); (C.L.); (Q.X.); (G.C.)
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32
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Luo W, Tang Y, Li S, Zhang L, Liu Y, Zhang R, Diao X, Yu J. The m 6 A reader SiYTH1 enhances drought tolerance by affecting the messenger RNA stability of genes related to stomatal closure and reactive oxygen species scavenging in Setaria italica. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:2569-2586. [PMID: 37861067 DOI: 10.1111/jipb.13575] [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: 05/10/2023] [Accepted: 10/19/2023] [Indexed: 10/21/2023]
Abstract
Foxtail millet (Setaria italica), a vital drought-resistant crop, plays a significant role in ensuring food and nutritional security. However, its drought resistance mechanism is not fully understood. N6 -methyladenosine (m6 A) modification of RNA, a prevalent epi-transcriptomic modification in eukaryotes, provides a binding site for m6 A readers and affects plant growth and stress responses by regulating RNA metabolism. In this study, we unveiled that the YT521-B homology (YTH) family gene SiYTH1 positively regulated the drought tolerance of foxtail millet. Notably, the siyth1 mutant exhibited reduced stomatal closure and augmented accumulation of excessive H2 O2 under drought stress. Further investigations demonstrated that SiYTH1 positively regulated the transcripts harboring m6 A modification related to stomatal closure and reactive oxygen species (ROS) scavenging under drought stress. SiYTH1 was uniformly distributed in the cytoplasm of SiYTH1-GFP transgenic foxtail millet. It formed dynamic liquid-like SiYTH1 cytosol condensates in response to drought stress. Moreover, the cytoplasmic protein SiYTH1 was identified as a distinct m6 A reader, facilitating the stabilization of its directly bound SiARDP and ROS scavenging-related transcripts under drought stress. Furthermore, natural variation analysis revealed SiYTH1AGTG as the dominant allele responsible for drought tolerance in foxtail millet. Collectively, this study provides novel insights into the intricate mechanism of m6 A reader-mediated drought tolerance and presents a valuable genetic resource for improving drought tolerance in foxtail millet breeding.
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Affiliation(s)
- Weiwei Luo
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yuxiang Tang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Shenglan Li
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Linlin Zhang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yuwei Liu
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- College of Life Sciences, Hebei Agricultural University, Baoding, 071001, China
| | - Renliang Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jingjuan Yu
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
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Zhang J, Fang Z, Song C. Molecular characteristics and clinical implications of serine/arginine-rich splicing factors in human cancer. Aging (Albany NY) 2023; 15:13287-13311. [PMID: 38015716 DOI: 10.18632/aging.205241] [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: 07/17/2023] [Accepted: 10/17/2023] [Indexed: 11/30/2023]
Abstract
As critical splicing regulators, serine/arginine-rich splicing factors (SRSFs) play pivotal roles in carcinogenesis. As dysregulation of SRSFs may confer potential cancer risks, targeting SRSFs could provide important insights into cancer therapy. However, a global and comprehensive pattern to elaborate the molecular characteristics, mechanisms, and clinical links of SRSFs in a wide variety of human cancer is still lacking. In this study, a systematic analysis was conducted to reveal the molecular characteristics and clinical implications of SRSFs covering more than 10000 tumour samples of 33 human cancer types. We found that SRSFs experienced prevalent genomic alterations and expression perturbations in multiple cancer types. The DNA methylation, m6A modification, and miRNA regulation of SRSFs were all cancer context-dependent. Importantly, we found that SRSFs were strongly associated with cancer immunity, and were capable of predicting response to immunotherapy. And SRSFs had colossal potential for predicting survival in multiple cancer types, including those that have received immunotherapy. Moreover, we also found that SRSFs could indicate the drug sensitivity of targeted therapy and chemotherapy. Our research highlights the significance of SRSFs in cancer occurrence and development, and provides sufficient resources for understanding the biological characteristics of SRSFs, offering a new and unique perspective for developing cancer therapeutic strategies.
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Affiliation(s)
- Jinjin Zhang
- Department of Emergency Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Zhicheng Fang
- Department of Emergency Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Congkuan Song
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, China
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Xu J, He J, Hu B, Hou N, Guo J, Wang C, Li X, Li Z, Zhai J, Zhang T, Ma C, Ma F, Guan Q. Global hypermethylation of the N6-methyladenosine RNA modification associated with apple heterografting. PLANT PHYSIOLOGY 2023; 193:2513-2537. [PMID: 37648253 PMCID: PMC10663141 DOI: 10.1093/plphys/kiad470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 07/20/2023] [Indexed: 09/01/2023]
Abstract
Grafting can facilitate better scion performance and is widely used in plants. Numerous studies have studied the involvement of mRNAs, small RNAs, and epigenetic regulations in the grafting process. However, it remains unclear whether the mRNA N6-methyladenosine (m6A) modification participates in the apple (Malus x domestica Borkh.) grafting process. Here, we decoded the landscape of m6A modification profiles in 'Golden delicious' (a cultivar, Gd) and Malus prunifolia 'Fupingqiuzi' (a unique rootstock with resistance to environmental stresses, Mp), as well as their heterografted and self-grafted plants. Interestingly, global hypermethylation of m6A occurred in both heterografted scion and rootstock compared with their self-grafting controls. Gene Ontology (GO) term enrichment analysis showed that grafting-induced differentially m6A-modified genes were mainly involved in RNA processing, epigenetic regulation, stress response, and development. Differentially m6A-modified genes harboring expression alterations were mainly involved in various stress responses and fatty acid metabolism. Furthermore, grafting-induced mobile mRNAs with m6A and gene expression alterations mainly participated in ABA synthesis and transport (e.g. carotenoid cleavage dioxygenase 1 [CCD1] and ATP-binding cassette G22 [ABCG22]) and abiotic and biotic stress responses, which might contribute to the better performance of heterografted plants. Additionally, the DNA methylome analysis also demonstrated the DNA methylation alterations during grafting. Downregulated expression of m6A methyltransferase gene MdMTA (ortholog of METTL3) in apples induced the global m6A hypomethylation and distinctly activated the expression level of DNA demethylase gene MdROS1 (REPRESSOR OF SILENCING 1) showing the possible association between m6A and 5mC methylation in apples. Our results reveal the m6A modification profiles in the apple grafting process and enhance our understanding of the m6A regulatory mechanism in plant biological processes.
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Affiliation(s)
- Jidi Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jieqiang He
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Bichun Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Nan Hou
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Junxing Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Caixia Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Xuewei Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Zhongxing Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jingjing Zhai
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Ting Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Chuang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Qingmei Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
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35
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Liu T, Feng Y, Yang S, Ge Y, Zhang T, Li J, Li C, Ruan Y, Luo B, Liang G. Depicting the Profile of METTL3-Mediated lncRNA m6A Modification Variants and Identified SNHG7 as a Prognostic Indicator of MNNG-Induced Gastric Cancer. TOXICS 2023; 11:944. [PMID: 37999596 PMCID: PMC10674297 DOI: 10.3390/toxics11110944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 11/25/2023]
Abstract
As a representative example of an environmental chemical carcinogen, MNNG exposure is closely associated with the onset of gastric cancer (GC) where N6-methyladenosine (m6A) RNA methylation tends to be the critical epigenetic event. However, the effect of m6A modification on long non-coding RNAs (lncRNAs) in MNNG-induced GC onset is still unclear. To address the above issue, based on the Methylated RNA immunoprecipitation sequencing (MeRIP-seq) data of MNNG-induced malignant cells (MCs) and GC cells, we comprehensively analyzed the MNNG exposure-associated vital lncRNAs. MeRIP-seq analysis identified 1432 lncRNA transcripts in the MC cell, and 3520 lncRNA transcripts were found to be m6A modified in the GC cell, respectively. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that MNNG exposure could spark cellular localization change, which might be the critical cellular note variation for malignant transformation. We demonstrated that METTL3 is responsible for N6 methylation of lncRNAs and identified SNHG7 as a downstream target of METTL3. More importantly, we observed that SNHG7 was progressively up-regulated during gastric carcinogenesis by MNNG exposure. Finally, we investigated SNHG7 expression in different stages of GC malignancies and found that elevated SNHG7 expression correlated with advanced clinical features and poor prognosis in GC. In conclusion, our study found for the first time that METTL3 regulates the m6A methylation level of lncRNA SNHG7 and its expression in MNNG exposure-induced GC, suggesting that SNHG7 as a predictive biomarker or therapeutic target for GC.
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Affiliation(s)
- Tong Liu
- Institute of Occupational Health and Environmental Health, School of Public Health, Lanzhou University, Lanzhou 730000, China; (T.L.); (C.L.); (Y.R.); (B.L.)
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China; (Y.F.); (S.Y.); (Y.G.); (T.Z.); (J.L.)
| | - Yanlu Feng
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China; (Y.F.); (S.Y.); (Y.G.); (T.Z.); (J.L.)
| | - Sheng Yang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China; (Y.F.); (S.Y.); (Y.G.); (T.Z.); (J.L.)
| | - Yiling Ge
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China; (Y.F.); (S.Y.); (Y.G.); (T.Z.); (J.L.)
| | - Tianyi Zhang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China; (Y.F.); (S.Y.); (Y.G.); (T.Z.); (J.L.)
| | - Jie Li
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China; (Y.F.); (S.Y.); (Y.G.); (T.Z.); (J.L.)
| | - Chengyun Li
- Institute of Occupational Health and Environmental Health, School of Public Health, Lanzhou University, Lanzhou 730000, China; (T.L.); (C.L.); (Y.R.); (B.L.)
| | - Ye Ruan
- Institute of Occupational Health and Environmental Health, School of Public Health, Lanzhou University, Lanzhou 730000, China; (T.L.); (C.L.); (Y.R.); (B.L.)
| | - Bin Luo
- Institute of Occupational Health and Environmental Health, School of Public Health, Lanzhou University, Lanzhou 730000, China; (T.L.); (C.L.); (Y.R.); (B.L.)
| | - Geyu Liang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China; (Y.F.); (S.Y.); (Y.G.); (T.Z.); (J.L.)
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36
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Zhou L, Gao G, Li X, Wang W, Tian S, Qin G. The pivotal ripening gene SlDML2 participates in regulating disease resistance in tomato. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2291-2306. [PMID: 37466912 PMCID: PMC10579708 DOI: 10.1111/pbi.14130] [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: 01/11/2023] [Revised: 06/14/2023] [Accepted: 07/06/2023] [Indexed: 07/20/2023]
Abstract
Fruit ripening and disease resistance are two essential biological processes for quality formation and maintenance. DNA methylation, in the form of 5-methylcytosine (5mC), has been elucidated to modulate fruit ripening, but its role in regulating fruit disease resistance remains poorly understood. In this study, we show that mutation of SlDML2, the DNA demethylase gene essential for fruit ripening, affects multiple developmental processes of tomato besides fruit ripening, including seed germination, leaf length and width and flower branching. Intriguingly, loss of SlDML2 function decreased the resistance of tomato fruits against the necrotrophic fungal pathogen Botrytis cinerea. Comparative transcriptomic analysis revealed an obvious transcriptome reprogramming caused by SlDML2 mutation during B. cinerea invasion. Among the thousands of differentially expressed genes, SlβCA3 encoding a β-carbonic anhydrase and SlFAD3 encoding a ω-3 fatty acid desaturase were demonstrated to be transcriptionally activated by SlDML2-mediated DNA demethylation and positively regulate tomato resistance to B. cinerea probably in the same genetic pathway with SlDML2. We further show that the pericarp tissue surrounding B. cinerea infection exhibited a delay in ripening with singnificant decrease in expression of ripening genes that are targeted by SlDML2 and increase in expression of SlβCA3 and SlFAD3. Taken together, our results uncover an essential layer of gene regulation mediated by DNA methylation upon B. cinerea infection and raise the possible that the DNA demethylase gene SlDML2, as a multifunctional gene, participates in modulating the trade-off between fruit ripening and disease resistance.
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Affiliation(s)
- Leilei Zhou
- Key Laboratory of Plant Resources, Institute of BotanyChinese Academy of SciencesBeijingChina
- China National Botanical GardenBeijingChina
| | - Guangtong Gao
- Key Laboratory of Plant Resources, Institute of BotanyChinese Academy of SciencesBeijingChina
- China National Botanical GardenBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xiaojing Li
- Key Laboratory of Plant Resources, Institute of BotanyChinese Academy of SciencesBeijingChina
- China National Botanical GardenBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Weihao Wang
- Key Laboratory of Plant Resources, Institute of BotanyChinese Academy of SciencesBeijingChina
- China National Botanical GardenBeijingChina
| | - Shiping Tian
- Key Laboratory of Plant Resources, Institute of BotanyChinese Academy of SciencesBeijingChina
- China National Botanical GardenBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Guozheng Qin
- Key Laboratory of Plant Resources, Institute of BotanyChinese Academy of SciencesBeijingChina
- China National Botanical GardenBeijingChina
- University of Chinese Academy of SciencesBeijingChina
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37
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Ming Y, Jiang L, Ji D. Epigenetic regulation in tomato fruit ripening. FRONTIERS IN PLANT SCIENCE 2023; 14:1269090. [PMID: 37780524 PMCID: PMC10539587 DOI: 10.3389/fpls.2023.1269090] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 08/31/2023] [Indexed: 10/03/2023]
Abstract
Fruit ripening is a crucial stage in quality development, influenced by a diverse array of internal and external factors. Among these factors, epigenetic regulation holds significant importance and has garnered substantial research attention in recent years. Here, this review aims to discuss the breakthrough in epigenetic regulation of tomato (Solanum lycopersicum) fruit ripening, including DNA methylation, N6-Methyladenosine mRNA modification, histone demethylation/deacetylation, and non-coding RNA. Through this brief review, we seek to enhance our understanding of the regulatory mechanisms governing tomato fruit ripening, while providing fresh insights for the precise modulation of these mechanisms.
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Affiliation(s)
| | - Libo Jiang
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China
| | - Dongchao Ji
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China
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38
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Liufu Y, Xi F, Wu L, Zhang Z, Wang H, Wang H, Zhang J, Wang B, Kou W, Gao J, Zhao L, Zhang H, Gu L. Inhibition of DNA and RNA methylation disturbs root development of moso bamboo. TREE PHYSIOLOGY 2023; 43:1653-1674. [PMID: 37294626 DOI: 10.1093/treephys/tpad074] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 04/25/2023] [Accepted: 06/03/2023] [Indexed: 06/11/2023]
Abstract
DNA methylation (5mC) and N6-methyladenosine (m6A) are two important epigenetics regulators, which have a profound impact on plant growth development. Phyllostachys edulis (P. edulis) is one of the fastest spreading plants due to its well-developed root system. However, the association between 5mC and m6A has seldom been reported in P. edulis. In particular, the connection between m6A and several post-transcriptional regulators remains uncharacterized in P. edulis. Here, our morphological and electron microscope observations showed the phenotype of increased lateral root under RNA methylation inhibitor (DZnepA) and DNA methylation inhibitor (5-azaC) treatment. RNA epitranscriptome based on Nanopore direct RNA sequencing revealed that DZnepA treatment exhibits significantly decreased m6A level in the 3'-untranslated region (3'-UTR), which was accompanied by increased gene expression, full-length ratio, higher proximal poly(A) site usage and shorter poly(A) tail length. DNA methylation levels of CG and CHG were reduced in both coding sequencing and transposable element upon 5-azaC treatment. Cell wall synthesis was impaired under methylation inhibition. In particular, differentially expressed genes showed a high percentage of overlap between DZnepA and 5-azaC treatment, which suggested a potential correlation between two methylations. This study provides preliminary information for a better understanding of the link between m6A and 5mC in root development of moso bamboo.
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Affiliation(s)
- Yuxiang Liufu
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province 350002, China
| | - Feihu Xi
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lin Wu
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province 350002, China
| | - Zeyu Zhang
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province 350002, China
| | - Huihui Wang
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province 350002, China
| | - Huiyuan Wang
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province 350002, China
| | - Jun Zhang
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province 350002, China
| | - Baijie Wang
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province 350002, China
| | - Wenjing Kou
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province 350002, China
| | - Jian Gao
- Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Liangzhen Zhao
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hangxiao Zhang
- Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, College of Forestry, School of Future Technology, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province 350002, China
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Dong Y, Li S, Wu H, Gao Y, Feng Z, Zhao X, Shan L, Zhang Z, Ren H, Liu X. Advances in understanding epigenetic regulation of plant trichome development: a comprehensive review. HORTICULTURE RESEARCH 2023; 10:uhad145. [PMID: 37691965 PMCID: PMC10483894 DOI: 10.1093/hr/uhad145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 07/14/2023] [Indexed: 09/12/2023]
Abstract
Plant growth and development are controlled by a complex gene regulatory network, which is currently a focal point of research. It has been established that epigenetic factors play a crucial role in plant growth. Trichomes, specialized appendages that arise from epidermal cells, are of great significance in plant growth and development. As a model system for studying plant development, trichomes possess both commercial and research value. Epigenetic regulation has only recently been implicated in the development of trichomes in a limited number of studies, and microRNA-mediated post-transcriptional regulation appears to dominate in this context. In light of this, we have conducted a review that explores the interplay between epigenetic regulations and the formation of plant trichomes, building upon existing knowledge of hormones and transcription factors in trichome development. Through this review, we aim to deepen our understanding of the regulatory mechanisms underlying trichome formation and shed light on future avenues of research in the field of epigenetics as it pertains to epidermal hair growth.
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Affiliation(s)
- Yuming Dong
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Sen Li
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Haoying Wu
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Yiming Gao
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Zhongxuan Feng
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Xi Zhao
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Li Shan
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Zhongren Zhang
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Huazhong Ren
- College of Horticulture, China Agricultural University, Beijing 100193, China
- Sanya Institute of China Agricultural University, Sanya Hainan 572000, China
| | - Xingwang Liu
- College of Horticulture, China Agricultural University, Beijing 100193, China
- Sanya Institute of China Agricultural University, Sanya Hainan 572000, China
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40
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Kang H, Xu T. N6-methyladenosine RNA methylation modulates liquid‒liquid phase separation in plants. THE PLANT CELL 2023; 35:3205-3213. [PMID: 37032432 PMCID: PMC10473200 DOI: 10.1093/plcell/koad103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/13/2023] [Accepted: 03/17/2023] [Indexed: 06/19/2023]
Abstract
Membraneless biomolecular condensates form distinct subcellular compartments that enable a cell to orchestrate numerous biochemical reactions in a spatiotemporal-specific and dynamic manner. Liquid‒liquid phase separation (LLPS) facilitates the formation of membraneless biomolecular condensates, which are crucial for many cellular processes in plants, including embryogenesis, the floral transition, photosynthesis, pathogen defense, and stress responses. The main component required for LLPS is a protein harboring key characteristic features, such as intrinsically disordered regions, low-complexity sequence domains, and prion-like domains. RNA is an additional component involved in LLPS. Increasing evidence indicates that modifications in proteins and RNAs play pivotal roles in LLPS. In particular, recent studies have indicated that N6-methyladenosine (m6A) modification of messenger RNA is crucial for LLPS in plants and animals. In this review, we provide an overview of recent developments in the role of mRNA methylation in LLPS in plant cells. Moreover, we highlight the major challenges in understanding the pivotal roles of RNA modifications and elucidating how m6A marks are interpreted by RNA-binding proteins crucial for LLPS.
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Affiliation(s)
- Hunseung Kang
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu Joint International Center of Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, Jiangsu Province, China
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea
| | - Tao Xu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu Joint International Center of Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, Jiangsu Province, China
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41
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Han X, Guo J, Wang M, Zhang N, Ren J, Yang Y, Chi X, Chen Y, Yao H, Zhao YL, Yang YG, Sun Y, Xu J. Dynamic DNA 5-hydroxylmethylcytosine and RNA 5-methycytosine Reprogramming During Early Human Development. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:805-822. [PMID: 35644351 PMCID: PMC10787118 DOI: 10.1016/j.gpb.2022.05.005] [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: 12/06/2021] [Revised: 04/18/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
After implantation, complex and highly specialized molecular events render functionally distinct organ formation, whereas how the epigenome shapes organ-specific development remains to be fully elucidated. Here, nano-hmC-Seal, RNA bisulfite sequencing (RNA-BisSeq), and RNA sequencing (RNA-Seq) were performed, and the first multilayer landscapes of DNA 5-hydroxymethylcytosine (5hmC) and RNA 5-methylcytosine (m5C) epigenomes were obtained in the heart, kidney, liver, and lung of the human foetuses at 13-28 weeks with 123 samples in total. We identified 70,091 and 503 organ- and stage-specific differentially hydroxymethylated regions (DhMRs) and m5C-modified mRNAs, respectively. The key transcription factors (TFs), T-box transcription factor 20 (TBX20), paired box 8 (PAX8), krueppel-like factor 1 (KLF1), transcription factor 21 (TCF21), and CCAAT enhancer binding protein beta (CEBPB), specifically contribute to the formation of distinct organs at different stages. Additionally, 5hmC-enriched Alu elements may participate in the regulation of expression of TF-targeted genes. Our integrated studies reveal a putative essential link between DNA modification and RNA methylation, and illustrate the epigenetic maps during human foetal organogenesis, which provide a foundation for for an in-depth understanding of the epigenetic mechanisms underlying early development and birth defects.
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Affiliation(s)
- Xiao Han
- Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Jia Guo
- Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Mengke Wang
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Nan Zhang
- Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Jie Ren
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Ying Yang
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China; Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Xu Chi
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Yusheng Chen
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huan Yao
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong-Liang Zhao
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yun-Gui Yang
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China; Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.
| | - Yingpu Sun
- Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China.
| | - Jiawei Xu
- Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China.
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Xing K, Liu Z, Liu L, Zhang J, Qanmber G, Wang Y, Liu L, Gu Y, Zhang C, Li S, Zhang Y, Yang Z. N 6 -Methyladenosine mRNA modification regulates transcripts stability associated with cotton fiber elongation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:967-985. [PMID: 37158663 DOI: 10.1111/tpj.16274] [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: 02/01/2023] [Revised: 04/29/2023] [Accepted: 05/04/2023] [Indexed: 05/10/2023]
Abstract
N6 -Methyladenosine (m6 A) is the most abundant methylation modification in eukaryotic mRNA. The discovery of the dynamic and reversible regulatory mechanism of m6 A has greatly promoted the development of m6 A-led epitranscriptomics. However, the characterization of m6 A in cotton fiber is still unknown. Here, we reveal the potential link between m6 A modification and cotton fiber elongation by parallel m6 A-immunoprecipitation-sequencing (m6 A-seq) and RNA-seq analysis of fibers from the short fiber mutants Ligonliness-2 (Li2 ) and wild-type (WT). This study demonstrated a higher level of m6 A in the Li2 mutant, with the enrichment of m6 A modifications in the stop codon, 3'-untranslated region and coding sequence regions than in WT cotton. In the correlation analysis between genes containing differential m6 A modifications and differentially expressed genes, we identified several genes that could potentially regulate fiber elongation, including cytoskeleton, microtubule binding, cell wall and transcription factors (TFs). We further confirmed that the methylation of m6 A affected the mRNA stability of these fiber elongation-related genes including the TF GhMYB44, which showed the highest expression level in the RNA-seq data and m6 A methylation in the m6 A-seq data. Next, the overexpression of GhMYB44 reduces fiber elongation, whereas the silencing of GhMYB44 produces longer fibers. In summary, these results uncover that m6 A methylation regulated the expression of genes related to fiber development by affecting mRNA's stability, ultimately affecting cotton fiber elongation.
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Affiliation(s)
- Kun Xing
- Hebei Research Base,National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, College of Agronomy, Hebei Agricultural University, Baoding, 071001, Hebei, China
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization,Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Zhao Liu
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Le Liu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization,Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Jie Zhang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization,Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Ghulam Qanmber
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Ye Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization,Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Lisen Liu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization,Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Yu Gu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization,Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Changsheng Zhang
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Shuaijie Li
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Yan Zhang
- Hebei Research Base,National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, College of Agronomy, Hebei Agricultural University, Baoding, 071001, Hebei, China
| | - Zuoren Yang
- Hebei Research Base,National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, College of Agronomy, Hebei Agricultural University, Baoding, 071001, Hebei, China
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization,Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, Xinjiang, China
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Zhu C, Zhang S, Zhou C, Tian C, Shi B, Xu K, Huang L, Sun Y, Lin Y, Lai Z, Guo Y. RNA Methylome Reveals the m 6A-mediated Regulation of Flavor Metabolites in Tea Leaves under Solar-withering. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:769-787. [PMID: 36791953 PMCID: PMC10787128 DOI: 10.1016/j.gpb.2023.02.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 11/20/2022] [Accepted: 02/05/2023] [Indexed: 02/16/2023]
Abstract
The epitranscriptomic mark N6-methyladenosine (m6A), which is the predominant internal modification in RNA, is important for plant responses to diverse stresses. Multiple environmental stresses caused by the tea-withering process can greatly influence the accumulation of specialized metabolites and the formation of tea flavor. However, the effects of the m6A-mediated regulatory mechanism on flavor-related metabolic pathways in tea leaves remain relatively uncharacterized. We performed an integrated RNA methylome and transcriptome analysis to explore the m6A-mediated regulatory mechanism and its effects on flavonoid and terpenoid metabolism in tea (Camellia sinensis) leaves under solar-withering conditions. Dynamic changes in global m6A level in tea leaves were mainly controlled by two m6A erasers (CsALKBH4A and CsALKBH4B) during solar-withering treatments. Differentially methylated peak-associated genes following solar-withering treatments with different shading rates were assigned to terpenoid biosynthesis and spliceosome pathways. Further analyses indicated that CsALKBH4-driven RNA demethylation can directly affect the accumulation of volatile terpenoids by mediating the stability and abundance of terpenoid biosynthesis-related transcripts and also indirectly influence the flavonoid, catechin, and theaflavin contents by triggering alternative splicing-mediated regulation. Our findings revealed a novel layer of epitranscriptomic gene regulation in tea flavor-related metabolic pathways and established a link between the m6A-mediated regulatory mechanism and the formation of tea flavor under solar-withering conditions.
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Affiliation(s)
- Chen Zhu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Tea Industry Research Institute, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shuting Zhang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chengzhe Zhou
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Tea Industry Research Institute, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Caiyun Tian
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Tea Industry Research Institute, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Biying Shi
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Tea Industry Research Institute, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Kai Xu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Tea Industry Research Institute, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Linjie Huang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Tea Industry Research Institute, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yun Sun
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Tea Industry Research Institute, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuling Lin
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhongxiong Lai
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Yuqiong Guo
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Tea Industry Research Institute, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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Lv Y, Han F, Liu M, Zhang T, Cui G, Wang J, Yang Y, Yang YG, Yang W. Characteristics of N 6-methyladenosine Modification During Sexual Reproduction of Chlamydomonas reinhardtii. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:756-768. [PMID: 35550876 PMCID: PMC10787120 DOI: 10.1016/j.gpb.2022.04.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/12/2022] [Accepted: 04/24/2022] [Indexed: 06/15/2023]
Abstract
The unicellular green alga Chlamydomonas reinhardtii (hereafter Chlamydomonas) possesses both plant and animal attributes, and it is an ideal model organism for studying fundamental processes such as photosynthesis, sexual reproduction, and life cycle. N6-methyladenosine (m6A) is the most prevalent mRNA modification, and it plays important roles during sexual reproduction in animals and plants. However, the pattern and function of m6A modification during the sexual reproduction of Chlamydomonas remain unknown. Here, we performed transcriptome and methylated RNA immunoprecipitation sequencing (MeRIP-seq) analyses on six samples from different stages during sexual reproduction of the Chlamydomonas life cycle. The results show that m6A modification frequently occurs at the main motif of DRAC (D = G/A/U, R = A/G) in Chlamydomonas mRNAs. Moreover, m6A peaks in Chlamydomonas mRNAs are mainly enriched in the 3' untranslated regions (3'UTRs) and negatively correlated with the abundance of transcripts at each stage. In particular, there is a significant negative correlation between the expression levels and the m6A levels of genes involved in the microtubule-associated pathway, indicating that m6A modification influences the sexual reproduction and the life cycle of Chlamydomonas by regulating microtubule-based movement. In summary, our findings are the first to demonstrate the distribution and the functions of m6A modification in Chlamydomonas mRNAs and provide new evolutionary insights into m6A modification in the process of sexual reproduction in other plant organisms.
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Affiliation(s)
- Ying Lv
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fei Han
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mengxia Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ting Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Guanshen Cui
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Jiaojiao Wang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China; Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Yun-Gui Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China; Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenqiang Yang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China; Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100093, China.
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45
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Zhang Y, Han X, Su D, Liu C, Chen Q, Qi Z. An analysis of differentially expressed and differentially m6A-modified transcripts in soybean roots treated with lead. JOURNAL OF HAZARDOUS MATERIALS 2023; 453:131370. [PMID: 37043855 DOI: 10.1016/j.jhazmat.2023.131370] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/23/2023] [Accepted: 04/03/2023] [Indexed: 05/03/2023]
Abstract
Lead is one of the most common toxic heavy metal pollutants in nature, and exposure to lead can cause serious toxicity to many organisms. In this study, we collected root growth data from soybean plants exposed to lead for seven days and confirmed that lead significantly inhibited root growth. We performed a transcriptome-wide m6A methylation analysis to study the response of soybean RNA methylation groups to lead. The m6A modified regions were enriched near the 3'UTR region and stop codon, and m6A methylation was positively correlated with transcript abundance. In the presence of lead, the transcriptome range of m6A RNA methylation peaks increased, and we identified 1144 m6A modification peaks and 1094 differentially expressed genes. The integration of m6A methylation and transcriptomic results enabled us to identify 16 candidate genes whose transcripts were differentially methylated and differentially expressed under lead stress. Annotation results suggest that these genes may promote abiotic stress tolerance by impacting lead uptake, transport, and accumulation through ROS pathways, enzymes, transporters, and hormones. These results provide candidate genes for future studies of lead stress tolerance mechanisms in soybean roots and provide genetic resources for studying plant heavy metal stress in soybean breeding.
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Affiliation(s)
- Yu Zhang
- National Research Center of Soybean Engineering and Technology, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Xue Han
- National Research Center of Soybean Engineering and Technology, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Daiqun Su
- National Research Center of Soybean Engineering and Technology, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Chunyan Liu
- National Research Center of Soybean Engineering and Technology, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Qingshan Chen
- National Research Center of Soybean Engineering and Technology, Northeast Agricultural University, Harbin, Heilongjiang 150030, China.
| | - Zhaoming Qi
- National Research Center of Soybean Engineering and Technology, Northeast Agricultural University, Harbin, Heilongjiang 150030, China.
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Wang W, Wang Y, Chen T, Qin G, Tian S. Current insights into posttranscriptional regulation of fleshy fruit ripening. PLANT PHYSIOLOGY 2023; 192:1785-1798. [PMID: 36250906 PMCID: PMC10315313 DOI: 10.1093/plphys/kiac483] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/27/2022] [Indexed: 05/26/2023]
Abstract
Fruit ripening is a complicated process that is accompanied by the formation of fruit quality. It is not only regulated at the transcriptional level via transcription factors or DNA methylation but also fine-tuned after transcription occurs. Here, we review recent advances in our understanding of key regulatory mechanisms of fleshy fruit ripening after transcription. We mainly highlight the typical mechanisms by which fruit ripening is controlled, namely, alternative splicing, mRNA N6-methyladenosine RNA modification methylation, and noncoding RNAs at the posttranscriptional level; regulation of translation efficiency and upstream open reading frame-mediated translational repression at the translational level; and histone modifications, protein phosphorylation, and protein ubiquitination at the posttranslational level. Taken together, these posttranscriptional regulatory mechanisms, along with transcriptional regulation, constitute the molecular framework of fruit ripening. We also critically discuss the potential usage of some mechanisms to improve fruit traits.
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Affiliation(s)
- Weihao Wang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yuying Wang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Tong Chen
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Guozheng Qin
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Shiping Tian
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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47
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Ji Y, Wang A. Recent advances in epigenetic triggering of climacteric fruit ripening. PLANT PHYSIOLOGY 2023; 192:1711-1717. [PMID: 37002826 PMCID: PMC10315304 DOI: 10.1093/plphys/kiad206] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/03/2023] [Accepted: 03/18/2023] [Indexed: 06/19/2023]
Abstract
During ripening, fleshy fruits undergo irreversible changes in color, texture, sugar content, aroma, and flavor to appeal to seed-dispersal vectors. The onset of climacteric fruit ripening is accompanied by an ethylene burst. Understanding the factors triggering this ethylene burst is important for manipulating climacteric fruit ripening. Here, we review the current understanding and recent insights into the possible factors triggering climacteric fruit ripening: DNA methylation and histone modification, including methylation and acetylation. Understanding the initiation factors of fruit ripening is important for exploring and accurately regulating the mechanisms of fruit ripening. Lastly, we discuss the potential mechanisms responsible for climacteric fruit ripening.
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Affiliation(s)
- Yinglin Ji
- Key Laboratory of Fruit Postharvest Biology (Liaoning Province), Key Laboratory of Protected Horticulture (Ministry of Education), National and Local Joint Engineering Research Center of Northern Horticultural Facilities Design and Application Technology (Liaoning), College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Aide Wang
- Key Laboratory of Fruit Postharvest Biology (Liaoning Province), Key Laboratory of Protected Horticulture (Ministry of Education), National and Local Joint Engineering Research Center of Northern Horticultural Facilities Design and Application Technology (Liaoning), College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
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48
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Zhang Y, Wang J, Ma W, Lu N, Fu P, Yang Y, Zhao L, Hu J, Qu G, Wang N. Transcriptome-wide m6A methylation in natural yellow leaf of Catalpa fargesii. FRONTIERS IN PLANT SCIENCE 2023; 14:1167789. [PMID: 37404531 PMCID: PMC10315917 DOI: 10.3389/fpls.2023.1167789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 05/30/2023] [Indexed: 07/06/2023]
Abstract
N6-methyladenosine (m6A) is the most abundant internal modification in eukaryotic messenger RNA, and involved in various biological processes in plants. However, the distribution features and functions of mRNA m6A methylation have been poorly explored in woody perennial plants. In this study, a new natural variety with yellow-green leaves, named Maiyuanjinqiu, was screened from the seedlings of Catalpa fargesii. Based on the preliminary experiment, the m6A methylation levels in the leaves of Maiyuanjinqiu were significantly higher than those in C. fargesii. Furthermore, a parallel analysis of m6A-seq and RNA-seq was carried out in different leaf color sectors. The result showed that m6A modification were mostly identified around the 3'-untranslated regions (3'-UTR), which was slightly negatively correlated with the mRNA abundance. KEGG and GO analyses showed that m6A methylation genes were associated with photosynthesis, pigments biosynthesis and metabolism, oxidation-reduction and response to stress, etc. The overall increase of m6A methylation levels in yellow-green leaves might be associated with the decreased the expression of RNA demethylase gene CfALKBH5. The silencing of CfALKBH5 caused a chlorotic phenotype and increased m6A methylation level, which further confirmed our hypothesis. Our results suggested that mRNA m6A methylation could be considered as a vital epigenomic mark and contribute to the natural variations in plants.
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Affiliation(s)
- Yu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry and Northeast Forestry University, Beijing, China
| | - Junhui Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry and Northeast Forestry University, Beijing, China
| | - Wenjun Ma
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry and Northeast Forestry University, Beijing, China
| | - Nan Lu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry and Northeast Forestry University, Beijing, China
| | - Pengyue Fu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry and Northeast Forestry University, Beijing, China
| | - Yingying Yang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry and Northeast Forestry University, Beijing, China
| | - Linjiao Zhao
- Hekou Yao Autonomous County Forestry and Grassland Bureau, Hekou, China
| | - Jiwen Hu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry and Northeast Forestry University, Beijing, China
| | - Guanzheng Qu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry and Northeast Forestry University, Beijing, China
| | - Nan Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry and Northeast Forestry University, Beijing, China
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Li B, Zhang M, Sun W, Yue D, Ma Y, Zhang B, Duan L, Wang M, Lindsey K, Nie X, Zhang X, Yang X. N6-methyladenosine RNA modification regulates cotton drought response in a Ca 2+ and ABA-dependent manner. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:1270-1285. [PMID: 36949572 DOI: 10.1111/pbi.14036] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 02/10/2023] [Accepted: 02/24/2023] [Indexed: 05/27/2023]
Abstract
N6 -methyladenosine (m6 A) is the most prevalent internal modification present in mRNAs, and is considered to participate in a range of developmental and biological processes. Drought response is highly regulated at the genomic, transcriptional and post-transcriptional levels. However, the biological function and regulatory mechanism of m6 A modification in the drought stress response is still poorly understood. We generated a transcriptome-wide m6 A map using drought-resistant and drought-sensitive varieties of cotton under different water deficient conditions to uncover patterns of m6 A methylation in cotton response to drought stress. The results reveal that m6 A represents a common modification and exhibit dramatic changes in distribution during drought stress. More 5'UTR m6 A was deposited in the drought-resistant variety and was associated with a positive effect on drought resistance by regulating mRNA abundance. Interestingly, we observed that increased m6 A abundance was associated with increased mRNA abundance under drought, contributing to drought resistance, and vice versa. The demethylase GhALKBH10B was found to decrease m6 A levels, facilitating the mRNA decay of ABA signal-related genes (GhZEP, GhNCED4 and GhPP2CA) and Ca2+ signal-related genes (GhECA1, GhCNGC4, GhANN1 and GhCML13), and mutation of GhALKBH10B enhanced drought resistance at seedling stage in cotton. Virus-induced gene silencing (VIGS) of two Ca2+ -related genes, GhECA1 and GhCNGC4, reduced drought resistance with the decreased m6 A enrichment on silenced genes in cotton. Collectively, we reveal a novel mechanism of post-transcriptional modification involved in affecting drought response in cotton, by mediating m6 A methylation on targeted transcripts in the ABA and Ca2+ signalling transduction pathways.
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Affiliation(s)
- Baoqi Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Mengmeng Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Weinan Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Dandan Yue
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yizan Ma
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Boyang Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Lingfeng Duan
- College of Engineering, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Keith Lindsey
- Department of Biosciences, Durham University, Durham, UK
| | - Xinhui Nie
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Bingtuan, Agricultural College, Shihezi University, Xinjiang, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xiyan Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
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50
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Prall W, Ganguly DR, Gregory BD. The covalent nucleotide modifications within plant mRNAs: What we know, how we find them, and what should be done in the future. THE PLANT CELL 2023; 35:1801-1816. [PMID: 36794718 PMCID: PMC10226571 DOI: 10.1093/plcell/koad044] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/16/2022] [Accepted: 01/09/2023] [Indexed: 05/30/2023]
Abstract
Although covalent nucleotide modifications were first identified on the bases of transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs), a number of these epitranscriptome marks have also been found to occur on the bases of messenger RNAs (mRNAs). These covalent mRNA features have been demonstrated to have various and significant effects on the processing (e.g. splicing, polyadenylation, etc.) and functionality (e.g. translation, transport, etc.) of these protein-encoding molecules. Here, we focus our attention on the current understanding of the collection of covalent nucleotide modifications known to occur on mRNAs in plants, how they are detected and studied, and the most outstanding future questions of each of these important epitranscriptomic regulatory signals.
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Affiliation(s)
- Wil Prall
- Department of Biology, University of Pennsylvania, School of Arts and Sciences, 433 S. University Ave., Philadelphia, PA 19104, USA
| | - Diep R Ganguly
- Department of Biology, University of Pennsylvania, School of Arts and Sciences, 433 S. University Ave., Philadelphia, PA 19104, USA
| | - Brian D Gregory
- Department of Biology, University of Pennsylvania, School of Arts and Sciences, 433 S. University Ave., Philadelphia, PA 19104, USA
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