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Huang J, Jia Y, Pan Y, Lin H, Lv S, Nawaz M, Song B, Nie X. Genome-wide identification of m6A-related gene family and the involvement of TdFIP37 in salt stress in wild emmer wheat. PLANT CELL REPORTS 2024; 43:254. [PMID: 39373738 DOI: 10.1007/s00299-024-03339-z] [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: 03/27/2024] [Accepted: 09/23/2024] [Indexed: 10/08/2024]
Abstract
KEY MESSAGE The genomic organization, phylogenetic relationship, expression patterns, and genetic variations of m6A-related genes were systematically investigated in wild emmer wheat and the function of TdFIP37 regulating salt tolerance was preliminarily determined. m6A modification is one of the most abundant and crucial RNA modifications in eukaryotics, playing the indispensable role in growth and development as well as stress response in plants. However, its significance in wild emmer wheat remains elusive. Here, a genome-wide search of m6A-related genes was conducted in wild emmer wheat to obtain 64 candidates, including 21 writers, 17 erasers, and 26 readers. Phylogenetic and collinearity analysis demonstrated that segmental duplication and polyploidization contributed mainly to the expansion of m6A-related genes in wild emmer. A number of cis-acting elements involving in stress and hormonal regulation were found in the promoter regions of them, such as MBS, LTR, and ABRE. Genetic variation of them was also investigated using resequencing data and obvious genetic bottleneck was occurred on them during wild emmer wheat domestication process. Furthermore, the salt-responsive candidates were investigated through RNA-seq data and qRT-PCR validation using the salt-tolerant and -sensitive genotypes and the co-expression analysis showed that they played the hub role in regulating salt stress response. Finally, the loss-function mutant of Tdfip37 displayed the significantly higher salt-sensitive compared to WT and then RNA-seq analysis demonstrated that FIP37 mediated the MAPK pathway, hormone signal transduction, as well as transcription factor to regulate salt tolerance. This study provided the potential m6A genes for functional analysis, which will contribute to better understand the regulatory roles of m6A modification and also improve the salt tolerance from the perspective of epigenetic approach in emmer wheat and other crops.
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Affiliation(s)
- Jiaqian Huang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261325, Shandong, China
| | - Yanze Jia
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yan Pan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Huiyuan Lin
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Shuzuo Lv
- Luoyang Academy of Agriculture and Forestry Science, Luoyang Key Laboratory of Crop Molecular Biology and Germplasm Enhancement, Luoyang, 471000, Henan, China
| | - Mohsin Nawaz
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Baoxing Song
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261325, Shandong, China
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Fang Z, Ding H, Han J, Fu L, Jin J, Feng W. Functions of N6-methyladenosine (m6A) RNA modifications in acute myeloid leukemia. J Leukoc Biol 2024; 116:662-671. [PMID: 38721720 DOI: 10.1093/jleuko/qiae106] [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: 11/15/2023] [Revised: 04/14/2024] [Accepted: 04/15/2024] [Indexed: 10/03/2024] Open
Abstract
N6-methyladenosine is the most common modification of eukaryotic RNA. N6-methyladenosine participates in RNA splicing, nuclear export, translation, and degradation through regulation by methyltransferases, methylation readers, and demethylases, affecting messenger RNA stability and translation efficiency. Through the dynamic and reversible regulatory network composed of "writers, erasers, and readers," N6-methyladenosine modification plays a unique role in the process of hematopoiesis. Acute myeloid leukemia is a heterogeneous disease characterized by malignant proliferation of hematopoietic stem cells/progenitor cells. Many studies have shown that N6-methyladenosine-related proteins are abnormally expressed in acute myeloid leukemia and play an important role in the occurrence and development of acute myeloid leukemia, acting as carcinogenic or anticancer factors. Here, we describe the mechanisms of action of reversing N6-methyladenosine modification in hematopoiesis and acute myeloid leukemia occurrence and progression to provide a basis for further research on the role of N6-methyladenosine methylation and its regulatory factors in normal hematopoiesis and acute myeloid leukemia, to ultimately estimate its potential clinical value.
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Affiliation(s)
- Zehao Fang
- Department of Hematology, Shaoxing People's Hospital, 568 Zhongxing North Road, Shaoxing 312000, China
| | - Hanyi Ding
- Department of Hematology, Shaoxing People's Hospital, 568 Zhongxing North Road, Shaoxing 312000, China
| | - Jiongping Han
- Department of Hematology, Shaoxing People's Hospital, 568 Zhongxing North Road, Shaoxing 312000, China
| | - Leihua Fu
- Department of Hematology, Shaoxing People's Hospital, 568 Zhongxing North Road, Shaoxing 312000, China
| | - Jing Jin
- Department of Hematology, Shaoxing People's Hospital, 568 Zhongxing North Road, Shaoxing 312000, China
| | - Weiying Feng
- Department of Hematology, Shaoxing People's Hospital, 568 Zhongxing North Road, Shaoxing 312000, China
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3
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Piomponi V, Krepl M, Sponer J, Bussi G. Molecular Simulations to Investigate the Impact of N6-Methylation in RNA Recognition: Improving Accuracy and Precision of Binding Free Energy Prediction. J Phys Chem B 2024; 128:8896-8907. [PMID: 39240243 DOI: 10.1021/acs.jpcb.4c03397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2024]
Abstract
N6-Methyladenosine (m6A) is a prevalent RNA post-transcriptional modification that plays crucial roles in RNA stability, structural dynamics, and interactions with proteins. The YT521-B (YTH) family of proteins, which are notable m6A readers, functions through its highly conserved YTH domain. Recent structural investigations and molecular dynamics (MD) simulations have shed light on the mechanism of recognition of m6A by the YTHDC1 protein. Despite advancements, using MD to predict the stabilization induced by m6A on the free energy of binding between RNA and YTH proteins remains challenging due to inaccuracy of the employed force field and limited sampling. For instance, simulations often fail to sufficiently capture the hydration dynamics of the binding pocket. This study addresses these challenges through an innovative methodology that integrates metadynamics, alchemical simulations, and force-field refinement. Importantly, our research identifies hydration of the binding pocket as giving only a minor contribution to the binding free energy and emphasizes the critical importance of precisely tuning force-field parameters to experimental data. By employing a fitting strategy built on alchemical calculations, we refine the m6A partial charge parameters, thereby enabling the simultaneous reproduction of N6 methylation on both the protein binding free energy and the thermodynamic stability of nine RNA duplexes. Our findings underscore the sensitivity of binding free energies to partial charges, highlighting the necessity for thorough parametrization and validation against experimental observations across a range of structural contexts.
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Affiliation(s)
- Valerio Piomponi
- Scuola Internazionale Superiore di Studi Avanzati, SISSA, Via Bonomea 265, Trieste 34136, Italy
- Area Science Park, località Padriciano, 99, Trieste 34149, Italy
| | - Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolská 135, Brno 612 00, Czech Republic
| | - Jiri Sponer
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolská 135, Brno 612 00, Czech Republic
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati, SISSA, Via Bonomea 265, Trieste 34136, Italy
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Wang Q, Qin B, Yu H, Hu Y, Yu H, Zhong J, Liu J, Yao C, Zeng J, Fan J, Diao L. Advances in Circular RNA in the Pathogenesis of Epilepsy. Neuroscience 2024; 551:246-253. [PMID: 38843987 DOI: 10.1016/j.neuroscience.2024.05.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 05/23/2024] [Accepted: 05/27/2024] [Indexed: 06/15/2024]
Abstract
Recent studies evidenced the involvement of circular RNA (circRNA) in neuroinflammation, apoptosis, and synaptic remodeling suggesting an important role for circRNA in the occurrence and development of epilepsy. This review provides an overview of circRNAs considered to be playing regulatory roles in the process of epilepsy and to be involved in multiple biological epilepsy-related processes, such as hippocampal sclerosis, inflammatory response, cell apoptosis, synaptic remodeling, and cell proliferation and differentiation. This review covers the current research status of differential expression of circRNA-mediated seizures, m6A methylation, demethylation-mediated seizures in post transcriptional circRNA modification, as well as the mechanisms of m5C- and m7G-modified circRNA. In summary, this article reviews the research progress on the relationship between circRNA in non-coding RNA and epilepsy.
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Affiliation(s)
- Qin Wang
- Graduate School of First Clinical Medicine College, Guangxi University of Chinese Medicine, 13 Wuhe Avenue, Qingxiu District, Nanning, Guangxi 530001, China; Department of Neurology, The First Affiliated Hospital of Guangxi University of Chinese Medicine, 89-9 Dongge Road, Qingxiu District, Nanning, Guangxi 530023, China
| | - Baijun Qin
- Department of Gastroenterology, Chongqing Hospital of Traditional Chinese Medicine, 6 Seventh Branch Road, Panxi, Jiangbei District, Chongqing 400021, China
| | - Haichun Yu
- Guangxi Technological College of Machinery and Electricity, Nanning, Guangxi 30007, China
| | - Yueqiang Hu
- Department of Neurology, The First Affiliated Hospital of Guangxi University of Chinese Medicine, 89-9 Dongge Road, Qingxiu District, Nanning, Guangxi 530023, China
| | - Han Yu
- Harbin Medical University, 157 Baojian Road, Nangang District, Harbin, Heilongjiang 150081, China
| | - Jie Zhong
- Department of Neurology, The First Affiliated Hospital of Guangxi University of Chinese Medicine, 89-9 Dongge Road, Qingxiu District, Nanning, Guangxi 530023, China
| | - Jinwen Liu
- Graduate School of First Clinical Medicine College, Guangxi University of Chinese Medicine, 13 Wuhe Avenue, Qingxiu District, Nanning, Guangxi 530001, China; Department of Neurology, The First Affiliated Hospital of Guangxi University of Chinese Medicine, 89-9 Dongge Road, Qingxiu District, Nanning, Guangxi 530023, China
| | - Chunyuan Yao
- Graduate School of First Clinical Medicine College, Guangxi University of Chinese Medicine, 13 Wuhe Avenue, Qingxiu District, Nanning, Guangxi 530001, China; Department of Neurology, The First Affiliated Hospital of Guangxi University of Chinese Medicine, 89-9 Dongge Road, Qingxiu District, Nanning, Guangxi 530023, China
| | - Jiawei Zeng
- Graduate School of First Clinical Medicine College, Guangxi University of Chinese Medicine, 13 Wuhe Avenue, Qingxiu District, Nanning, Guangxi 530001, China; Department of Neurology, The First Affiliated Hospital of Guangxi University of Chinese Medicine, 89-9 Dongge Road, Qingxiu District, Nanning, Guangxi 530023, China
| | - Jingjing Fan
- Graduate School of First Clinical Medicine College, Guangxi University of Chinese Medicine, 13 Wuhe Avenue, Qingxiu District, Nanning, Guangxi 530001, China; Department of Neurology, The First Affiliated Hospital of Guangxi University of Chinese Medicine, 89-9 Dongge Road, Qingxiu District, Nanning, Guangxi 530023, China
| | - Limei Diao
- Graduate School of First Clinical Medicine College, Guangxi University of Chinese Medicine, 13 Wuhe Avenue, Qingxiu District, Nanning, Guangxi 530001, China; Department of Neurology, The First Affiliated Hospital of Guangxi University of Chinese Medicine, 89-9 Dongge Road, Qingxiu District, Nanning, Guangxi 530023, China.
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5
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Lühmann KL, Seemann S, Martinek N, Ostendorp S, Kehr J. The glycine-rich domain of GRP7 plays a crucial role in binding long RNAs and facilitating phase separation. Sci Rep 2024; 14:16018. [PMID: 38992080 PMCID: PMC11239674 DOI: 10.1038/s41598-024-66955-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 07/05/2024] [Indexed: 07/13/2024] Open
Abstract
Microscale thermophoresis (MST) is a well-established method to quantify protein-RNA interactions. In this study, we employed MST to analyze the RNA binding properties of glycine-rich RNA binding protein 7 (GRP7), which is known to have multiple biological functions related to its ability to bind different types of RNA. However, the exact mechanism of GRP7's RNA binding is not fully understood. While the RNA-recognition motif of GRP7 is known to be involved in RNA binding, the glycine-rich region (known as arginine-glycine-glycine-domain or RGG-domain) also influences this interaction. To investigate to which extend the RGG-domain of GRP7 is involved in RNA binding, mutation studies on putative RNA interacting or modulating sites were performed. In addition to MST experiments, we examined liquid-liquid phase separation of GRP7 and its mutants, both with and without RNA. Furthermore, we systemically investigated factors that might affect RNA binding selectivity of GRP7 by testing RNAs of different sizes, structures, and modifications. Consequently, our study revealed that GRP7 exhibits a high affinity for a variety of RNAs, indicating a lack of pronounced selectivity. Moreover, we established that the RGG-domain plays a crucial role in binding longer RNAs and promoting phase separation.
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Affiliation(s)
- Kim Lara Lühmann
- Department of Biology, Molecular Plant Genetics, Institute of Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany
| | - Silja Seemann
- Department of Biology, Molecular Plant Genetics, Institute of Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany
| | - Nina Martinek
- Department of Biology, Molecular Plant Genetics, Institute of Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany
| | - Steffen Ostendorp
- Department of Biology, Molecular Plant Genetics, Institute of Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany
| | - Julia Kehr
- Department of Biology, Molecular Plant Genetics, Institute of Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany.
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6
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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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7
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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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8
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Liu C, Mentzelopoulou A, Hatzianestis IH, Tzagkarakis E, Skaltsogiannis V, Ma X, Michalopoulou VA, Romero-Campero FJ, Romero-Losada AB, Sarris PF, Marhavy P, Bölter B, Kanterakis A, Gutierrez-Beltran E, Moschou PN. A proxitome-RNA-capture approach reveals that processing bodies repress coregulated hub genes. THE PLANT CELL 2024; 36:559-584. [PMID: 37971938 PMCID: PMC10896293 DOI: 10.1093/plcell/koad288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/18/2023] [Accepted: 10/18/2023] [Indexed: 11/19/2023]
Abstract
Cellular condensates are usually ribonucleoprotein assemblies with liquid- or solid-like properties. Because these subcellular structures lack a delineating membrane, determining their compositions is difficult. Here we describe a proximity-biotinylation approach for capturing the RNAs of the condensates known as processing bodies (PBs) in Arabidopsis (Arabidopsis thaliana). By combining this approach with RNA detection, in silico, and high-resolution imaging approaches, we studied PBs under normal conditions and heat stress. PBs showed a much more dynamic RNA composition than the total transcriptome. RNAs involved in cell wall development and regeneration, plant hormonal signaling, secondary metabolism/defense, and RNA metabolism were enriched in PBs. RNA-binding proteins and the liquidity of PBs modulated RNA recruitment, while RNAs were frequently recruited together with their encoded proteins. In PBs, RNAs follow distinct fates: in small liquid-like PBs, RNAs get degraded while in more solid-like larger ones, they are stored. PB properties can be regulated by the actin-polymerizing SCAR (suppressor of the cyclic AMP)-WAVE (WASP family verprolin homologous) complex. SCAR/WAVE modulates the shuttling of RNAs between PBs and the translational machinery, thereby adjusting ethylene signaling. In summary, we provide an approach to identify RNAs in condensates that allowed us to reveal a mechanism for regulating RNA fate.
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Affiliation(s)
- Chen Liu
- Department of Biology, University of Crete, Heraklion 70013, Greece
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden
| | - Andriani Mentzelopoulou
- Department of Biology, University of Crete, Heraklion 70013, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion 70013, Greece
| | - Ioannis H Hatzianestis
- Department of Biology, University of Crete, Heraklion 70013, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion 70013, Greece
| | | | - Vasileios Skaltsogiannis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion 70013, Greece
| | - Xuemin Ma
- Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), Umeå, Sweden
| | - Vassiliki A Michalopoulou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion 70013, Greece
| | - Francisco J Romero-Campero
- Department of Computer Science and Artificial Intelligence, Universidad de Sevilla, Avenida Reina Mercedes s/n, Seville 41012, Spain
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla and Consejo Superior de Investigaciones Científicas (CSIC), Seville, Spain
| | - Ana B Romero-Losada
- Department of Computer Science and Artificial Intelligence, Universidad de Sevilla, Avenida Reina Mercedes s/n, Seville 41012, Spain
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla and Consejo Superior de Investigaciones Científicas (CSIC), Seville, Spain
| | - Panagiotis F Sarris
- Department of Biology, University of Crete, Heraklion 70013, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion 70013, Greece
- Biosciences, University of Exeter, Exeter, UK
| | - Peter Marhavy
- Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), Umeå, Sweden
| | - Bettina Bölter
- Ludwig Maximilians University Munich, Plant Biochemistry, Großhadernerstr. 2-4, Planegg-Martinsried 82152, Germany
| | - Alexandros Kanterakis
- Institute of Computer Science, Foundation for Research and Technology-Hellas, Heraklion, Greece
| | - Emilio Gutierrez-Beltran
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla and Consejo Superior de Investigaciones Científicas (CSIC), Seville, Spain
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
| | - Panagiotis N Moschou
- Department of Biology, University of Crete, Heraklion 70013, Greece
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion 70013, Greece
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9
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Ramakrishnan M, Rajan KS, Mullasseri S, Ahmad Z, Zhou M, Sharma A, Ramasamy S, Wei Q. Exploring N6-methyladenosine (m 6A) modification in tree species: opportunities and challenges. HORTICULTURE RESEARCH 2024; 11:uhad284. [PMID: 38371641 PMCID: PMC10871907 DOI: 10.1093/hr/uhad284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 12/17/2023] [Indexed: 02/20/2024]
Abstract
N 6-methyladenosine (m6A) in eukaryotes is the most common and widespread internal modification in mRNA. The modification regulates mRNA stability, translation efficiency, and splicing, thereby fine-tuning gene regulation. In plants, m6A is dynamic and critical for various growth stages, embryonic development, morphogenesis, flowering, stress response, crop yield, and biomass. Although recent high-throughput sequencing approaches have enabled the rapid identification of m6A modification sites, the site-specific mechanism of this modification remains unclear in trees. In this review, we discuss the functional significance of m6A in trees under different stress conditions and discuss recent advancements in the quantification of m6A. Quantitative and functional insights into the dynamic aspect of m6A modification could assist researchers in engineering tree crops for better productivity and resistance to various stress conditions.
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Affiliation(s)
- Muthusamy Ramakrishnan
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing 210037, Jiangsu, China
| | - K Shanmugha Rajan
- Department of Chemical and Structural Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Sileesh Mullasseri
- Department of Zoology, St. Albert’s College (Autonomous), Kochi 682018, Kerala, India
| | - Zishan Ahmad
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing 210037, Jiangsu, China
| | - Mingbing Zhou
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Lin’an, Hangzhou 311300, Zhejiang, China
- Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Zhejiang A&F University, Lin’an, Hangzhou 311300, Zhejiang, China
| | - Anket Sharma
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Lin’an, Hangzhou 311300, Zhejiang, China
| | - Subbiah Ramasamy
- Cardiac Metabolic Disease Laboratory, Department of Biochemistry, School of Biological Sciences, Madurai Kamaraj University, Madurai 625 021, Tamilnadu, India
| | - Qiang Wei
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing 210037, Jiangsu, China
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10
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Chen Y, Li P, Lin M, Jiang Y, Tan G, Huang L, Song D. Silencing of METTL3 prevents the proliferation, migration, epithelial-mesenchymal transition, and renal fibrosis of high glucose-induced HK2 cells by mediating WISP1 in m6A-dependent manner. Aging (Albany NY) 2024; 16:1237-1248. [PMID: 38289593 PMCID: PMC10866449 DOI: 10.18632/aging.205401] [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: 08/19/2023] [Accepted: 11/13/2023] [Indexed: 02/06/2024]
Abstract
Diabetic nephropathy (DN) is one of the most serious complications in diabetic patients. And m6A modifications mediated by METTL3 are involved multiple biological processes. However, the specific function and mechanism of METTL3 in DN remains unclear. DN model mice were first established with streptozotocin, and WISP1 expression was confirmed by qRT-PCR. Then the influences of WISP1 or/and METTL3 on the proliferation, migration, and epithelial-mesenchymal transition (EMT) and fibrosis-related proteins of high glucose (HG)-induced HK2 cells or HK2 cells were tested through CCK-8, wound healing, and western blot. We first revealed that WISP1 was highly expressed in renal tissues of DN model mice and HG-induced HK2 cells. Functionally, WISP1 or METTL3 silencing could weaken the proliferation, migration, EMT, and fibrosis of HG-treated HK2 cells, and WISP1 or METTL3 overexpression could induce the proliferation, migration, EMT, and fibrosis of HK2 cells. Additionally, METTL3 silencing could decrease WISP1 m6A modification, and silencing of METTL3 also could notably suppress the biological functions of HG-induced HK2 cells by downregulating WISP1. Silencing of METTL3 prevents DN development process by decreasing WISP1 with m6A modification pattern. Therefore, we suggest that METTL3/WISP1 axis might be a novel therapeutic target for DN.
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Affiliation(s)
- Yuanzhen Chen
- Department of Nephrology, Shenzhen Guangming District People’s Hospital, Guangming, Shenzhen 518000, China
| | - Ping Li
- Department of Nephrology, Shenzhen Guangming District People’s Hospital, Guangming, Shenzhen 518000, China
| | - Mei Lin
- Department of Nephrology, Shenzhen Guangming District People’s Hospital, Guangming, Shenzhen 518000, China
| | - Ying Jiang
- Department of Nephrology, Shenzhen Guangming District People’s Hospital, Guangming, Shenzhen 518000, China
| | - Guiping Tan
- Department of Nephrology, Shenzhen Guangming District People’s Hospital, Guangming, Shenzhen 518000, China
| | - Lianfang Huang
- Department of Nephrology, Shenzhen Guangming District People’s Hospital, Guangming, Shenzhen 518000, China
| | - Dan Song
- Department of Nephrology, Shenzhen Guangming District People’s Hospital, Guangming, Shenzhen 518000, China
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11
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Liang L, Wang X, Lan H, Wei S, Lei Y, Zhang S, Zhai H, Hu Y, Lv Y. Comprehensive analysis of aflatoxin B 1 biosynthesis in Aspergillus flavus via transcriptome-wide m 6A methylome response to cycloleucine. JOURNAL OF HAZARDOUS MATERIALS 2024; 461:132677. [PMID: 37797576 DOI: 10.1016/j.jhazmat.2023.132677] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/22/2023] [Accepted: 09/28/2023] [Indexed: 10/07/2023]
Abstract
Aspergillus flavus and its toxic aflatoxins secondary metabolites contaminate food and grains, posing a severe threat to human health and leading to liver cancer. Here, we demonstrated that cycloleucine blocked aflatoxin B1 synthesis by inhibiting N6-methyladenosine (m6A) methylation modification of messenger RNA (mRNA). m6A Methylation Immunoprecipitation Sequencing (m6A MeRIP-Seq)-based comprehensive transcriptome-wide m6A profiling identified 102 differentially expressed genes that underwent m6A modification, of which 22 hypermethylated genes were downregulated and 49 hypomethylated genes were upregulated, suggesting a negative correlation between m6A methylation and gene expression. Notably, cycloleucine inhibited aflatoxin B1 production via multiple targets. The m6A sites of several key genes involved in the aflatoxin B1 biosynthesis pathway were significantly enriched in the coding sequence and around the stop codon, resulting in their downregulation. Furthermore, m6A methylation on genes related to the aflatoxin B1 biosynthesis pathway led to reduced mRNA stability. Cycloleucine inhibition of aflatoxin B1 production highlights its potential as an agent for removing mycotoxins in environmental pollution. ENVIRONMENTAL IMPLICATION: Aflatoxins, highly carcinogenic secondary metabolites produced by Aspergillus flavus, frequently contaminate crops such as peanut, corn, wheat and sesame leading to irreversible loss in the quality and yield of agricultural products and posing serious threats to food safety. Aflatoxins has also been linked to developmental delays and liver cancer in humans. In our study, 'monitoring aflatoxin concentrations and its bioaccumulation in organisms' has been conducted. The results demonstrated that aflatoxin production in A. flavus was completely blocked after cycloleucine treatment. Additionally, we demonstrated that inhibition of aflatoxin was linked to N6-methyladenosine methylation of multiple genes in aflatoxin biosynthesis pathway.
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Affiliation(s)
- Liuke Liang
- College of biological engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Xiaoyan Wang
- College of biological engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Haier Lan
- College of biological engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Shan Wei
- College of biological engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Yang Lei
- College of biological engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Shuaibing Zhang
- College of biological engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Huanchen Zhai
- College of biological engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Yuansen Hu
- College of biological engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Yangyong Lv
- College of biological engineering, Henan University of Technology, Zhengzhou 450001, China.
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12
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Fan S, Xu X, Chen J, Yin Y, Zhao Y. Genome-wide identification, characterization, and expression analysis of m6A readers-YTH domain-containing genes in alfalfa. BMC Genomics 2024; 25:18. [PMID: 38166738 PMCID: PMC10759653 DOI: 10.1186/s12864-023-09926-w] [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: 09/04/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024] Open
Abstract
Eukaryotic messenger RNAs (mRNAs) are often modified with methyl groups at the N6 position of adenosine (m6A), and these changes are interpreted by YTH domain-containing proteins to regulate the metabolism of m6A-modified mRNAs. Although alfalfa (Medicago sativa) is an established model organism for forage development, the understanding of YTH proteins in alfalfa is still limited. In the present investigation, 53 putative YTH genes, each encoding a YT521 domain-containing protein, were identified within the alfalfa genome. These genes were categorized into two subfamilies: YTHDF (49 members) and YTHDC (four members). Each subfamily demonstrates analogous motif distributions and domain architectures. Specifically, proteins encoded by MsYTHDF genes incorporate a single domain structure, while those corresponding to MsYTH5, 8, 12, 16 who are identified as members of the MsYTHDC subfamily, exhibit CCCH-type zinc finger repeats at their N-termini. It is also observed that the predicted aromatic cage pocket that binds the m6A residue of MsYTHDC consists of a sequence of two tryptophan residues and one tyrosine residue (WWY). Conversely, in MsYTHDF, the binding pocket comprises two highly conserved tryptophan residues and either one tryptophan residue (WWW) or tyrosine residue (WWY) in MsYTHDF.Through comparative analysis of qRT-PCR data, we observed distinct expression patterns in specific genes under abiotic stress, indicating their potential regulatory roles. Notably, five genes (MsYTH2, 14, 26, 27, 48) consistently exhibit upregulation, and two genes (MsYTH33, 35) are downregulated in response to both cold and salt stress. This suggests a common mechanism among these YTH proteins in response to various abiotic stressors in alfalfa. Further, integrating qRT-PCR with RNA-seq data revealed that MsYTH2, MsYTH14, and MsYTH16 are highly expressed in leaves at various development stages, underscoring their potential roles in regulating the growth of these plant parts. The obtained findings shed further light on the biological functions of MsYTH genes and may aid in the selection of suitable candidate genes for future genetic enhancement endeavors aimed at improving salt and cold tolerance in alfalfa.
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Affiliation(s)
- Shugao Fan
- School of Resources and Environmental Engineering, Ludong University, Yantai, China
| | - Xiao Xu
- School of Resources and Environmental Engineering, Ludong University, Yantai, China
| | - Jianmin Chen
- School of Resources and Environmental Engineering, Ludong University, Yantai, China
| | - Yanling Yin
- School of Resources and Environmental Engineering, Ludong University, Yantai, China.
| | - Ying Zhao
- School of Resources and Environmental Engineering, Ludong University, Yantai, China.
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13
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Xie Y, Chan LY, Cheung MY, Li MW, Lam HM. Current technical advancements in plant epitranscriptomic studies. THE PLANT GENOME 2023; 16:e20316. [PMID: 36890704 DOI: 10.1002/tpg2.20316] [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: 12/14/2022] [Accepted: 02/05/2023] [Indexed: 06/18/2023]
Abstract
The growth and development of plants are the result of the interplay between the internal developmental programming and plant-environment interactions. Gene expression regulations in plants are made up of multi-level networks. In the past few years, many studies were carried out on co- and post-transcriptional RNA modifications, which, together with the RNA community, are collectively known as the "epitranscriptome." The epitranscriptomic machineries were identified and their functional impacts characterized in a broad range of physiological processes in diverse plant species. There is mounting evidence to suggest that the epitranscriptome provides an additional layer in the gene regulatory network for plant development and stress responses. In the present review, we summarized the epitranscriptomic modifications found so far in plants, including chemical modifications, RNA editing, and transcript isoforms. The various approaches to RNA modification detection were described, with special emphasis on the recent development and application potential of third-generation sequencing. The roles of epitranscriptomic changes in gene regulation during plant-environment interactions were discussed in case studies. This review aims to highlight the importance of epitranscriptomics in the study of gene regulatory networks in plants and to encourage multi-omics investigations using the recent technical advancements.
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Affiliation(s)
- Yichun Xie
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Long-Yiu Chan
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Ming-Yan Cheung
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Man-Wah Li
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Hon-Ming Lam
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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14
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Prall W, Sheikh AH, Bazin J, Bigeard J, Almeida-Trapp M, Crespi M, Hirt H, Gregory BD. Pathogen-induced m6A dynamics affect plant immunity. THE PLANT CELL 2023; 35:4155-4172. [PMID: 37610247 PMCID: PMC10615206 DOI: 10.1093/plcell/koad224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 08/24/2023]
Abstract
Posttranscriptional regulation of mRNA mediated by methylation at the N6 position of adenine (N6-methyladenosine [m6A]) has profound effects on transcriptome regulation in plants. Focused studies across eukaryotes offer glimpses into the processes governed by m6A throughout developmental and disease states. However, we lack an understanding of the dynamics and the regulatory potential of m6A during biotic stress in plants. Here, we provide a comprehensive look into the effects of m6A on both the short-term and long-term responses to pathogen signaling in Arabidopsis (Arabidopsis thaliana). We demonstrate that m6A-deficient plants are more resistant to bacterial and fungal pathogen infections and have altered immune responses. Furthermore, m6A deposition is specifically coordinated on transcripts involved in defense and immunity prior to and proceeding the pathogen signal flagellin. Consequently, the dynamic modulation of m6A on specific stress-responsive transcripts is correlated with changes in abundance and cleavage of these transcripts. Overall, we show that the m6A methylome is regulated prior to and during simulated and active pathogen stress and functions in the coordination and balancing of normal growth and pathogen responses.
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Affiliation(s)
- Wil Prall
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104,USA
| | - Arsheed H Sheikh
- Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal 23955-6900,Saudi Arabia
| | - Jeremie Bazin
- CNRS, INRA, Institute of Plant Sciences Paris-Saclay IPS2, Universite Paris Sud, Universite Evry, Universite Paris-Diderot, Sorbonne Paris-Cite, Universite Paris-Saclay, 91190 Gif-sur-Yvette,France
| | - Jean Bigeard
- CNRS, INRA, Institute of Plant Sciences Paris-Saclay IPS2, Universite Paris Sud, Universite Evry, Universite Paris-Diderot, Sorbonne Paris-Cite, Universite Paris-Saclay, 91190 Gif-sur-Yvette,France
| | - Marilia Almeida-Trapp
- Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal 23955-6900,Saudi Arabia
| | - Martin Crespi
- CNRS, INRA, Institute of Plant Sciences Paris-Saclay IPS2, Universite Paris Sud, Universite Evry, Universite Paris-Diderot, Sorbonne Paris-Cite, Universite Paris-Saclay, 91190 Gif-sur-Yvette,France
| | - Heribert Hirt
- Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal 23955-6900,Saudi Arabia
- Max F. Perutz Laboratories, University of Vienna, 1030 Vienna,Austria
| | - Brian D Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104,USA
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15
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Yao S, Zhang J, Cheng X, Wang D, Yu W, Ji K, Yu Q. Genome-Wide Identification and Characterization of the YTH Domain-Containing RNA-Binding Protein Family in Liriodendron chinense. Int J Mol Sci 2023; 24:15189. [PMID: 37894868 PMCID: PMC10606907 DOI: 10.3390/ijms242015189] [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: 08/31/2023] [Revised: 10/03/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023] Open
Abstract
N6-methyladenosine (m6A) is becoming one of the most important RNA modifications in plant growth and development, including defense, cell differentiation, and secondary metabolism. YT521-B homology (YTH) domain-containing RNA-binding proteins, identified as m6A readers in epitranscriptomics, could affect the fate of m6A-containing RNA by recognizing and binding the m6A site. Therefore, the identification and study of the YTH gene family in Liriodendron chinense (L. chinense) can provide a molecular basis for the study of the role of m6A in L. chinense, but studies on the YTH gene in L. chinense have not been reported. We identified nine putative YTH gene models in the L. chinense genome, which can be divided into DF subgroups and DC subgroups. Domain sequence analysis showed that the LcYTH protein had high sequence conservation. A LcYTH aromatic cage bag is composed of tryptophan and tryptophan (WWW). PrLDs were found in the protein results of YTH, suggesting that these genes may be involved in the process of liquid-liquid phase separation. LcYTH genes have different tissue expression patterns, but the expression of LcYTHDF2 is absolutely dominant in all tissues. In addition, the expression of the LcYTH genes is changed in response to ABA and MeJA. In this study, We identified and analyzed the expression pattern of LcYTH genes. Our results laid a foundation for further study of the function of the LcYTH gene and further genetic and functional analyses of m6A RNA modification in forest trees.
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Affiliation(s)
- Sheng Yao
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; (S.Y.); (J.Z.); (X.C.); (D.W.); (W.Y.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland, Nanjing Forestry University, 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.); (J.Z.); (X.C.); (D.W.); (W.Y.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland, Nanjing Forestry University, 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.); (J.Z.); (X.C.); (D.W.); (W.Y.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland, Nanjing Forestry University, 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.); (J.Z.); (X.C.); (D.W.); (W.Y.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland, Nanjing Forestry University, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Wenya Yu
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; (S.Y.); (J.Z.); (X.C.); (D.W.); (W.Y.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland, Nanjing Forestry University, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Kongshu Ji
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; (S.Y.); (J.Z.); (X.C.); (D.W.); (W.Y.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland, Nanjing Forestry University, 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.); (J.Z.); (X.C.); (D.W.); (W.Y.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland, Nanjing Forestry University, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
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16
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Dai Z, Asgari S. ALKBH8 as a potential N 6 -methyladenosine (m 6 A) eraser in insects. INSECT MOLECULAR BIOLOGY 2023; 32:461-468. [PMID: 37119026 DOI: 10.1111/imb.12843] [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: 11/10/2022] [Accepted: 04/13/2023] [Indexed: 06/19/2023]
Abstract
The N6 -methyladenosine (m6 A) machinery functions through three groups of proteins in eukaryotic cells, including m6 A writers, erasers and readers. The m6 A cellular machinery has mostly been characterised in mammalian species, and the relevant literature on insects is currently scant. While homologues of m6 A writers and readers have been reported from insects, no erasers have been described so far. Here, using BLAST search, we searched for potential erasers in insects. While we found homologues of human m6 A eraser ALKBH5 in termites, beetles and true bugs, they could not be found in representative dipteran and lepidopteran species. However, a potential m6 A eraser, ALKBH8, was identified and experimentally investigated. Our results showed that ALKBH8 can reduce the m6 A levels of Aedes aegypti and Drosophila melanogaster RNAs, suggesting that AeALKBH8 could be a candidate m6 A eraser in insects.
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Affiliation(s)
- Zhenkai Dai
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Sassan Asgari
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
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17
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Ao Q, Qiu T, Liao F, Hu Z, Yang Y. Knockout of SlYTH2, encoding a YTH domain-containing protein, caused plant dwarfing, delayed fruit internal ripening, and increased seed abortion rate in tomato. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 335:111807. [PMID: 37479087 DOI: 10.1016/j.plantsci.2023.111807] [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: 06/04/2023] [Revised: 07/13/2023] [Accepted: 07/18/2023] [Indexed: 07/23/2023]
Abstract
The m6A is one of the most abundant and widespread modifications in eukaryotic mRNAs, which regulates gene expression at the post-transcriptional level and plays key roles in many physiological processes. The YT521-B homologous (YTH) domain-containing proteins act as m6A readers to regulate m6A-RNA metabolism processes and mediate the various functions of m6A modification. Previously, we reported tomato contains 9 YTH genes, among which SlYTH2 is relatively highly expressed. This study reports the physiological functions of SlYTH2 in tomato. SlYTH2 protein is distributed in the nucleus and cytoplasm, and its three-dimensional structure is highly similar to human HsYTHDF1. SlYTH2 knockout through Crispr/Cas9 gene editing technology leaded to pleiotropic phenotypes, including dwarfing plant, delayed fruit internal ripening process, and increased seed abortion rate. The deletion of SlYTH2 gene increased the accumulation of endogenous ABA, decreased the content of endogenous GA3, and enhanced the sensitivity of seed germination to exogenous ABA and seedling growth to exogenous GA3. RNA-Seq data showed that the expression levels of multiple hormone-related genes were altered in SlYTH2 knockout line. These facts suggested SlYTH2 plays its physiological roles related to ABA, gibberellin and other hormones in tomato.
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Affiliation(s)
- Qiujing Ao
- Bioengineering College, Chongqing University, Chongqing 400044, China
| | - Tiaoshuang Qiu
- Bioengineering College, Chongqing University, Chongqing 400044, China
| | - Feng Liao
- Bioengineering College, Chongqing University, Chongqing 400044, China
| | - Zichao Hu
- Bioengineering College, Chongqing University, Chongqing 400044, China
| | - Yingwu Yang
- Bioengineering College, Chongqing University, Chongqing 400044, China.
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18
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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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Hu J, Xue C, Wang Q. N 6-methyladenosine modification: an important player in the tumor immune microenvironment. Biomed Pharmacother 2023; 165:115171. [PMID: 37494788 DOI: 10.1016/j.biopha.2023.115171] [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: 06/04/2023] [Revised: 07/05/2023] [Accepted: 07/12/2023] [Indexed: 07/28/2023] Open
Abstract
The decoration of RNA with N6-methyladenosine (m6A) is a reversible post-transcriptional modification that plays an important regulatory role in all eukaryotic life activities. The m6A modification of RNA regulates the development and progression of tumors, including bladder cancer, melanoma, Lewis lung carcinoma, and hepatocellular carcinoma. The tumor immune microenvironment (TIME) includes immune cells, cytokines, and cell surface molecules, which interact with each other and ultimately determine the flow of tumor immunity. The onset of cancer implies that the TIME has been reshaped into a pro-tumor state. The key to cancer treatment lies in reshaping the TIME to reset the anti-tumor immune response. Here, we have reviewed how RNA m6A modification affects the TIME, and discussed the merits of using m6A regulator inhibitors as an individual treatment strategy as well as in combination with immune checkpoint blockade therapy.
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Affiliation(s)
- Jiaxiang Hu
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou 310058, China; Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China; The Key Laboratory for Immunity and Inflammatory Diseases of Zhejiang Province, Hangzhou 310058, China
| | - Chen Xue
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Qingqing Wang
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou 310058, China; Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China; The Key Laboratory for Immunity and Inflammatory Diseases of Zhejiang Province, Hangzhou 310058, China.
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20
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Chen G, Ren D, Wang Y, Wang H, Zhang J, Yang S. YTHDF2 negatively correlates with tumor immune infiltration in small cell lung cancer. J Mol Histol 2023; 54:365-377. [PMID: 37357252 DOI: 10.1007/s10735-023-10129-6] [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: 12/08/2022] [Accepted: 05/18/2023] [Indexed: 06/27/2023]
Abstract
In recent times, RNA modifications have garnered increased attention due to their involvement in the onset and progression of tumors, with N6-methyladenosine (m6A) modification being the most prevalent form. YTHDF2 is an m6A reading protein that can modulate RNA stability, transcription, and translation. This study aimed to explore the role of YTHDF2 in small cell lung cancer (SCLC) by collecting 20 SCLC patients from our hospital (cohort 1) and 48 Chinese SCLC patients from the GEO database (cohort 2). We evaluated the prognostic value of YTHDF2 using Kaplan-Meier survival analysis, Log-rank test, and Cox regression analysis. Additionally, we employed Gene Set Enrichment Analysis (GSEA) to screen different signaling pathways. We also investigated the correlation between the expression of m6A-related genes and SCLC molecular subtype and tumor immune microenvironment (TIME). Furthermore, we utilized multiplex immunofluorescence (mIF) staining to validate the immune infiltration of SCLC patient tissue sections. Our study revealed that YTHDF2 is an independent prognostic factor, which high expression is associated with low overall survival rate in SCLC. Low expression of YTHDF2 in SCLC tumors may enhance the molecular subtype transition from neuroendocrine (NE) to non-neuroendocrine (non-NE) subtype. Low YTHDF2 expression was closely associated with high immune infiltration, immune checkpoints, and other immune-related molecular features. Additionally, mIF detection showed a correlation between the low expression of YTHDF2 and CD4 + T cells and CD8 + T cells. Taken together, YTHDF2 could serve as a potential prognostic biomarker negatively correlated with tumor immune infiltration in SCLC.
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Affiliation(s)
- Gang Chen
- Department of Esophageal Mediastinal and Lymphatic Oncology (Chemoradiotherapy), Zhongnan Hospital of Wuhan University, Wuhan, Hubei, P.R. China
| | - Dandan Ren
- Genecast Biotechnology Co., Ltd, Wuxi, Jiangsu, P.R. China
| | - Yuanhan Wang
- Department of Thoracic Surgery, The Affiliated Cancer Hospital of Guizhou Medical University, Guiyang, Guizhou, P.R. China
| | - Hui Wang
- Department of Thoracic and Cardiovascular Surgery, The Second Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, P.R. China
| | - Junhong Zhang
- Department of Pulmonary Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, P.R. China.
| | - Song Yang
- Department of Thoracic Surgery, The Affiliated Cancer Hospital of Guizhou Medical University, Guiyang, Guizhou, P.R. China.
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21
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Guo T, Yang Z, Bao R, Fu X, Wang N, Liu C, Ma F. The m 6A reader MhYTP2 regulates the stability of its target mRNAs contributing to low nitrogen tolerance in apple ( Malus domestica). HORTICULTURE RESEARCH 2023; 10:uhad094. [PMID: 37350799 PMCID: PMC10282597 DOI: 10.1093/hr/uhad094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 04/26/2023] [Indexed: 06/24/2023]
Abstract
Studies have shown that the m6A reader primarily affects genes expression by participating in the regulation of mRNA localization, splicing, degradation, translation, and other metabolic processes. Previously, we discovered that the apple (Malus domestica) m6A reader MhYTP2 bound with and destabilized m6A-modified MdMLO19 mRNA. In addition, it enhanced the translation efficiency of m6A-modified mRNA of MdGDH1L, encoding a glutamate dehydrogenase, which confers resistance to powdery mildew. In this study, we report the function of MhYTP2 in the regulation of resistance to low nitrogen (N). The overexpression of MhYTP2 enhances the resistance of apple to low N. We show that MhYTP2 binds with and stabilizes the mRNAs of MdALN, which participates in the allantoin catabolic process and cellular response to N starvation in apple; MdPIDL, which participates in root hair elongation; MdTTG1, which is involved in the differentiation process of trichomes; and MdATG8A, which is a core participant in the regulation of autophagy. In addition, MhYTP2 accelerates the degradation of MdRHD3 mRNA, which regulates root development. RNA immunoprecipitation-seq and electrophoretic mobility shift assays show that the mRNAs of MdALN, MdATG8A, MdPIDL, MdTTG1, and MdRHD3 are the direct targets of MhYTP2. Overexpressing or knocking down the above genes in MhYTP2 overexpressing plants dismisses the function of MhYTP2 under low N, suggesting the role of MhYTP2 is dependent on those genes. Together, these results demonstrate that MhYTP2 enhances the resistance of apple to N deficiency by affecting the stability of the bound mRNAs.
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Affiliation(s)
- Tianli Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zehua Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ru Bao
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaomin Fu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Na Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
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22
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Manavella PA, Godoy Herz MA, Kornblihtt AR, Sorenson R, Sieburth LE, Nakaminami K, Seki M, Ding Y, Sun Q, Kang H, Ariel FD, Crespi M, Giudicatti AJ, Cai Q, Jin H, Feng X, Qi Y, Pikaard CS. Beyond transcription: compelling open questions in plant RNA biology. THE PLANT CELL 2023; 35:1626-1653. [PMID: 36477566 PMCID: PMC10226580 DOI: 10.1093/plcell/koac346] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/14/2022] [Accepted: 12/06/2022] [Indexed: 05/30/2023]
Abstract
The study of RNAs has become one of the most influential research fields in contemporary biology and biomedicine. In the last few years, new sequencing technologies have produced an explosion of new and exciting discoveries in the field but have also given rise to many open questions. Defining these questions, together with old, long-standing gaps in our knowledge, is the spirit of this article. The breadth of topics within RNA biology research is vast, and every aspect of the biology of these molecules contains countless exciting open questions. Here, we asked 12 groups to discuss their most compelling question among some plant RNA biology topics. The following vignettes cover RNA alternative splicing; RNA dynamics; RNA translation; RNA structures; R-loops; epitranscriptomics; long non-coding RNAs; small RNA production and their functions in crops; small RNAs during gametogenesis and in cross-kingdom RNA interference; and RNA-directed DNA methylation. In each section, we will present the current state-of-the-art in plant RNA biology research before asking the questions that will surely motivate future discoveries in the field. We hope this article will spark a debate about the future perspective on RNA biology and provoke novel reflections in the reader.
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Affiliation(s)
- Pablo A Manavella
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe 3000, Argentina
| | - Micaela A Godoy Herz
- Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Universidad de Buenos Aires (UBA), Buenos Aires C1428EHA, Argentina
| | - Alberto R Kornblihtt
- Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Universidad de Buenos Aires (UBA), Buenos Aires C1428EHA, Argentina
| | - Reed Sorenson
- School of Biological Sciences, University of UtahSalt Lake City 84112, USA
| | - Leslie E Sieburth
- School of Biological Sciences, University of UtahSalt Lake City 84112, USA
| | - Kentaro Nakaminami
- Center for Sustainable Resource Science, RIKEN, Kanagawa 230-0045, Japan
| | - Motoaki Seki
- Center for Sustainable Resource Science, RIKEN, Kanagawa 230-0045, Japan
- Cluster for Pioneering Research, RIKEN, Saitama 351-0198, Japan
- Kihara Institute for Biological Research, Yokohama City University, Kanagawa 244-0813, Japan
| | - Yiliang Ding
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Qianwen Sun
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Hunseung Kang
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea
| | - Federico D Ariel
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe 3000, Argentina
| | - Martin Crespi
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Evry, Université Paris-Saclay, Bâtiment 630, Orsay 91405, France
- Institute of Plant Sciences Paris-Saclay IPS2, Université de Paris, Bâtiment 630, Orsay 91405, France
| | - Axel J Giudicatti
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe 3000, Argentina
| | - Qiang Cai
- State Key Laboratory of Hybrid Rice, College of Life Science, Wuhan University, Wuhan 430072, China
| | - Hailing Jin
- Department of Microbiology and Plant Pathology and Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, California 92507, USA
| | - Xiaoqi Feng
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Yijun Qi
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Craig S Pikaard
- Howard Hughes Medical Institute, Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA
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23
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Mateos JL, Staiger D. Toward a systems view on RNA-binding proteins and associated RNAs in plants: Guilt by association. THE PLANT CELL 2023; 35:1708-1726. [PMID: 36461946 PMCID: PMC10226577 DOI: 10.1093/plcell/koac345] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/08/2022] [Accepted: 11/17/2022] [Indexed: 05/30/2023]
Abstract
RNA-binding proteins (RBPs) have a broad impact on most biochemical, physiological, and developmental processes in a plant's life. RBPs engage in an on-off relationship with their RNA partners, accompanying virtually every stage in RNA processing and function. While the function of a plethora of RBPs in plant development and stress responses has been described, we are lacking a systems-level understanding of components in RNA-based regulation. Novel techniques have substantially enlarged the compendium of proteins with experimental evidence for binding to RNAs in the cell, the RNA-binding proteome. Furthermore, ribonomics methods have been adapted for use in plants to profile the in vivo binding repertoire of RBPs genome-wide. Here, we discuss how recent technological achievements have provided novel insights into the mode of action of plant RBPs at a genome-wide scale. Furthermore, we touch upon two emerging topics, the connection of RBPs to phase separation in the cell and to extracellular RNAs. Finally, we define open questions to be addressed to move toward an integrated understanding of RBP function.
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Affiliation(s)
- Julieta L Mateos
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-CONICET-UBA), Buenos Aires, Argentina
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Dorothee Staiger
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
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24
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Tian MQ, Li J, Shu XM, Lang CH, Chen J, Peng LY, Lei WT, Yang CJ. The increase of Nrf2 m6A modification induced by FTO downregulation promotes hippocampal neuron injury and aggravates the progression of epilepsy in a rat model. Synapse 2023; 77:e22270. [PMID: 37122072 DOI: 10.1002/syn.22270] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 02/02/2023] [Accepted: 03/27/2023] [Indexed: 05/02/2023]
Abstract
Epilepsy is a common chronic neurological disorder characterized by widespread neuronal death. The purpose of this study was to investigate the role of nuclear factor erythroid 2-related factor 2 (Nrf2) m6A methylation in epilepsy. To create epileptic models, the rats were given Lithium chloride and pilocarpine, and isolated primary rat hippocampal neurons were cultured in an Mg2+ -free medium. The frequency of seizures was recorded in the epilepsy group of rats. The functional tests included TUNEL, MTT, and flow cytometry. Mechanistically, RNA degradation assay, RNA immunoprecipitation, and methylated RNA immunoprecipitation were performed. In epileptic models, Nrf2 and fat mass and obesity-associated (FTO) levels were downregulated, whereas YT521-B homology (YTH) domain family protein 2 (YTHDF2) was upregulated. Additionally, in epileptic models, there was a rise in the m6A methylation level of Nrf2 mRNA. Overexpressing FTO increased cell viability and reduced apoptosis, but Nrf2 interference reversed these effects. Meanwhile, FTO overexpression decreased the m6A methylation of Nrf2 mRNA. Moreover, YTHDF2 bound to Nrf2 mRNA and decreased its stability. Furthermore, FTO overexpression reduced seizure frequency in rats and inhibited hippocampal neuron apoptosis via lowering the m6A methylation level of Nrf2 mRNA. Overexpressing FTO reduced m6A methylation of Nrf2 mRNA, increased cell viability, suppressed apoptosis, and slowed the progression of epileptic diseases, which is linked to YTHDF2 binding to m6A-modified Nrf2 and promoting its degradation, as well as downregulating Nrf2 expression in hippocampal neurons.
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Affiliation(s)
- Mao-Qiang Tian
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Department of Pediatrics, Guizhou Children's Hospital, Zunyi, China
| | - Juan Li
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Department of Pediatrics, Guizhou Children's Hospital, Zunyi, China
| | - Xiao-Mei Shu
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Department of Pediatrics, Guizhou Children's Hospital, Zunyi, China
| | - Chang-Hui Lang
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Department of Pediatrics, Guizhou Children's Hospital, Zunyi, China
| | - Jing Chen
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Department of Pediatrics, Guizhou Children's Hospital, Zunyi, China
| | - Long-Ying Peng
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Department of Pediatrics, Guizhou Children's Hospital, Zunyi, China
| | - Wen-Ting Lei
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Department of Pediatrics, Guizhou Children's Hospital, Zunyi, China
| | - Chang-Jian Yang
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Department of Pediatrics, Guizhou Children's Hospital, Zunyi, China
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25
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Tang J, Zhang J, Lu Y, He J, Wang H, Liu B, Tu C, Li Z. Novel insights into the multifaceted roles of m 6A-modified LncRNAs in cancers: biological functions and therapeutic applications. Biomark Res 2023; 11:42. [PMID: 37069649 PMCID: PMC10111779 DOI: 10.1186/s40364-023-00484-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 04/11/2023] [Indexed: 04/19/2023] Open
Abstract
N6-methyladenosine (m6A) is considered as the most common and important internal transcript modification in several diseases like type 2 diabetes, schizophrenia and especially cancer. As a main target of m6A methylation, long non-coding RNAs (lncRNAs) have been proved to regulate cellular processes at various levels, including epigenetic modification, transcriptional, post-transcriptional, translational and post-translational regulation. Recently, accumulating evidence suggests that m6A-modified lncRNAs greatly participate in the tumorigenesis of cancers. In this review, we systematically summarized the biogenesis of m6A-modified lncRNAs and the identified m6A-lncRNAs in a variety of cancers, as well as their potential diagnostic and therapeutic applications as biomarkers and therapeutic targets, hoping to shed light on the novel strategies for cancer treatment.
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Affiliation(s)
- Jinxin Tang
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
- Xiangya School of Medicine, Central South University, Changsha, Hunan, 410011, China
| | - Jinhui Zhang
- Xiangya School of Medicine, Central South University, Changsha, Hunan, 410011, China
| | - Yu Lu
- Xiangya School of Medicine, Central South University, Changsha, Hunan, 410011, China
| | - Jieyu He
- Department of Geriatrics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Hua Wang
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
- Xiangya School of Medicine, Central South University, Changsha, Hunan, 410011, China
| | - Binfeng Liu
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Chao Tu
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China.
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China.
| | - Zhihong Li
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China.
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China.
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26
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Pierroz G. 2D or not 2D: how mRNA methylation regulates the transition to 3-dimensional growth in Physcomitrium patens. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:5-6. [PMID: 36974889 DOI: 10.1111/tpj.16173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
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27
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Liu L, Liang L, Li H, Shao W, Yang C, Lin F, Liu J, Zhang J. The role of m6A-mediated PD-1/PD-L1 in antitumor immunity. Biochem Pharmacol 2023; 210:115460. [PMID: 36822438 DOI: 10.1016/j.bcp.2023.115460] [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: 12/18/2022] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 02/25/2023]
Abstract
N6-methyladenosine (m6A) is the most prevalent, abundant and conserved type of internal posttranscriptional RNA modification in eukaryotic cells. Emerging evidence suggests that m6A modifications perform important functions that affect antitumor immunity. Programmed death 1 (PD-1) and programmed cell death-ligand 1 (PD-L1) are the two most well-studied immune checkpoint pathways. The interaction of PD-L1 with its receptor PD-1 inhibits cytotoxic T-cell-mediated tumor responses, and blockade of this interaction has proven to be an effective immunotherapy strategy in various cancers. Unfortunately, few cancer patients benefit from the two tools due to uncertain resistance. m6A plays an important role in affecting RNA biogenesis and process in various cancers. Understanding the molecular mechanism of drug resistance will promote the development of personalized clinical management. In this review, we systematically discussed the mechanisms by which m6A regulates PD-1 and PD-L1 expression and further their functions in the process of tumor immunotherapy and the potential application prospects of m6A-associated molecules. Moreover, mounting m6Ascore is established to evaluate the prognosis of cancer.
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Affiliation(s)
- Li Liu
- The First Affiliated Hospital, Department of Clinical Laboratory Medicine, Institution of Microbiology and Infectious Diseases, Hengyang Medical School, University of South China, Hengyang, 421001 Hunan, China
| | - Long Liang
- Hunan Province Key Laboratory of Basic and Applied Hematology, Molecular Biology Research Center & Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, 410078 Hunan, China
| | - Hui Li
- Hunan Province Key Laboratory of Basic and Applied Hematology, Molecular Biology Research Center & Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, 410078 Hunan, China; Department of Dermatology, Hunan Key Laboratory of Skin Cancer and Psoriasis, Hunan Engineering Research Center of Skin Health and Disease, Xiangya Clinical Research Center for Cancer Immunotherapy, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Wenjun Shao
- The First Affiliated Hospital, Department of Clinical Laboratory Medicine, Institution of Microbiology and Infectious Diseases, Hengyang Medical School, University of South China, Hengyang, 421001 Hunan, China
| | - Chaoying Yang
- Hunan Province Key Laboratory of Basic and Applied Hematology, Molecular Biology Research Center & Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, 410078 Hunan, China
| | - Feng Lin
- Department of Urology Surgery, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, 518033 Guangdong, China.
| | - Jing Liu
- Department of Dermatology, Hunan Key Laboratory of Skin Cancer and Psoriasis, Hunan Engineering Research Center of Skin Health and Disease, Xiangya Clinical Research Center for Cancer Immunotherapy, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.
| | - Ji Zhang
- The First Affiliated Hospital, Department of Clinical Laboratory Medicine, Institution of Microbiology and Infectious Diseases, Hengyang Medical School, University of South China, Hengyang, 421001 Hunan, China; The Affiliated Nanhua Hospital, Department of Clinical Laboratory, Hengyang Medical School, University of South China, Hengyang, 421002 Hunan, China.
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28
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Chuong NN, Doan PPT, Wang L, Kim JH, Kim J. Current Insights into m 6A RNA Methylation and Its Emerging Role in Plant Circadian Clock. PLANTS (BASEL, SWITZERLAND) 2023; 12:624. [PMID: 36771711 PMCID: PMC9920239 DOI: 10.3390/plants12030624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/24/2023] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
N6-adenosine methylation (m6A) is a prevalent form of RNA modification found in the expressed transcripts of many eukaryotic organisms. Moreover, m6A methylation is a dynamic and reversible process that requires the functioning of various proteins and their complexes that are evolutionarily conserved between species and include methylases, demethylases, and m6A-binding proteins. Over the past decade, the m6A methylation process in plants has been extensively studied and the understanding thereof has drastically increased, although the regulatory function of some components relies on information derived from animal systems. Notably, m6A has been found to be involved in a variety of factors in RNA processing, such as RNA stability, alternative polyadenylation, and miRNA regulation. The circadian clock in plants is a molecular timekeeping system that regulates the daily and rhythmic activity of many cellular and physiological processes in response to environmental changes such as the day-night cycle. The circadian clock regulates the rhythmic expression of genes through post-transcriptional regulation of mRNA. Recently, m6A methylation has emerged as an additional layer of post-transcriptional regulation that is necessary for the proper functioning of the plant circadian clock. In this review, we have compiled and summarized recent insights into the molecular mechanisms behind m6A modification and its various roles in the regulation of RNA. We discuss the potential role of m6A modification in regulating the plant circadian clock and outline potential future directions for the study of mRNA methylation in plants. A deeper understanding of the mechanism of m6A RNA regulation and its role in plant circadian clocks will contribute to a greater understanding of the plant circadian clock.
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Affiliation(s)
- Nguyen Nguyen Chuong
- Interdisciplinary Graduate Program in Advanced Convergence Technology & Science, Jeju National University, Jeju 690756, Republic of Korea
| | - Phan Phuong Thao Doan
- Interdisciplinary Graduate Program in Advanced Convergence Technology & Science, Jeju National University, Jeju 690756, Republic of Korea
| | - Lanshuo Wang
- Interdisciplinary Graduate Program in Advanced Convergence Technology & Science, Jeju National University, Jeju 690756, Republic of Korea
| | - Jin Hee Kim
- Subtropical Horticulture Research Institute, Jeju National University, Jeju 690756, Republic of Korea
| | - Jeongsik Kim
- Interdisciplinary Graduate Program in Advanced Convergence Technology & Science, Jeju National University, Jeju 690756, Republic of Korea
- Subtropical Horticulture Research Institute, Jeju National University, Jeju 690756, Republic of Korea
- Faculty of Science Education, Jeju National University, Jeju 690756, Republic of Korea
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Abstract
Cardiovascular disease (CVD) is the major cause of disability-adjusted life years (DALY) and death globally. The most common internal modification of mRNA is N6-adenosylate methylation (m6A). Recently, a growing number of studies have been devoted to researching cardiac remodeling mechanisms, especially m6A RNA methylation, revealing a connection between m6A and cardiovascular diseases. This review summarized the current understanding regarding m6A and elucidated the dynamic modifications of writers, erasers, and readers. Furthermore, we highlighted m6A RNA methylation related to cardiac remodeling and summarized its potential mechanisms. Finally, we discussed the potential of m6A RNA methylation in the treatment of cardiac remodeling.
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Rudy E, Grabsztunowicz M, Arasimowicz-Jelonek M, Tanwar UK, Maciorowska J, Sobieszczuk-Nowicka E. N 6-methyladenosine (m 6A) RNA modification as a metabolic switch between plant cell survival and death in leaf senescence. FRONTIERS IN PLANT SCIENCE 2023; 13:1064131. [PMID: 36684776 PMCID: PMC9846058 DOI: 10.3389/fpls.2022.1064131] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Crop losses caused by climate change and various (a)biotic stressors negatively affect agriculture and crop production. Therefore, it is vital to develop a proper understanding of the complex response(s) to (a)biotic stresses and delineate them for each crop plant as a means to enable translational research. In plants, the improvement of crop quality by m6A editing is believed to be a promising strategy. As a reaction to environmental changes, m6A modification showed a high degree of sensitivity and complexity. We investigated differences in gene medleys between dark-induced leaf senescence (DILS) and developmental leaf senescence in barley, including inter alia RNA modifications active in DILS. The identified upregulated genes in DILS include RNA methyltransferases of different RNA types, embracing enzymes modifying mRNA, tRNA, and rRNA. We have defined a decisive moment in the DILS model which determines the point of no return, but the mechanism of its control is yet to be uncovered. This indicates the possibility of an unknown additional switch between cell survival and cell death. Discoveries of m6A RNA modification changes in certain RNA species in different stages of leaf senescence may uncover the role of such modifications in metabolic reprogramming. Nonetheless, there is no such data about the process of leaf senescence in plants. In this scope, the prospect of finding connections between the process of senescence and m6A modification of RNA in plants seems to be compelling.
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Affiliation(s)
- Elżbieta Rudy
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, Poznań, Poland
| | - Magda Grabsztunowicz
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, Poznań, Poland
| | - Magdalena Arasimowicz-Jelonek
- Department of Plant Ecophysiology, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, Poznań, Poland
| | - Umesh Kumar Tanwar
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, Poznań, Poland
| | - Julia Maciorowska
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, Poznań, Poland
| | - Ewa Sobieszczuk-Nowicka
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, Poznań, Poland
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Tang L, Xue J, Ren X, Zhang Y, Du L, Ding F, Zhou K, Ma W. Genome-Wide Identification and Expression Analysis of m6A Writers, Erasers, and Readers in Litchi ( Litchi chinensis Sonn.). Genes (Basel) 2022; 13:genes13122284. [PMID: 36553551 PMCID: PMC9777543 DOI: 10.3390/genes13122284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/25/2022] [Accepted: 11/30/2022] [Indexed: 12/07/2022] Open
Abstract
N6-methyladenosine (m6A) RNA modification is the most prevalent type of RNA methylation and plays a pivotal role in the development of plants. However, knowledge of the m6A modification in litchi remains limited. In this study, a complete analysis of m6A writers, erasers, and readers in litchi was performed and 31 litchi m6A regulatory genes were identified in total, including 7 m6A writers, 12 m6A erases, and 12 readers. Phylogeny analysis showed that all three of the kinds of litchi m6A regulatory proteins could be divided into three groups; domains and motifs exhibited similar patterns in the same group. MiRNA target site prediction showed that 77 miRNA target sites were located in 25 (80.6%) litchi m6A regulatory genes. Cis-elements analysis exhibited that litchi m6A regulatory genes were mainly responsive to light and plant hormones, followed by environmental stress and plant development. Expression analysis revealed litchi m6A regulatory genes might play an important role during the peel coloration and fruit abscission of litchi. This study provided valuable and expectable information of litchi m6A regulatory genes and their potential epigenetic regulation mechanism in litchi.
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Affiliation(s)
- Liwen Tang
- Sanya Nanfan Research Institute of Hainan University, Sanya 572025, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Horticulture College, School of Horticulture, Haikou 570228, China
| | - Jiali Xue
- Sanya Nanfan Research Institute of Hainan University, Sanya 572025, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Horticulture College, School of Horticulture, Haikou 570228, China
| | - Xingyu Ren
- Sanya Nanfan Research Institute of Hainan University, Sanya 572025, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Horticulture College, School of Horticulture, Haikou 570228, China
| | - Yue Zhang
- Sanya Nanfan Research Institute of Hainan University, Sanya 572025, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Horticulture College, School of Horticulture, Haikou 570228, China
| | - Liqing Du
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture & Rural Affairs, South Subtropical Crops Research Institute of Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China
| | - Feng Ding
- Guangxi Crop Genetic Improvement and Biotechnology Key Laboratory, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Kaibing Zhou
- Sanya Nanfan Research Institute of Hainan University, Sanya 572025, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Horticulture College, School of Horticulture, Haikou 570228, China
| | - Wuqiang Ma
- Sanya Nanfan Research Institute of Hainan University, Sanya 572025, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Horticulture College, School of Horticulture, Haikou 570228, China
- Correspondence: ; Tel.: +86-158-1331-3342
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Zhang X, Li MJ, Xia L, Zhang H. The biological function of m6A methyltransferase KIAA1429 and its role in human disease. PeerJ 2022; 10:e14334. [PMID: 36389416 PMCID: PMC9657180 DOI: 10.7717/peerj.14334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/12/2022] [Indexed: 11/11/2022] Open
Abstract
KIAA1429 is a major m6A methyltransferase, which plays important biological and pharmacological roles in both human cancer or non-cancer diseases. KIAA1429 produce a tumorigenic role in various cancers through regulating DAPK3, ID2, GATA3, SMC1A, CDK1, SIRT1 and other targets, promoting cell proliferation, migration, invasion, metastasis and tumor growth . At the same time, KIAA1429 is also effective in non-tumor diseases, such as reproductive system and cardiovascular system diseases. The potential regulatory mechanism of KIAA1429 dependent on m6A modification is related to mRNA, lncRNA, circRNA and miRNAs. In this review, we summarized the current evidence on KIAA1429 in various human cancers or non-cancer diseases and its potential as a prognostic target.
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Affiliation(s)
- Xiaoyu Zhang
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Meng jiao Li
- Liaocheng Vocational and Technical College, Liaocheng, China
| | - Lei Xia
- Shandong University of Traditional Chinese Medicine, Department of Pathology, Jinan, China
| | - Hairong Zhang
- Shandong Provincial Third Hospital, Department of Obstetrics and Gynecology, Jinan, China
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Hunt AG. Review: Mechanisms underlying alternative polyadenylation in plants - looking in the right places. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 324:111430. [PMID: 36007628 DOI: 10.1016/j.plantsci.2022.111430] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 08/01/2022] [Accepted: 08/19/2022] [Indexed: 06/15/2023]
Abstract
Recent years have seen an explosion of interest in the subject of alternative polyadenylation in plants. Connections between the polyadenylation complex and numerous developmental and stress responses are well-established. However, those that link stimuli with the functioning of the polyadenylation complex are less well understood. To this end, it is imperative to clearly delineate the roles of the polyadenylation complex in both plant growth AND alternative polyadenylation. It is also necessary to understand the ways by which other molecular processes may contribute to alternative polyadenylation. This review discusses these issues, with a focus on instances that reveal mechanisms by which mRNA polyadenylation may be regulated. Insights from from characterizations of mutants affected in the polyadenylation complex are discussed, as are the limitations of such characterizations when it comes to teasing out cause and effect. These limitations encourage explorations to other processes that are beyond the core polyadenylation complex. Two such processes that sculpt the plant transcriptome - transcription termination and the epigenetic control of transposon activity - also contribute to regulated poly(A) site choice. These subjects define "the right places" - molecular mechanisms that contribute to the wide-ranging control of gene expression via mRNA polyadenylation.
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Affiliation(s)
- Arthur G Hunt
- Department of Plant and Soil Sciences, University of Kentucky, 301A Plant Science Building, 1405 Veterans Road, Lexington, KY 40546-0312, USA.
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Yin S, Ao Q, Qiu T, Tan C, Tu Y, Kuang T, Yang Y. Tomato SlYTH1 encoding a putative RNA m 6A reader affects plant growth and fruit shape. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 323:111417. [PMID: 35973580 DOI: 10.1016/j.plantsci.2022.111417] [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: 06/01/2022] [Revised: 08/08/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
N6-methyladenosine (m6A), the most abundant and common modification on eukaryotic mRNA, plays crucial roles in multiple biological processes through controlling endogenous gene activity in organisms. The m6A reader specifically recognizes the m6A mark to mediate the regulation of m6A on mRNA, and determines the fate of its target mRNA. In plants, the currently confirmed m6A readers are YTH (YT521B homology) domain-containing proteins. We previously reported that tomato contains 9 YTH genes, of which SlYTH1 has the strongest expression. The present study reports the functional characterization of SlYTH1 in tomato. SlYTH1 mutants generated via CRISPR/Cas9 technology exhibited pleiotropic phenotypes, including low seed germination rate, shortened seedling root, retarded plant growth and development during vegetative development, and elongated and longitudinally flattened fruit with reduced the locule number. SlYTH1 knockout reduced GA3 content and downregulated the expression of related genes in gibberellin biosynthesis pathway. Moreover, exogenous GA3 application could partially restore the phenotypic defects caused by SlYTH1 mutations. SlYTH1 knockout could alleviate the inhibition of seedling root elongation by exogenous GA3 application at relatively low concentration. These facts indicated SlYTH1 is involved in regulating gibberellin biosynthesis and plays important roles in multiple physiological processes in tomato.
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Affiliation(s)
- Shuangqin Yin
- Bioengineering College, Chongqing University, Chongqing 400044, China; State Key Laboratory of Trauma, Burns and Combined Injury, Department of Wound Infection and Drug, Daping Hospital, Army Medical University, Chongqing 400042, China
| | - Qiujing Ao
- Bioengineering College, Chongqing University, Chongqing 400044, China
| | - Tiaoshuang Qiu
- Bioengineering College, Chongqing University, Chongqing 400044, China
| | - Caiyun Tan
- Bioengineering College, Chongqing University, Chongqing 400044, China
| | - Yun Tu
- Bioengineering College, Chongqing University, Chongqing 400044, China
| | - Tianyin Kuang
- State Key Laboratory of Trauma, Burns and Combined Injury, Department of Wound Infection and Drug, Daping Hospital, Army Medical University, Chongqing 400042, China
| | - Yingwu Yang
- Bioengineering College, Chongqing University, Chongqing 400044, China.
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Tian M, Mao L, Zhang L. Crosstalk among N6-methyladenosine modification and RNAs in central nervous system injuries. Front Cell Neurosci 2022; 16:1013450. [PMID: 36246528 PMCID: PMC9556889 DOI: 10.3389/fncel.2022.1013450] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/09/2022] [Indexed: 11/13/2022] Open
Abstract
Central nervous system (CNS) injuries, including traumatic brain injury (TBI), intracerebral hemorrhage (ICH) and ischemic stroke, are the most common cause of death and disability around the world. As the most common modification on ribonucleic acids (RNAs), N6-methyladenosine (m6A) modification has recently attracted great attentions due to its functions in determining the fate of RNAs through changes in splicing, translation, degradation and stability. A large number of studies have suggested that m6A modification played an important role in brain development and involved in many neurological disorders, particularly in CNS injuries. It has been proposed that m6A modification could improve neurological impairment, inhibit apoptosis, suppress inflammation, reduce pyroptosis and attenuate ferroptosis in CNS injuries via different molecules including phosphatase and tensin homolog (PTEN), NLR family pyrin domain containing 3 (NLRP3), B-cell lymphoma 2 (Bcl-2), glutathione peroxidase 4 (GPX4), and long non-coding RNA (lncRNA). Therefore, m6A modification showed great promise as potential targets in CNS injuries. In this article, we present a review highlighting the role of m6A modification in CNS injuries. Hence, on the basis of these properties and effects, m6A modification may be developed as therapeutic agents for CNS injury patients.
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Affiliation(s)
- Mi Tian
- Department of Anesthesiology, Affiliated Zhongda Hospital of Southeast University, Nanjing, Jiangsu, China
| | - Lei Mao
- Department of Neurosurgery, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, Jiangsu, China
| | - Li Zhang
- Department of Neurosurgery, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, Jiangsu, China
- *Correspondence: Li Zhang,
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36
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Effects of N6-Methyladenosine Regulators on LAG3 and Immune Infiltrates in Lung Adenocarcinoma. DISEASE MARKERS 2022; 2022:1829528. [PMID: 36051357 PMCID: PMC9427291 DOI: 10.1155/2022/1829528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 06/30/2022] [Accepted: 07/19/2022] [Indexed: 11/17/2022]
Abstract
Background. Lung adenocarcinoma (LUAD) is the most common histological subtype of lung cancer, which is one of the most commonly diagnosed tumors and the leading causes of death from cancer around the world. Since RNA methylation is a posttranscriptional modification and affects so much biological progress, it is urged to explore the role of N6-methyladenosine (m6A) methylation in LUAD. Methods. We explored the expression of 24 m6A methylation genes, as well as their correlations with LAG3 in 561 LUAD samples from TCGA. Consensus clustering was applied to m6A methylation genes, and two LUAD subgroups were identified. The expression of m6A genes was analyzed by the Wilcoxon test. KEGG and GO enrichment analyses were performed to indicate the pathway affected by differentially expressed genes in the two groups. A prognostic model based on LASSO regression using an eleven-m6A gene signature was constructed according to the expression of these genes. Receiver operating characteristic (ROC) curve was used to confirm the accuracy of the model in the TCGA cohort, as well as in the test cohort from the Gene Expression Omnibus (GEO) database. Results. Compared to cluster 1, cluster 2 showed poorer overall survival (OS) and higher LAG3 expression. In addition, KEGG and GO enrichment analyses indicated that differentially expressed genes are enriched in the immune response. We also observed that the expression of LAG3 is positively correlated with IGF2BP2, CBLL1, and HNRNPA2B1 and negatively correlated with YTHDF2, YTHDF3, and FTO. For patients in the TCGA cohort, the AUC score is 0.7, and the AUC score for the GSE50081 cohort is 0.675. Patients with lower risk scores exhibited better overall survival and lower expression of LAG3 than patients with higher risk scores. Conclusions. In brief, our results indicated the important role of m6 methylation in affecting the tumor immune microenvironment and the survival of patients with LUAD. The m6A methylation gene signatures might serve as promising therapeutic targets and help the immunotherapy of LUAD in the future.
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37
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Dagan Y, Yesharim Y, Bonneau AR, Frankovits T, Schwartz S, Reddien PW, Wurtzel O. m6A is required for resolving progenitor identity during planarian stem cell differentiation. EMBO J 2022; 41:e109895. [PMID: 35971838 PMCID: PMC9627665 DOI: 10.15252/embj.2021109895] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 07/10/2022] [Accepted: 07/12/2022] [Indexed: 12/13/2022] Open
Abstract
Regeneration and tissue homeostasis require accurate production of missing cell lineages. Cell production is driven by changes to gene expression, which is shaped by multiple layers of regulation. Here, we find that the ubiquitous mRNA base-modification, m6A, is required for proper cell fate choice and cellular maturation in planarian stem cells (neoblasts). We mapped m6A-enriched regions in 7,600 planarian genes and found that perturbation of the m6A pathway resulted in progressive deterioration of tissues and death. Using single-cell RNA sequencing of >20,000 cells following perturbation of the m6A pathway, we identified an increase in expression of noncanonical histone variants, and that inhibition of the pathway resulted in accumulation of undifferentiated cells throughout the animal in an abnormal transcriptional state. Analysis of >1,000 planarian gene expression datasets revealed that the inhibition of the chromatin modifying complex NuRD had almost indistinguishable consequences, unraveling an unappreciated link between m6A and chromatin modifications. Our findings reveal that m6A is critical for planarian stem cell homeostasis and gene regulation in tissue maintenance and regeneration.
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Affiliation(s)
- Yael Dagan
- The George S. Wise Faculty of Life Sciences, School of Neurobiology, Biochemistry, and Biophysics, Tel Aviv University, Tel Aviv, Israel
| | - Yarden Yesharim
- The George S. Wise Faculty of Life Sciences, School of Neurobiology, Biochemistry, and Biophysics, Tel Aviv University, Tel Aviv, Israel
| | - Ashley R Bonneau
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Tamar Frankovits
- The George S. Wise Faculty of Life Sciences, School of Neurobiology, Biochemistry, and Biophysics, Tel Aviv University, Tel Aviv, Israel
| | - Schraga Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Peter W Reddien
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Omri Wurtzel
- The George S. Wise Faculty of Life Sciences, School of Neurobiology, Biochemistry, and Biophysics, Tel Aviv University, Tel Aviv, Israel.,Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
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Yang X, Patil S, Joshi S, Jamla M, Kumar V. Exploring epitranscriptomics for crop improvement and environmental stress tolerance. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 183:56-71. [PMID: 35567875 DOI: 10.1016/j.plaphy.2022.04.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/27/2022] [Accepted: 04/30/2022] [Indexed: 06/15/2023]
Abstract
Climate change and stressful environmental conditions severely hamper crop growth, development and yield. Plants respond to environmental perturbations, through their plasticity provided by key-genes, governed at post-/transcriptional levels. Gene-regulation in plants is a multilevel process controlled by diverse cellular entities that includes transcription factors (TF), epigenetic regulators and non-coding RNAs beside others. There are successful studies confirming the role of epigenetic modifications (DNA-methylation/histone-modifications) in gene expression. Recent years have witnessed emergence of a highly specialized field the "Epitranscriptomics". Epitranscriptomics deals with investigating post-transcriptional RNA chemical-modifications present across the life forms that change structural, functional and biological characters of RNA. However, deeper insights on of epitranscriptomic modifications, with >140 types known so far, are to be understood fully. Researchers have identified epitranscriptome marks (writers, erasers and readers) and mapped the site-specific RNA modifications (m6A, m5C, 3' uridylation, etc.) responsible for fine-tuning gene expression in plants. Simultaneous advancement in sequencing platforms, upgraded bioinformatic tools and pipelines along with conventional labelled techniques have further given a statistical picture of these epitranscriptomic modifications leading to their potential applicability in crop improvement and developing climate-smart crops. We present herein the insights on epitranscriptomic machinery in plants and how epitranscriptome and epitranscriptomic modifications underlying plant growth, development and environmental stress responses/adaptations. Third-generation sequencing technology, advanced bioinformatics tools and databases being used in plant epitranscriptomics are also discussed. Emphasis is given on potential exploration of epitranscriptome engineering for crop-improvement and developing environmental stress tolerant plants covering current status, challenges and future directions.
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Affiliation(s)
- Xiangbo Yang
- College of Agriculture, Jilin Agricultural Science and Technology University, Jilin, 132101, PR China.
| | - Suraj Patil
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Ganeshkhind, Pune, 411016, India
| | - Shrushti Joshi
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Ganeshkhind, Pune, 411016, India
| | - Monica Jamla
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Ganeshkhind, Pune, 411016, India
| | - Vinay Kumar
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Ganeshkhind, Pune, 411016, India.
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Immune Infiltration and N(6)-Methyladenosine ncRNA Isoform Detection in Acute Lung Injury. JOURNAL OF ONCOLOGY 2022; 2022:3922299. [PMID: 35813860 PMCID: PMC9262529 DOI: 10.1155/2022/3922299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 12/02/2022]
Abstract
Acute lung injury (ALI) is a severe form of sepsis that is associated with a high rate of morbidity and death in critically ill individuals. The emergence of ALI is the result of several factors at work. Case mortality rates might range from 40% to 70%. Researchers have discovered that epigenetic alterations are important in the pathophysiology of ALI and that using epigenetic inhibitors may help reduce symptoms. In embryonic development, circadian rhythm, the cell cycle, and cancer, methylation of m6A seems to be relevant all along the way. According to recent research, posttranscriptional methylation is a key player in the development of alveolar lymphoma. In this study, we clustered ALI based on m6A-related factors, analyzed different classes of immune cell enrichment and inflammatory cytokine expression, screened clustered differential genes for ALI to construct coexpression networks, screened key ALI genes potentially regulated by m6A modifications, and then typed the disease based on key genes to compare the consistency of different clustering results. Our findings have revealed a hitherto undiscovered prognostic sign and a therapeutic target for ALI therapy in m6A and immune invading cells, respectively.
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40
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Immune Infiltration of Ulcerative Colitis and Detection of the m6A Subtype. J Immunol Res 2022; 2022:7280977. [PMID: 35795532 PMCID: PMC9252851 DOI: 10.1155/2022/7280977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/09/2022] [Indexed: 11/17/2022] Open
Abstract
Ulcerative colitis (UC) is an inflammatory bowel disease characterized by persistent colon inflammation. N6-methyladenosine (m6A) methylation is one of the most prevalent RNA modifications with key roles in both normal and illness, but m6A methylation in ulcerative colitis is unknown. This research investigated m6A methylation in UC. We examined the expression of known m6A RNA methylation regulators in UC using the Gene Expression Omnibus database (GEO database). First, we used m6A regulators to examine m6A change in UC samples. These two patient groups were created by clustering three m6A gene expression datasets. These genes were then utilized to build an m6A gene network using WGCNA and PPI. These networks were built using differentially expressed genes. The 12 m6A regulators were found to be dispersed throughout the chromosome. The study’s data were then connected, revealing positive or negative relationships between genes or signaling pathways. Then, PCA of the 12 m6A-regulated genes indicated that the two patient groups could be discriminated in both PC1 and PC2 dimensions. The ssGSEA algorithm found that immune invading cells could be easily distinguished across diverse patient groups. Both groups had varied levels of popular cytokines. The differential gene analysis of the two samples yielded 517 genes like FTO and RFX7. It found 9 hub genes among 121 genes in the blue module, compared their expression in two groups of samples, and found that the differences in expression of these 9 genes were highly significant. The identification of 9 possible m6A methylation-dependent gene regulatory networks suggests that m6A methylation is involved in UC pathogenesis. Nine candidate genes have been identified as possible markers for assessing UC severity and developing innovative UC targeted therapeutic approaches.
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Zhang Y, Li T, Pan C, Khan IA, Chen Z, Yue Y, Yang M. Intergenerational toxic effects of parental exposure to bisphenol AF on offspring and epigenetic modulations in zebrafish. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 823:153714. [PMID: 35143790 DOI: 10.1016/j.scitotenv.2022.153714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/28/2022] [Accepted: 02/02/2022] [Indexed: 06/14/2023]
Abstract
Bisphenol AF (BPAF), an endocrine-disrupting chemical, has been detected in various environmental media because of its wide industrial applications. Meanwhile, substances that are known to be toxic to the reproductive system have been observed to interfere with the development of the offspring following parental exposure. This study was aimed at determining the gender-dependent intergenerational effects of BPAF on offspring development following either paternal or maternal exposure of adult zebrafish to an environmental concentration of BPAF. Four-month-old zebrafish (F0) were exposed to 10 μg/L of BPAF for 28 days, the developmental endpoints of F1 embryos were then tested without further treatment with BPAF. The results show that paternal BPAF exposure decreased the hatching rate, increased mortality, and shortened the body lengths of F1 larval offspring. In addition, it changed DNA and m6A RNA methylation gene expression levels in F0 testes and F1 larvae. Although maternal exposure increased mortality and enhanced antioxidant enzyme activities in F1 larvae, only DNA methylation gene expression was altered in F0 ovaries and F1 larvae. In addition, a short term BPAF exposure of zebrafish embryos from 4 h post-fertilization (hpf) until 120 hpf similarly impaired the early development of the larvae but only at a level relatively higher than 10 μg/L; and DNA and RNA methylation gene expression was regulated to some extent in BPAF exposure groups. Overall, our results indicate the gender-specific effects of BPAF on offspring development and epigenetic modulations, suggesting a relatively high susceptibility within the exposure window during gametogenesis and early embryonic developmental stages to environmental chemicals.
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Affiliation(s)
- Yuanyuan Zhang
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, China
| | - Tianjie Li
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, China
| | - Chenyuan Pan
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, China
| | - Imran Ahamed Khan
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, China
| | - Zhong Chen
- Department of Cardiology, the Affiliated Sixth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201306, China.
| | - Yihong Yue
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, China
| | - Ming Yang
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, China.
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Li W, Yu Y, Chen X, Fang Q, Yang A, Chen X, Wu L, Wang C, Wu D, Ye S, Wu D, Sun G. N6-Methyladenosine dynamic changes and differential methylation in wheat grain development. PLANTA 2022; 255:125. [PMID: 35567638 DOI: 10.1007/s00425-022-03893-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 04/02/2022] [Indexed: 06/15/2023]
Abstract
More methylation changes occur in late interval than in early interval of wheat seed development with protein and the starch synthesis-related pathway enriched in the later stages. Wheat seed development is a critical process to determining wheat yield and quality, which is controlled by genetics, epigenetics and environments. The N6-methyladenosine (m6A) modification is a reversible and dynamic process and plays regulatory role in plant development and stress responses. To better understand the role of m6A in wheat grain development, we characterized the m6A modification at 10 day post-anthesis (DPA), 20 DPA and 30 DPA in wheat grain development. m6A-seq identified 30,615, 30,326, 27,676 high confidence m6A peaks from the 10DPA, 20DPA, and 30DPA, respectively, and enriched at 3'UTR. There were 29,964, 29,542 and 26,834 unique peaks identified in AN0942_10d, AN0942_20d and AN0942_30d. One hundred and forty-two genes were methylated by m6A throughout seed development, 940 genes methylated in early grain development (AN0942_20d vs AN0942_10d), 1542 genes in late grain development (AN0942_30d vs AN0942_20d), and 1190 genes between early and late development stage (AN0942_30d vs AN0942_10d). KEGG enrichment analysis found that protein-related pathways and the starch synthesis-related pathway were significantly enriched in the later stages of seed development. Our results provide novel knowledge on m6A dynamic changes and its roles in wheat grain development.
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Affiliation(s)
- Wenxiang Li
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Yi Yu
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Xuanrong Chen
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Qian Fang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Anqi Yang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Xinyu Chen
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Lei Wu
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Chengyu Wang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China
- Key Laboratory of Wheat Biology and Genetic Improvement on South Yellow and Huai River Valley, Ministry of Agriculture, Hefei, 230036, China
| | - Dechuan Wu
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Sihong Ye
- Cotton Institute, Anhui Academy of Agricultural Sciences, Hefei, 230001, Anhui, China.
| | - Dexiang Wu
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China.
| | - Genlou Sun
- Biology Department, Saint Mary's University, Halifax, NS, B3H 3C3, Canada.
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Lei L, Li N, Yuan P, Liu D. A new risk model based on a 11-m 6A-related lncRNA signature for predicting prognosis and monitoring immunotherapy for gastric cancer. BMC Cancer 2022; 22:365. [PMID: 35382776 PMCID: PMC8981748 DOI: 10.1186/s12885-021-09062-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 11/22/2021] [Indexed: 12/16/2022] Open
Abstract
Objective N6-methyladenosine (m6A) mRNA modification triggers malignant behaviors of tumor cells and thereby drives malignant progression in gastric cancer (GC). However, data regarding the prognostic values of m6A RNA methylation-related long non-coding RNAs (lncRNAs) in GC are very limited in the literature. We aimed to investigate the prognostic potential of m6A-related lncRNAs in predicting prognosis and monitoring immunotherapy efficacy in GC patients. Methods Transcriptome and clinical data were obtained from GC biopsies from Cancer Genome Atlas (TCGA). M6A-related lncRNAs associated with GC were identified by constructing a co-expression network, and the gene pairs differentially expressed in GC were selected using univariate analysis. We constructed a risk model based on prognosis-related lncRNA pairs selected using the LASSO algorithm and quantified the best cutoff by comparing the area under the curve (AUC) for risk stratification. A risk model with the optimal discrimination between high- and low-risk GC patients was established. Its feasibility for overall survival prediction and discrimination of clinicopathological features, tumor-infiltrating immune cells, and biomarkers of immune checkpoint inhibitors between high- and low-risk groups were assessed. Results Finally, we identified 11 m6A-related lncRNA pairs associated with GC prognosis based on transcriptome analysis of 375 GC specimens and 32 normal tissues. A risk model was constructed with an AUC of 0.8790. We stratified GC patients into high- and low-risk groups at a cutoff of 1.442. As expected, patients in the low-risk group had longer overall survival versus the high-risk group. Infiltration of cancer-associated fibroblasts, endothelial cells, macrophages, particularly M2 macrophages, and monocytes was more severe in high-risk patients than low-risk individuals, who exhibited high CD4+ Th1 cell infiltration in GC. Altered expressions of immune-related genes were observed in both groups. PD-1 and LAG3 expressions were found higher in low-risk patients than high-risk patients. Immunotherapy, either single or combined use of PD-1 or CTLA4 inhibitors, had better efficacy in low-risk patients than high-risk patients. Conclusion The new risk model based on a 11-m6A-related lncRNA signature can serve as an independent predictor for GC prognosis prediction and may aid in the development of personalized immunotherapy strategies for patients. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-09062-2.
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Affiliation(s)
- Liangliang Lei
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, No.24 Jinghua Road, Jianxi District, Luoyang, 471003, China
| | - Nannan Li
- Department of Ultrasonography, The Sixth People's Hospital of Luoyang, Luoyang, 471003, China
| | - Pengfei Yuan
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, No.24 Jinghua Road, Jianxi District, Luoyang, 471003, China.
| | - Dechun Liu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, No.24 Jinghua Road, Jianxi District, Luoyang, 471003, China.
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Ponnu J, Hoecker U. Signaling Mechanisms by Arabidopsis Cryptochromes. FRONTIERS IN PLANT SCIENCE 2022; 13:844714. [PMID: 35295637 PMCID: PMC8918993 DOI: 10.3389/fpls.2022.844714] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 02/04/2022] [Indexed: 05/29/2023]
Abstract
Cryptochromes (CRYs) are blue light photoreceptors that regulate growth, development, and metabolism in plants. In Arabidopsis thaliana (Arabidopsis), CRY1 and CRY2 possess partially redundant and overlapping functions. Upon exposure to blue light, the monomeric inactive CRYs undergo phosphorylation and oligomerization, which are crucial to CRY function. Both the N- and C-terminal domains of CRYs participate in light-induced interaction with multiple signaling proteins. These include the COP1/SPA E3 ubiquitin ligase, several transcription factors, hormone signaling intermediates and proteins involved in chromatin-remodeling and RNA N6 adenosine methylation. In this review, we discuss the mechanisms of Arabidopsis CRY signaling in photomorphogenesis and the recent breakthroughs in Arabidopsis CRY research.
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Affiliation(s)
| | - Ute Hoecker
- *Correspondence: Ute Hoecker, , orcid.org/0000-0002-5636-9777
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Yue J, Wei Y, Zhao M. The Reversible Methylation of m6A Is Involved in Plant Virus Infection. BIOLOGY 2022; 11:biology11020271. [PMID: 35205137 PMCID: PMC8869485 DOI: 10.3390/biology11020271] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/20/2022] [Accepted: 02/06/2022] [Indexed: 02/01/2023]
Abstract
Simple Summary N6-methyladenosine (m6A) is the most prevalent modification in the mRNAs of many eukaryotic species. The abundance and effects of m6A are determined by dynamic interactions between its methyltransferases (“writers”), demethylases (“erasers”), and binding proteins (“readers”). It has been indicated that there is a strong correlation between m6A and virus infection in mammals. In the case of plant virus infection, it appears that m6A plays a dual role. On the one hand, m6A acts as a plant immune response induced by virus infection, inhibiting viral replication or translation through methylation of viral genome RNAs. On the other hand, m6A acts as part of an infection strategy employed by plant viruses to overcome the host immune system by interacting with m6A-related proteins. We proposed that antagonists of m6A-related proteins might be used to design new strategies for plant virus control in the future. Abstract In recent years, m6A RNA methylation has attracted broad interest and is becoming a hot research topic. It has been demonstrated that there is a strong association between m6A and viral infection in the human system. The life cycles of plant RNA viruses are often coordinated with the mechanisms of their RNA modification. Here, we reviewed recent advances in m6A methylation in plant viruses. It appears that m6A methylation plays a dual role during viral infection in plants. On the one hand, m6A methylation acts as an antiviral immune response induced by virus infection, which inhibits viral replication or translation through the methylation of viral genome RNAs. On the other hand, plant viruses could disrupt the m6A methylation through interacting with the key proteins of the m6A pathway to avoid modification. Those plant viruses containing ALKB domain are discussed as well. Based on this mechanism, we propose that new strategies for plant virus control could be designed with competitive antagonists of m6A-associated proteins.
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46
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Zhang M, Chen Y, Chen H, Shen Y, Pang L, Wu W, Yu Z. Tanshinone IIA alleviates cardiac hypertrophy through m6A modification of galectin-3. Bioengineered 2022; 13:4260-4270. [PMID: 35191812 PMCID: PMC8973617 DOI: 10.1080/21655979.2022.2031388] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Cardiac hypertrophy results from the adaptive response of the myocardium to pressure overload on the heart. Tanshinone IIA (Tan IIA) is the major active compound extracted from Salvia miltiorrhiza Bunge, which possesses various pharmacological benefits. In the present study, the effect and mechanism of action of Tan IIA on cardiac hypertrophy were studied. Ang II–induced and transverse aortic constriction (TAC)-induced cardiomyocyte hypertrophy models were used to evaluate the effect of Tan IIA. An adenoviral vector system was utilized to overexpress galectin-3. The results revealed that Tan IIA significantly inhibited Ang II–induced hypertrophy in vitro and TAC-induced cardiac hypertrophy in vivo. Furthermore, Tan IIA notably inhibited the expression of galectin-3. Rescue experiments indicated that galectin-3 overexpression reversed the effects of Tan IIA, which further validated the interaction between Tan IIA and galectin-3. Additionally, Tan IIA suppressed alkB homolog 5, RNA demethylase (ALKBH5)-mediated N6-methyladenosine (m6A) modification of galectin-3. In summary, the results of the present study indicated that Tan IIA attenuates cardiac hypertrophy by targeting galectin-3, suggesting that galectin-3 plays a critical role in cardiac hypertrophy and represents a new therapeutic target.
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Affiliation(s)
- Meiqi Zhang
- Department of Intensive Care Unit, Hangzhou Hospital of Traditional Chinese Medicine (Dingqiao District), Guangxing Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Yun Chen
- Department of Intensive Care Unit, Hangzhou Hospital of Traditional Chinese Medicine (Dingqiao District), Guangxing Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Huan Chen
- Department of Emergency Medicine, Zhejiang Provincial People' s Hospital (People's Hospital of Hangzhou Medical College), Hangzhou, Zhejiang, China
| | - Ye Shen
- Department of Emergency Medicine, Zhejiang Provincial People' s Hospital (People's Hospital of Hangzhou Medical College), Hangzhou, Zhejiang, China
| | - Lingxiao Pang
- Department of Emergency Medicine, Zhejiang Provincial People' s Hospital (People's Hospital of Hangzhou Medical College), Hangzhou, Zhejiang, China
| | - Weihua Wu
- Department of Intensive Care Unit, Hangzhou Hospital of Traditional Chinese Medicine (Dingqiao District), Guangxing Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Zhenfei Yu
- Department of Intensive Care Unit, Hangzhou Hospital of Traditional Chinese Medicine (Dingqiao District), Guangxing Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
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Li H, Xiao W, He Y, Wen Z, Cheng S, Zhang Y, Li Y. Novel Insights Into the Multifaceted Functions of RNA n 6-Methyladenosine Modification in Degenerative Musculoskeletal Diseases. Front Cell Dev Biol 2022; 9:766020. [PMID: 35024366 PMCID: PMC8743268 DOI: 10.3389/fcell.2021.766020] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 11/05/2021] [Indexed: 12/13/2022] Open
Abstract
N6-methyladenosine (m6A) is an important modification of eukaryotic mRNA. Since the first discovery of the corresponding demethylase and the subsequent identification of m6A as a dynamic modification, the function and mechanism of m6A in mammalian gene regulation have been extensively investigated. “Writer”, “eraser” and “reader” proteins are key proteins involved in the dynamic regulation of m6A modifications, through the anchoring, removal, and interpretation of m6A modifications, respectively. Remarkably, such dynamic modifications can regulate the progression of many diseases by affecting RNA splicing, translation, export and degradation. Emerging evidence has identified the relationship between m6A modifications and degenerative musculoskeletal diseases, such as osteoarthritis, osteoporosis, sarcopenia and degenerative spinal disorders. Here, we have comprehensively summarized the evidence of the pathogenesis of m6A modifications in degenerative musculoskeletal diseases. Moreover, the potential molecular mechanisms, regulatory functions and clinical implications of m6A modifications are thoroughly discussed. Our review may provide potential prospects for addressing key issues in further studies.
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Affiliation(s)
- Hengzhen Li
- Department of Orthopedics, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - WenFeng Xiao
- Department of Orthopedics, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Yuqiong He
- Department of Orthopedics, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Zeqin Wen
- Department of Clinical Medicine, Xiangya School of Medicine of Central South University, Changsha, China
| | - Siyuan Cheng
- Department of Clinical Medicine, Xiangya School of Medicine of Central South University, Changsha, China
| | - Yi Zhang
- Department of Orthopedics, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Yusheng Li
- Department of Orthopedics, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
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Yu G, Su Q, Chen Y, Wu L, Wu S, Li H. Epigenetics in neurodegenerative disorders induced by pesticides. Genes Environ 2021; 43:55. [PMID: 34893084 PMCID: PMC8662853 DOI: 10.1186/s41021-021-00224-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 10/21/2021] [Indexed: 12/15/2022] Open
Abstract
Neurodegenerative diseases are becoming major socio-economic burdens. However, most of them still have no effective treatment. Growing evidence indicates excess exposure to pesticides are involved in the development of various forms of neurodegenerative and neurological diseases through trigger epigenetic changes and inducing disruption of the epigenome. This review summaries studies on epigenetics alterations in nervous systems in relation to different kinds of pesticides, highlighting potential mechanism in the etiology, precision prevention and target therapy of various neurodegenerative diseases. In addition, the current gaps in research and future areas for study were also discussed.
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Affiliation(s)
- Guangxia Yu
- Fujian Key Lab of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, Fujian Province, China.,Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou, Fujian Province, China.,Key Lab of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou, Fujian Province, China
| | - Qianqian Su
- Fujian Key Lab of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, Fujian Province, China.,Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou, Fujian Province, China
| | - Yao Chen
- Fujian Key Lab of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, Fujian Province, China.,Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou, Fujian Province, China
| | - Lingyan Wu
- Fujian Key Lab of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, Fujian Province, China.,Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou, Fujian Province, China
| | - Siying Wu
- Fujian Key Lab of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, Fujian Province, China. .,Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou, Fujian Province, China.
| | - Huangyuan Li
- Fujian Key Lab of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, Fujian Province, China. .,Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou, Fujian Province, China. .,Key Lab of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou, Fujian Province, China.
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Zhang G, Lv Z, Diao S, Liu H, Duan A, He C, Zhang J. Unique features of the m 6A methylome and its response to drought stress in sea buckthorn ( Hippophae rhamnoides Linn.). RNA Biol 2021; 18:794-803. [PMID: 34806556 DOI: 10.1080/15476286.2021.1992996] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
In plants, recent studies have revealed that N6-methyladenosine (m6A) methylation of mRNA has potential regulatory functions of this mRNA modification in many biological processes. m6A methyltransferase, m6A demethylase and m6A-binding proteins can cause differential phenotypes, indicating that m6A may have critical roles in the plant. In this study, we depicted the m6A map of sea buckthorn (Hippophae rhamnoides Linn.) transcriptome. Similar to A. thaliana, m6A sites of sea buckthorn transcriptome is significantly enriched around the stop codon and within 3'-untranslated regions (3'UTR). Gene ontology analysis shows that the m6A modification genes are associated with metabolic biosynthesis. In addition, we identified 13,287 different m6A peaks (DMPs) between leaf under drought (TR) and control (CK) treatment. It reveals that m6A has a high level of conservation and has a positive correlation with mRNA abundance in plants. GO and KEGG enrichment results showed that DMP modification DEGs in TR were particularly associated with ABA biosynthesis. Interestingly, our results showed three m6A demethylase (HrALKBH10B, HrALKBH10C and HrALKBH10D) genes were significantly increased following drought stress, which indicated that it may contributed the decreased m6A levels. This exhaustive m6A map provides a basis and resource for the further functional study of mRNA m6A modification in abiotic stress.
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Affiliation(s)
- Guoyun Zhang
- State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Zhongrui Lv
- State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Songfeng Diao
- Non-timber Forestry Research and Development Center, Chinese Academy of Forestry & Key Laboratory of Non-timber Forest Germplasm Enhancement & Utilization of National Forestry and Grassland Administration, Zhengzhou, China
| | - Hong Liu
- State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Aiguo Duan
- State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Caiyun He
- State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Jianguo Zhang
- State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.,Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
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50
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Manavski N, Vicente A, Chi W, Meurer J. The Chloroplast Epitranscriptome: Factors, Sites, Regulation, and Detection Methods. Genes (Basel) 2021; 12:genes12081121. [PMID: 34440296 PMCID: PMC8394491 DOI: 10.3390/genes12081121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/20/2021] [Accepted: 07/22/2021] [Indexed: 12/24/2022] Open
Abstract
Modifications in nucleic acids are present in all three domains of life. More than 170 distinct chemical modifications have been reported in cellular RNAs to date. Collectively termed as epitranscriptome, these RNA modifications are often dynamic and involve distinct regulatory proteins that install, remove, and interpret these marks in a site-specific manner. Covalent nucleotide modifications-such as methylations at diverse positions in the bases, polyuridylation, and pseudouridylation and many others impact various events in the lifecycle of an RNA such as folding, localization, processing, stability, ribosome assembly, and translational processes and are thus crucial regulators of the RNA metabolism. In plants, the nuclear/cytoplasmic epitranscriptome plays important roles in a wide range of biological processes, such as organ development, viral infection, and physiological means. Notably, recent transcriptome-wide analyses have also revealed novel dynamic modifications not only in plant nuclear/cytoplasmic RNAs related to photosynthesis but especially in chloroplast mRNAs, suggesting important and hitherto undefined regulatory steps in plastid functions and gene expression. Here we report on the latest findings of known plastid RNA modifications and highlight their relevance for the post-transcriptional regulation of chloroplast gene expression and their role in controlling plant development, stress reactions, and acclimation processes.
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Affiliation(s)
- Nikolay Manavski
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, 82152 Planegg-Martinsried, Germany; (N.M.); (A.V.)
| | - Alexandre Vicente
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, 82152 Planegg-Martinsried, Germany; (N.M.); (A.V.)
| | - Wei Chi
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China;
| | - Jörg Meurer
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, 82152 Planegg-Martinsried, Germany; (N.M.); (A.V.)
- Correspondence: ; Tel.: +49-89-218074556
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