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Cai Z, Tang Q, Song P, Tian E, Yang J, Jia G. The m6A reader ECT8 is an abiotic stress sensor that accelerates mRNA decay in Arabidopsis. THE PLANT CELL 2024:koae149. [PMID: 38835286 DOI: 10.1093/plcell/koae149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/11/2024] [Indexed: 06/06/2024]
Abstract
N 6-methyladenosine (m6A) is the most abundant mRNA modification and plays diverse roles in eukaryotes, including plants. It regulates various processes, including plant growth, development, and responses to external or internal stress responses. However, the mechanisms underlying how m6A is related to environmental stresses in both mammals and plants remain elusive. Here, we identified EVOLUTIONARILY CONSERVED C-TERMINAL REGION 8 (ECT8) as an m6A reader protein and showed that its m6A-binding capability is required for salt stress responses in Arabidopsis (Arabidopsis thaliana). ECT8 accelerates the degradation of its target transcripts through direct interaction with the decapping protein DECAPPING 5 within processing bodies. We observed a significant increase in the ECT8 expression level under various environmental stresses. Using salt stress as a representative stressor, we found that the transcript and protein levels of ECT8 rise in response to salt stress. The increased abundance of ECT8 protein results in the enhanced binding capability to m6A-modified mRNAs, thereby accelerating their degradation, especially those of negative regulators of salt stress responses. Our results demonstrated that ECT8 acts as an abiotic stress sensor, facilitating mRNA decay, which is vital for maintaining transcriptome homeostasis and enhancing stress tolerance in plants. Our findings not only advance the understanding of epitranscriptomic gene regulation but also offer potential applications for breeding more resilient crops in the face of rapidly changing environmental conditions.
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Affiliation(s)
- Zhihe Cai
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Qian Tang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Peizhe Song
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Enlin Tian
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Junbo Yang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Guifang Jia
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- Beijing Advanced Center of RNA Biology, Peking University, Beijing 100871, China
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2
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Tang Y, Yang X, Huang A, Seong K, Ye M, Li M, Zhao Q, Krasileva K, Gu Y. Proxiome assembly of the plant nuclear pore reveals an essential hub for gene expression regulation. NATURE PLANTS 2024; 10:1005-1017. [PMID: 38773271 DOI: 10.1038/s41477-024-01698-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 04/11/2024] [Indexed: 05/23/2024]
Abstract
The nuclear pore complex (NPC) is vital for nucleocytoplasmic communication. Recent evidence emphasizes its extensive association with proteins of diverse functions, suggesting roles beyond cargo transport. Yet, our understanding of NPC's composition and functionality at this extended level remains limited. Here, through proximity-labelling proteomics, we uncover both local and global NPC-associated proteome in Arabidopsis, comprising over 500 unique proteins, predominantly associated with NPC's peripheral extension structures. Compositional analysis of these proteins revealed that the NPC concentrates chromatin remodellers, transcriptional regulators and mRNA processing machineries in the nucleoplasmic region while recruiting translation regulatory machinery on the cytoplasmic side, achieving a remarkable orchestration of the genetic information flow by coupling RNA transcription, maturation, transport and translation regulation. Further biochemical and structural modelling analyses reveal that extensive interactions with nucleoporins, along with phase separation mediated by substantial intrinsically disordered proteins, may drive the formation of the unexpectedly large nuclear pore proteome assembly.
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Affiliation(s)
- Yu Tang
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Institute of Advanced Agricultural Sciences, Peking University, Weifang, Shandong, China
| | - Xiangyun Yang
- Institute of Advanced Agricultural Sciences, Peking University, Weifang, Shandong, China
| | - Aobo Huang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Kyungyong Seong
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Mao Ye
- Institute of Advanced Agricultural Sciences, Peking University, Weifang, Shandong, China
| | - Mengting Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Qiao Zhao
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Ksenia Krasileva
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Yangnan Gu
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
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3
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Song P, Cai Z, Jia G. Principles, functions, and biological implications of m 6A in plants. RNA (NEW YORK, N.Y.) 2024; 30:491-499. [PMID: 38531642 PMCID: PMC11019739 DOI: 10.1261/rna.079951.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 02/09/2024] [Indexed: 03/28/2024]
Abstract
Over the past decade, N 6-methyladenosine (m6A) has emerged as a prevalent and dynamically regulated modification across the transcriptome; it has been reversibly installed, removed, and interpreted by specific binding proteins, and has played crucial roles in molecular and biological processes. Within this scope, we consolidate recent advancements of m6A research in plants regarding gene expression regulation, diverse physiologic and pathogenic processes, as well as crop trial implications, to guide discussions on challenges associated with and leveraging epitranscriptome editing for crop improvement.
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Affiliation(s)
- Peizhe Song
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Zhihe Cai
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Guifang Jia
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- PKU-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- Beijing Advanced Center of RNA Biology, Peking University, Beijing 100871, China
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4
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Ma C, Ma S, Yu Y, Feng H, Wang Y, Liu C, He S, Yang M, Chen Q, Xin D, Wang J. Transcriptome-wide m 6A methylation profiling identifies GmAMT1;1 as a promoter of lead and cadmium tolerance in soybean nodules. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133263. [PMID: 38118200 DOI: 10.1016/j.jhazmat.2023.133263] [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: 10/01/2023] [Revised: 12/01/2023] [Accepted: 12/12/2023] [Indexed: 12/22/2023]
Abstract
Lead (Pb) and cadmium (Cd) are common heavy metal pollutants that are often found in the soil in soybean agricultural production, adversely impacting symbiotic nitrogen fixation in soybean nodules. In this study, the exposure of soybean nodules to Pb and Cd stress was found to reduce nitrogenase activity. Shifts in the RNA methylation profiles of nodules were subsequently examined by profiling the differential expression of genes responsible for regulating m6A modifications and conducting transcriptome-wide analyses of m6A methylation profiles under Pb and Cd stress condition. Differentially methylated genes (DMGs) that were differentially expressed were closely related to reactive oxygen species activity and integral membrane components. Overall, 19 differentially expressed DMGs were ultimately determined to be responsive to both Pb and Cd stress, including Glyma.20G082450, which encodes GmAMT1;1 and was confirmed to be a positive regulator of nodules tolerance to Pb and Cd. Together, these results are the first published data corresponding to transcriptome-wide m6A methylation patterns in soybean nodules exposed to Cd and Pb stress, and provide novel molecular insight into the regulation of Pb and Cd stress responses in nodules, highlighting promising candidate genes related to heavy metal tolerance, that may also be amenable to application in agricultural production. ENVIRONMENTAL IMPLICATIONS: Lead (Pb) and cadmium (Cd) are prevalent heavy metal pollutants in soil, and pose a major threat to crop production, food security and human health. Here, MeRIP-seq approach was employed to analyze the regulatory network activated in soybean nodules under Pb and Cd stress, ultimately leading to the identification of 19 shared differentially expressed DMGs. When overexpressed, GmATM1;1 was found to enhance the Pb and Cd tolerance of soybean nodules. These results provide a theoretical basis for studies on tolerance to heavy metals in symbiotic nitrogen fixation, and provide an approach to enhancing Pb and Cd tolerance in soybean production.
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Affiliation(s)
- Chao Ma
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, People's Republic of China
| | - Shengnan Ma
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, People's Republic of China
| | - Yanyu Yu
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, People's Republic of China
| | - Haojie Feng
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, People's Republic of China
| | - Yue Wang
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, People's Republic of China
| | - Chunyan Liu
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, People's Republic of China
| | - Shanshan He
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, People's Republic of China
| | - Mingliang Yang
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, People's Republic of China
| | - Qingshan Chen
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, People's Republic of China
| | - Dawei Xin
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, People's Republic of China.
| | - Jinhui Wang
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, People's Republic of China.
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5
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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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Amara U, Hu J, Park SJ, Kang H. ECT12, an YTH-domain protein, is a potential mRNA m 6A reader that affects abiotic stress responses by modulating mRNA stability in Arabidopsis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108255. [PMID: 38071803 DOI: 10.1016/j.plaphy.2023.108255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 11/15/2023] [Accepted: 11/29/2023] [Indexed: 02/15/2024]
Abstract
N6-methyladenosine (m6A), the most abundant modification found in eukaryotic mRNAs, is interpreted by m6A "readers," thus playing a crucial role in regulating RNA metabolism. The YT521-B homology-domain (YTHD) proteins, also known as EVOLUTIONARILY CONSERVED C-TERMINAL REGION (ECT), are recognized as m6A reader proteins in plants and animals. Among the 13 potential YTHD family proteins in Arabidopsis thaliana, the functions of only a few members are known. In this study, we determined the function of ECT12 (YTH11) as a potential m6A reader that plays a crucial role in response to abiotic stresses. The loss-of-function ect12 mutants showed no noticeable developmental defects under normal conditions but displayed hypersensitivity to salt or dehydration stress. The salt- or dehydration-hypersensitive phenotypes were correlated with altered levels of several m6A-modified stress-responsive transcripts. Notably, the increased or decreased transcript levels were associated with each transcript's reduced or enhanced decay, respectively. Electrophoretic mobility shift and RNA-immunoprecipitation assays showed that ECT12 binds to m6A-modified RNAs both in vitro and in planta, suggesting its role as an m6A reader. Collectively, these results indicate that the potential m6A reader ECT12 regulates the stability of m6A-modified RNA transcripts, thereby facilitating the response of Arabidopsis to abiotic stresses.
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Affiliation(s)
- Umme Amara
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, South Korea
| | - Jianzhong Hu
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, South Korea
| | - Su Jung Park
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, South Korea
| | - Hunseung Kang
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, South Korea.
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7
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Due Tankmar M, Reichel M, Arribas-Hernández L, Brodersen P. A YTHDF-PABP interaction is required for m 6 A-mediated organogenesis in plants. EMBO Rep 2023; 24:e57741. [PMID: 38009565 DOI: 10.15252/embr.202357741] [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: 07/01/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/29/2023] Open
Abstract
N6-methyladenosine (m6 A) in mRNA is key to eukaryotic gene regulation. Many m6 A functions involve RNA-binding proteins that recognize m6 A via a YT521-B Homology (YTH) domain. YTH domain proteins contain long intrinsically disordered regions (IDRs) that may mediate phase separation and interaction with protein partners, but whose precise biochemical functions remain largely unknown. The Arabidopsis thaliana YTH domain proteins ECT2, ECT3, and ECT4 accelerate organogenesis through stimulation of cell division in organ primordia. Here, we use ECT2 to reveal molecular underpinnings of this function. We show that stimulation of leaf formation requires the long N-terminal IDR, and we identify two short IDR elements required for ECT2-mediated organogenesis. Of these two, a 19-amino acid region containing a tyrosine-rich motif conserved in both plant and metazoan YTHDF proteins is necessary for binding to the major cytoplasmic poly(A)-binding proteins PAB2, PAB4, and PAB8. Remarkably, overexpression of PAB4 in leaf primordia partially rescues the delayed leaf formation in ect2 ect3 ect4 mutants, suggesting that the ECT2-PAB2/4/8 interaction on target mRNAs of organogenesis-related genes may overcome limiting PAB concentrations in primordial cells.
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Affiliation(s)
| | - Marlene Reichel
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Peter Brodersen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
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8
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Flores-Téllez D, Tankmar MD, von Bülow S, Chen J, Lindorff-Larsen K, Brodersen P, Arribas-Hernández L. Insights into the conservation and diversification of the molecular functions of YTHDF proteins. PLoS Genet 2023; 19:e1010980. [PMID: 37816028 PMCID: PMC10617740 DOI: 10.1371/journal.pgen.1010980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 10/31/2023] [Accepted: 09/17/2023] [Indexed: 10/12/2023] Open
Abstract
YT521-B homology (YTH) domain proteins act as readers of N6-methyladenosine (m6A) in mRNA. Members of the YTHDF clade determine properties of m6A-containing mRNAs in the cytoplasm. Vertebrates encode three YTHDF proteins whose possible functional specialization is debated. In land plants, the YTHDF clade has expanded from one member in basal lineages to eleven so-called EVOLUTIONARILY CONSERVED C-TERMINAL REGION1-11 (ECT1-11) proteins in Arabidopsis thaliana, named after the conserved YTH domain placed behind a long N-terminal intrinsically disordered region (IDR). ECT2, ECT3 and ECT4 show genetic redundancy in stimulation of primed stem cell division, but the origin and implications of YTHDF expansion in higher plants are unknown, as it is unclear whether it involves acquisition of fundamentally different molecular properties, in particular of their divergent IDRs. Here, we use functional complementation of ect2/ect3/ect4 mutants to test whether different YTHDF proteins can perform the same function when similarly expressed in leaf primordia. We show that stimulation of primordial cell division relies on an ancestral molecular function of the m6A-YTHDF axis in land plants that is present in bryophytes and is conserved over YTHDF diversification, as it appears in all major clades of YTHDF proteins in flowering plants. Importantly, although our results indicate that the YTH domains of all arabidopsis ECT proteins have m6A-binding capacity, lineage-specific neo-functionalization of ECT1, ECT9 and ECT11 happened after late duplication events, and involves altered properties of both the YTH domains, and, especially, of the IDRs. We also identify two biophysical properties recurrent in IDRs of YTHDF proteins able to complement ect2 ect3 ect4 mutants, a clear phase separation propensity and a charge distribution that creates electric dipoles. Human and fly YTHDFs do not have IDRs with this combination of properties and cannot replace ECT2/3/4 function in arabidopsis, perhaps suggesting different molecular activities of YTHDF proteins between major taxa.
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Affiliation(s)
- Daniel Flores-Téllez
- University of Copenhagen, Biology Department. Copenhagen, Denmark
- Universidad Francisco de Vitoria, Facultad de Ciencias Experimentales. Pozuelo de Alarcón (Madrid), Spain
| | | | - Sören von Bülow
- University of Copenhagen, Biology Department. Copenhagen, Denmark
| | - Junyu Chen
- University of Copenhagen, Biology Department. Copenhagen, Denmark
| | | | - Peter Brodersen
- University of Copenhagen, Biology Department. Copenhagen, Denmark
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9
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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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10
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Martínez‐Pérez M, Aparicio F, Arribas‐Hernández L, Tankmar MD, Rennie S, von Bülow S, Lindorff‐Larsen K, Brodersen P, Pallas V. Plant YTHDF proteins are direct effectors of antiviral immunity against an N6-methyladenosine-containing RNA virus. EMBO J 2023; 42:e113378. [PMID: 37431920 PMCID: PMC10505913 DOI: 10.15252/embj.2022113378] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 05/31/2023] [Accepted: 06/15/2023] [Indexed: 07/12/2023] Open
Abstract
In virus-host interactions, nucleic acid-directed first lines of defense that allow viral clearance without compromising growth are of paramount importance. Plants use the RNA interference pathway as a basal antiviral immune system, but additional RNA-based mechanisms of defense also exist. The infectivity of a plant positive-strand RNA virus, alfalfa mosaic virus (AMV), relies on the demethylation of viral RNA by the recruitment of the cellular N6-methyladenosine (m6 A) demethylase ALKBH9B, but how demethylation of viral RNA promotes AMV infection remains unknown. Here, we show that inactivation of the Arabidopsis cytoplasmic YT521-B homology domain (YTH)-containing m6 A-binding proteins ECT2, ECT3, and ECT5 is sufficient to restore AMV infectivity in partially resistant alkbh9b mutants. We further show that the antiviral function of ECT2 is distinct from its previously demonstrated function in the promotion of primordial cell proliferation: an ect2 mutant carrying a small deletion in its intrinsically disordered region is partially compromised for antiviral defense but not for developmental functions. These results indicate that the m6 A-YTHDF axis constitutes a novel branch of basal antiviral immunity in plants.
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Affiliation(s)
- Mireya Martínez‐Pérez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones CientíficasUniversitat Politècnica de ValènciaValenciaSpain
| | - Frederic Aparicio
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones CientíficasUniversitat Politècnica de ValènciaValenciaSpain
| | | | | | - Sarah Rennie
- Department of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Sören von Bülow
- Department of BiologyUniversity of CopenhagenCopenhagenDenmark
| | | | - Peter Brodersen
- Department of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Vicente Pallas
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones CientíficasUniversitat Politècnica de ValènciaValenciaSpain
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11
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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: 2] [Impact Index Per Article: 2.0] [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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12
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Swale C, Hakimi MA. 3'-end mRNA processing within apicomplexan parasites, a patchwork of classic, and unexpected players. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1783. [PMID: 36994829 DOI: 10.1002/wrna.1783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 01/17/2023] [Accepted: 01/25/2023] [Indexed: 03/31/2023]
Abstract
The 3'-end processing of mRNA is a co-transcriptional process that leads to the formation of a poly-adenosine tail on the mRNA and directly controls termination of the RNA polymerase II juggernaut. This process involves a megadalton complex composed of cleavage and polyadenylation specificity factors (CPSFs) that are able to recognize cis-sequence elements on nascent mRNA to then carry out cleavage and polyadenylation reactions. Recent structural and biochemical studies have defined the roles played by different subunits of the complex and provided a comprehensive mechanistic understanding of this machinery in yeast or metazoans. More recently, the discovery of small molecule inhibitors of CPSF function in Apicomplexa has stimulated interest in studying the specificities of this ancient eukaryotic machinery in these organisms. Although its function is conserved in Apicomplexa, the CPSF complex integrates a novel reader of the N6-methyladenosine (m6A). This feature, inherited from the plant kingdom, bridges m6A metabolism directly to 3'-end processing and by extension, to transcription termination. In this review, we will examine convergence and divergence of CPSF within the apicomplexan parasites and explore the potential of small molecule inhibition of this machinery within these organisms. This article is categorized under: RNA Processing > 3' End Processing RNA Processing > RNA Editing and Modification.
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Affiliation(s)
- Christopher Swale
- Team Host-Pathogen Interactions and Immunity to Infection, Institute for Advanced Biosciences, INSERM U1209, CNRS UMR5309, Grenoble Alpes University, Grenoble, France
| | - Mohamed-Ali Hakimi
- Team Host-Pathogen Interactions and Immunity to Infection, Institute for Advanced Biosciences, INSERM U1209, CNRS UMR5309, Grenoble Alpes University, Grenoble, France
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13
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Wang S, Wang H, Xu Z, Jiang S, Shi Y, Xie H, Wang S, Hua J, Wu Y. m6A mRNA modification promotes chilling tolerance and modulates gene translation efficiency in Arabidopsis. PLANT PHYSIOLOGY 2023; 192:1466-1482. [PMID: 36810961 PMCID: PMC10231368 DOI: 10.1093/plphys/kiad112] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/14/2022] [Accepted: 01/20/2023] [Indexed: 05/16/2023]
Abstract
N 6-methyladenosine (m6A), the most prevalent mRNA modification in eukaryotes, is an emerging player of gene regulation at transcriptional and translational levels. Here, we explored the role of m6A modification in response to low temperature in Arabidopsis (Arabidopsis thaliana). Knocking down mRNA adenosine methylase A (MTA), a key component of the modification complex, by RNA interference (RNAi) led to drastically reduced growth at low temperature, indicating a critical role of m6A modification in the chilling response. Cold treatment reduced the overall m6A modification level of mRNAs especially at the 3' untranslated region. Joint analysis of the m6A methylome, transcriptome and translatome of the wild type (WT) and the MTA RNAi line revealed that m6A-containing mRNAs generally had higher abundance and translation efficiency than non-m6A-containing mRNAs under normal and low temperatures. In addition, reduction of m6A modification by MTA RNAi only moderately altered the gene expression response to low temperature but led to dysregulation of translation efficiencies of one third of the genes of the genome in response to cold. We tested the function of the m6A-modified cold-responsive gene ACYL-COA:DIACYLGLYCEROL ACYLTRANSFERASE 1 (DGAT1) whose translation efficiency but not transcript level was reduced in the chilling-susceptible MTA RNAi plant. The dgat1 loss-of-function mutant exhibited reduced growth under cold stress. These results reveal a critical role of m6A modification in regulating growth under low temperature and suggest an involvement of translational control in chilling responses in Arabidopsis.
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Affiliation(s)
- Shuai Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210000, Jiangsu, China
| | - Haiyan Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210000, Jiangsu, China
| | - Zhihui Xu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210000, Jiangsu, China
| | - Shasha Jiang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210000, Jiangsu, China
| | - Yucheng Shi
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210000, Jiangsu, China
| | - Hairong Xie
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210000, Jiangsu, China
| | - Shu Wang
- Gene Sequencing Center, Jiangbei New Area Biopharmaceutical Public Service Platform Co., Ltd., Nanjing 210000, Jiangsu, China
| | - Jian Hua
- Plant Biology Section, School of Integrated Plant Science, Cornell University, Ithaca 14850, NY, USA
| | - Yufeng Wu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210000, Jiangsu, China
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14
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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: 6] [Impact Index Per Article: 6.0] [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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15
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Tang J, Chen S, Jia G. Detection, regulation, and functions of RNA N 6-methyladenosine modification in plants. PLANT COMMUNICATIONS 2023; 4:100546. [PMID: 36627844 DOI: 10.1016/j.xplc.2023.100546] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/22/2022] [Accepted: 01/05/2023] [Indexed: 05/11/2023]
Abstract
N6-Methyladenosine (m6A) is the most abundant internal chemical modification in eukaryotic mRNA and plays important roles in gene expression regulation, including transcriptional and post-transcriptional regulation. m6A is a reversible modification that is installed, removed, and recognized by methyltransferases (writers), demethylases (erasers), and m6A-binding proteins (readers), respectively. Recently, the breadth of research on m6A in plants has expanded, and the vital roles of m6A in plant development, biotic and abiotic stress responses, and crop trait improvement have been investigated. In this review, we discuss recent developments in research on m6A and highlight the detection methods, distribution, regulatory proteins, and molecular and biological functions of m6A in plants. We also offer some perspectives on future investigations, providing direction for subsequent research on m6A in plants.
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Affiliation(s)
- Jun Tang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Shuyan Chen
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Guifang Jia
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Beijing 100871, China.
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16
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Song P, Wei L, Chen Z, Cai Z, Lu Q, Wang C, Tian E, Jia G. m 6A readers ECT2/ECT3/ECT4 enhance mRNA stability through direct recruitment of the poly(A) binding proteins in Arabidopsis. Genome Biol 2023; 24:103. [PMID: 37122016 PMCID: PMC10150487 DOI: 10.1186/s13059-023-02947-4] [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: 10/26/2022] [Accepted: 04/20/2023] [Indexed: 05/02/2023] Open
Abstract
BACKGROUND RNA N6-methyladenosine (m6A) modification is critical for plant growth and crop yield. m6A reader proteins can recognize m6A modifications to facilitate the functions of m6A in gene regulation. ECT2, ECT3, and ECT4 are m6A readers that are known to redundantly regulate trichome branching and leaf growth, but their molecular functions remain unclear. RESULTS Here, we show that ECT2, ECT3, and ECT4 directly interact with each other in the cytoplasm and perform genetically redundant functions in abscisic acid (ABA) response regulation during seed germination and post-germination growth. We reveal that ECT2/ECT3/ECT4 promote the stabilization of their targeted m6A-modified mRNAs, but have no function in alternative polyadenylation and translation. We find that ECT2 directly interacts with the poly(A) binding proteins, PAB2 and PAB4, and maintains the stabilization of m6A-modified mRNAs. Disruption of ECT2/ECT3/ECT4 destabilizes mRNAs of ABA signaling-related genes, thereby promoting the accumulation of ABI5 and leading to ABA hypersensitivity. CONCLUSION Our study reveals a unified functional model of m6A mediated by m6A readers in plants. In this model, ECT2/ECT3/ECT4 promote stabilization of their target mRNAs in the cytoplasm.
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Affiliation(s)
- Peizhe Song
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, 100871, China
| | - Lianhuan Wei
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, 100871, China
| | - Zixin Chen
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, 100871, China
| | - Zhihe Cai
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, 100871, China
| | - Qiang Lu
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, 100871, China
| | - Chunling Wang
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, 100871, China
| | - Enlin Tian
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, 100871, China
| | - Guifang Jia
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, 100871, China.
- Peking-Tsinghua Center for Life Sciences, Beijing, 100871, China.
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17
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Wang H, Niu R, Zhou Y, Tang Z, Xu G, Zhou G. ECT9 condensates with ECT1 and regulates plant immunity. FRONTIERS IN PLANT SCIENCE 2023; 14:1140840. [PMID: 37113599 PMCID: PMC10126281 DOI: 10.3389/fpls.2023.1140840] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 03/28/2023] [Indexed: 06/19/2023]
Abstract
Mounting an efficient defense against pathogens requires RNA binding proteins (RBPs) to regulate immune mRNAs transcription, splicing, export, translation, storage, and degradation. RBPs often have multiple family members, raising the question of how they coordinate to carry out diverse cellular functions. In this study, we demonstrate that EVOLUTIONARILY CONSERVED C-TERMINAL REGION 9 (ECT9), a member of the YTH protein family in Arabidopsis, can condensate with its homolog ECT1 to control immune responses. Among the 13 YTH family members screened, only ECT9 can form condensates that decrease after salicylic acid (SA) treatment. While ECT1 alone cannot form condensates, it can be recruited to ECT9 condensates in vivo and in vitro. Notably, the ect1/9 double mutant, but not the single mutant, exhibits heightened immune responses to the avirulent pathogen. Our findings suggest that co-condensation is a mechanism by which RBP family members confer redundant functions.
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Affiliation(s)
- Hui Wang
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei, China
| | - Ruixia Niu
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei, China
| | - Yulu Zhou
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei, China
| | - Zhijuan Tang
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei, China
| | - Guoyong Xu
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei, China
- Hubei Hongshan Laboratory, Wuhan, Hubei, China
| | - Guilong Zhou
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei, China
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18
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Shen L, Ma J, Li P, Wu Y, Yu H. Recent advances in the plant epitranscriptome. Genome Biol 2023; 24:43. [PMID: 36882788 PMCID: PMC9990323 DOI: 10.1186/s13059-023-02872-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 02/12/2023] [Indexed: 03/09/2023] Open
Abstract
Chemical modifications of RNAs, known as the epitranscriptome, are emerging as widespread regulatory mechanisms underlying gene regulation. The field of epitranscriptomics advances recently due to improved transcriptome-wide sequencing strategies for mapping RNA modifications and intensive characterization of writers, erasers, and readers that deposit, remove, and recognize RNA modifications, respectively. Herein, we review recent advances in characterizing plant epitranscriptome and its regulatory mechanisms in post-transcriptional gene regulation and diverse physiological processes, with main emphasis on N6-methyladenosine (m6A) and 5-methylcytosine (m5C). We also discuss the potential and challenges for utilization of epitranscriptome editing in crop improvement.
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Affiliation(s)
- Lisha Shen
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore. .,Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore.
| | - Jinqi Ma
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.,Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore
| | - Ping Li
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Yujin Wu
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.,Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore
| | - Hao Yu
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore. .,Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore.
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19
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Yang J, Li L, Li X, Zhong M, Li X, Qu L, Zhang H, Tang D, Liu X, He C, Zhao X. The blue light receptor CRY1 interacts with FIP37 to promote N 6 -methyladenosine RNA modification and photomorphogenesis in Arabidopsis. THE NEW PHYTOLOGIST 2023; 237:840-854. [PMID: 36305219 DOI: 10.1111/nph.18583] [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: 02/08/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
Light is a particularly important environmental cue that regulates a variety of diverse plant developmental processes, such as photomorphogenesis. Blue light promotes photomorphogenesis mainly through the activation of the photoreceptor cryptochrome 1 (CRY1). However, the mechanism underlying the CRY1-mediated regulation of growth is not fully understood. Here, we found that blue light induced N6 -methyladenosine (m6 A) RNA modification during photomorphogenesis partially via CRY1. Cryptochrome 1 mediates blue light-induced expression of FKBP12-interacting protein 37 (FIP37), which is a component of m6 A writer. Moreover, we showed that CRY1 physically interacted with FIP37 in vitro and in vivo, and mediated blue light activation of FIP37 binding to RNA. Furthermore, CRY1 and FIP37 modulated m6 A on photomorphogenesis-related genes PIF3, PIF4, and PIF5, thereby accelerating the decay of their transcripts. Genetically, FIP37 repressed hypocotyl elongation under blue light, and fip37 mutation could partially rescue the short-hypocotyl phenotype of CRY1-overexpressing plants. Together, our results provide a new insight into CRY1 signal in modulating m6 A methylation and stability of PIFs, and establish an essential molecular link between m6 A modification and determination of photomorphogenesis in plants.
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Affiliation(s)
- Jiaxin Yang
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan Engineering and Technology Research enter of Hybrid Rapeseed, Hunan University, Changsha, 410082, China
- Shenzhen Institute, Hunan University, Shenzhen, 518057, China
| | - Lan Li
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan Engineering and Technology Research enter of Hybrid Rapeseed, Hunan University, Changsha, 410082, China
| | - Xin Li
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan Engineering and Technology Research enter of Hybrid Rapeseed, Hunan University, Changsha, 410082, China
- Shenzhen Institute, Hunan University, Shenzhen, 518057, China
| | - Ming Zhong
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan Engineering and Technology Research enter of Hybrid Rapeseed, Hunan University, Changsha, 410082, China
- Shenzhen Institute, Hunan University, Shenzhen, 518057, China
| | - Xinmei Li
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan Engineering and Technology Research enter of Hybrid Rapeseed, Hunan University, Changsha, 410082, China
- Shenzhen Institute, Hunan University, Shenzhen, 518057, China
| | - Lina Qu
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan Engineering and Technology Research enter of Hybrid Rapeseed, Hunan University, Changsha, 410082, China
- Shenzhen Institute, Hunan University, Shenzhen, 518057, China
| | - Hui Zhang
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan Engineering and Technology Research enter of Hybrid Rapeseed, Hunan University, Changsha, 410082, China
- Shenzhen Institute, Hunan University, Shenzhen, 518057, China
| | - Dongying Tang
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan Engineering and Technology Research enter of Hybrid Rapeseed, Hunan University, Changsha, 410082, China
| | - Xuanming Liu
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan Engineering and Technology Research enter of Hybrid Rapeseed, Hunan University, Changsha, 410082, China
| | - Chongsheng He
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan Engineering and Technology Research enter of Hybrid Rapeseed, Hunan University, Changsha, 410082, China
| | - Xiaoying Zhao
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan Engineering and Technology Research enter of Hybrid Rapeseed, Hunan University, Changsha, 410082, China
- Shenzhen Institute, Hunan University, Shenzhen, 518057, China
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20
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Artz O, Ackermann A, Taylor L, Koo PK, Pedmale UV. Light and temperature regulate m 6A-RNA modification to regulate growth in plants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.17.524395. [PMID: 36711495 PMCID: PMC9882139 DOI: 10.1101/2023.01.17.524395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
N6-methyladenosine is a highly dynamic, abundant mRNA modification which is an excellent potential mechanism for fine tuning gene expression. Plants adapt to their surrounding light and temperature environment using complex gene regulatory networks. The role of m6A in controlling gene expression in response to variable environmental conditions has so far been unexplored. Here, we map the transcriptome-wide m6A landscape under various light and temperature environments. Identified m6A-modifications show a highly specific spatial distribution along transcripts with enrichment occurring in 5'UTR regions and around transcriptional end sites. We show that the position of m6A modifications on transcripts might influence cellular transcript localization and the presence of m6A-modifications is associated with alternative polyadenylation, a process which results in multiple RNA isoforms with varying 3'UTR lengths. RNA with m6A-modifications exhibit a higher preference for shorter 3'UTRs. These shorter 3'UTR regions might directly influence transcript abundance and localization by including or excluding cis-regulatory elements. We propose that environmental stimuli might change the m6A landscape of plants as one possible way of fine tuning gene regulation through alternative polyadenylation and transcript localization.
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Affiliation(s)
- Oliver Artz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724. USA
| | - Amanda Ackermann
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724. USA
| | - Laura Taylor
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724. USA
| | - Peter K. Koo
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724. USA
| | - Ullas V. Pedmale
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724. USA
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21
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Lee HG, Kim J, Seo PJ. N 6-methyladenosine-modified RNA acts as a molecular glue that drives liquid-liquid phase separation in plants. PLANT SIGNALING & BEHAVIOR 2022; 17:2079308. [PMID: 35621186 PMCID: PMC9154792 DOI: 10.1080/15592324.2022.2079308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
Liquid-like condensates are organized by multivalent intrinsically disordered proteins and RNA molecules. We here demonstrate that N6-methyladenosine (m6A)-modified RNA is widespread in establishing diverse plant cell condensates. Several m6A-reader proteins contain putative prion-like domains, and the ect2/3/4 mutant exhibited reduced formation of key nuclear and cytoplasmic condensates in Arabidopsis.
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Affiliation(s)
- Hong Gil Lee
- Department of Chemistry, Seoul National University, Seoul, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea
| | - Jiwoo Kim
- Department of Chemistry, Seoul National University, Seoul, Korea
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea
- Research Institute of Basic Sciences, Seoul National University, Seoul, Korea
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22
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Zhang M, Zeng Y, Peng R, Dong J, Lan Y, Duan S, Chang Z, Ren J, Luo G, Liu B, Růžička K, Zhao K, Wang HB, Jin HL. N 6-methyladenosine RNA modification regulates photosynthesis during photodamage in plants. Nat Commun 2022; 13:7441. [PMID: 36460653 PMCID: PMC9718803 DOI: 10.1038/s41467-022-35146-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 11/18/2022] [Indexed: 12/04/2022] Open
Abstract
N6-methyladenosine (m6A) modification of mRNAs affects many biological processes. However, the function of m6A in plant photosynthesis remains unknown. Here, we demonstrate that m6A modification is crucial for photosynthesis during photodamage caused by high light stress in plants. The m6A modification levels of numerous photosynthesis-related transcripts are changed after high light stress. We determine that the Arabidopsis m6A writer VIRILIZER (VIR) positively regulates photosynthesis, as its genetic inactivation drastically lowers photosynthetic activity and photosystem protein abundance under high light conditions. The m6A levels of numerous photosynthesis-related transcripts decrease in vir mutants, extensively reducing their transcript and translation levels, as revealed by multi-omics analyses. We demonstrate that VIR associates with the transcripts of genes encoding proteins with functions related to photoprotection (such as HHL1, MPH1, and STN8) and their regulatory proteins (such as regulators of transcript stability and translation), promoting their m6A modification and maintaining their stability and translation efficiency. This study thus reveals an important mechanism for m6A-dependent maintenance of photosynthetic efficiency in plants under high light stress conditions.
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Affiliation(s)
- Man Zhang
- grid.411866.c0000 0000 8848 7685Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 510006 Guangzhou, People’s Republic of China ,grid.12981.330000 0001 2360 039XSchool of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, People’s Republic of China ,grid.484195.5Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, 510640 Guangzhou, People’s Republic of China
| | - Yunping Zeng
- grid.411866.c0000 0000 8848 7685Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 510006 Guangzhou, People’s Republic of China
| | - Rong Peng
- grid.411866.c0000 0000 8848 7685Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 510006 Guangzhou, People’s Republic of China
| | - Jie Dong
- grid.12981.330000 0001 2360 039XSchool of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, People’s Republic of China
| | - Yelin Lan
- grid.12981.330000 0001 2360 039XSchool of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, People’s Republic of China
| | - Sujuan Duan
- grid.411866.c0000 0000 8848 7685Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 510006 Guangzhou, People’s Republic of China
| | - Zhenyi Chang
- grid.411866.c0000 0000 8848 7685Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 510006 Guangzhou, People’s Republic of China
| | - Jian Ren
- grid.12981.330000 0001 2360 039XSchool of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, People’s Republic of China
| | - Guanzheng Luo
- grid.12981.330000 0001 2360 039XSchool of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, People’s Republic of China
| | - Bing Liu
- grid.12981.330000 0001 2360 039XSchool of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, People’s Republic of China
| | - Kamil Růžička
- grid.418095.10000 0001 1015 3316Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, 165 02 Prague 6, Czech Republic
| | - Kewei Zhao
- grid.411866.c0000 0000 8848 7685Guangzhou Key Laboratory of Chinese Medicine Research on Prevention and Treatment of Osteoporosis, The Third Affiliated Hospital of Guangzhou University of Chinese Medicine, No.263, Longxi Avenue, Guangzhou, People’s Republic of China
| | - Hong-Bin Wang
- grid.411866.c0000 0000 8848 7685Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 510006 Guangzhou, People’s Republic of China ,grid.419897.a0000 0004 0369 313XKey Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education, Guangzhou, People’s Republic of China ,grid.411866.c0000 0000 8848 7685State Key Laboratory of Dampness Syndrome of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, People’s Republic of China
| | - Hong-Lei Jin
- grid.411866.c0000 0000 8848 7685Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 510006 Guangzhou, People’s Republic of China ,grid.411866.c0000 0000 8848 7685Guangzhou Key Laboratory of Chinese Medicine Research on Prevention and Treatment of Osteoporosis, The Third Affiliated Hospital of Guangzhou University of Chinese Medicine, No.263, Longxi Avenue, Guangzhou, People’s Republic of China
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23
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Amara U, Shoaib Y, Kang H. ALKBH9C, a potential RNA m 6 A demethylase, regulates the response of Arabidopsis to abiotic stresses and abscisic acid. PLANT, CELL & ENVIRONMENT 2022; 45:3566-3581. [PMID: 36148771 DOI: 10.1111/pce.14447] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 07/25/2022] [Accepted: 09/05/2022] [Indexed: 06/16/2023]
Abstract
Although several studies have shown that AlkB homolog (ALKBH) proteins are potential RNA demethylases (referred to as 'erasers'), biological functions of only a few ALKBH proteins have been characterized to date. In this study, we determined the function of ALKBH9C (At4g36090) in seed germination and seedling growth of Arabidopsis thaliana in response to abiotic stress and abscisic acid (ABA). Seed germination of the alkbh9c mutant was delayed in response to salt, drought, cold and ABA. Moreover, seedling growth of the mutant was repressed under salt stress or ABA but enhanced under drought conditions. Notably, the stress-responsive phenotypes were associated with the altered expression of several m6 A-modified transcripts related to salt, drought or ABA response. Global m6 A levels were increased in the alkbh9c mutant, and ALKBH9C bound to m6 A-modified RNAs and had in vitro m6 A demethylase activity, suggesting its potential role as an m6 A eraser. The m6 A levels in several stress-responsive genes were increased in the alkbh9c mutant, and the stability of m6 A-modified transcripts was altered in the mutant. Collectively, our results suggest that m6 A eraser ALKBH9C is crucial for seed germination and seedling growth of Arabidopsis in response to abiotic stresses or ABA via affecting the stability of stress-responsive transcripts.
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Affiliation(s)
- Umme Amara
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Korea
| | - Yasira Shoaib
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Korea
| | - Hunseung Kang
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Korea
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24
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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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25
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Ma W, Cui S, Lu Z, Yan X, Cai L, Lu Y, Cai K, Zhou H, Ma R, Zhou S, Wang X. YTH Domain Proteins Play an Essential Role in Rice Growth and Stress Response. PLANTS 2022; 11:plants11172206. [PMID: 36079588 PMCID: PMC9460353 DOI: 10.3390/plants11172206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/19/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022]
Abstract
As the most prevalent epi-transcriptional modification, m6A modifications play essential roles in regulating RNA fate. The molecular functions of YTH521-B homology (YTH) domain proteins, the most known READER proteins of m6A modifications, have been well-studied in animals. Although plants contain more YTH domain proteins than other eukaryotes, little is known about their biological importance. In dicot species Arabidopsis thaliana, the YTHDFA clade members ECT2/3/4 and CPSF30-L are well-studied and important for cell proliferation, plant organogenesis, and nitrate transport. More emphasis is needed on the biological functions of plant YTH proteins, especially monocot YTHs. Here we presented a detailed phylogenetic relationship of eukaryotic YTH proteins and clustered plant YTHDFC clade into three subclades. To determine the importance of monocot YTH proteins, YTH knockout mutants and RNAi-induced knockdown plants were constructed and used for phenotyping, transcriptomic analysis, and stress treatments. Knocking out or knocking down OsYTHs led to the downregulation of multicellular organismal regulation genes and resulted in growth defects. In addition, loss-of-function ythdfa mutants led to better salinity tolerance whereas ythdfc mutants were more sensitive to abiotic stress. Overall, our study establishes the functional relevance of rice YTH genes in plant growth regulation and stress response.
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Affiliation(s)
- Weiwei Ma
- Institute of Crop Sciences, Ningbo Academy of Agricultural Sciences, Ningbo 315000, China
| | - Song Cui
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhenfei Lu
- Institute of Crop Sciences, Ningbo Academy of Agricultural Sciences, Ningbo 315000, China
| | - Xiaofeng Yan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Long Cai
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Yongfa Lu
- Institute of Crop Sciences, Ningbo Academy of Agricultural Sciences, Ningbo 315000, China
| | - Kefeng Cai
- Institute of Crop Sciences, Ningbo Academy of Agricultural Sciences, Ningbo 315000, China
| | - Huacheng Zhou
- Institute of Crop Sciences, Ningbo Academy of Agricultural Sciences, Ningbo 315000, China
| | - Rongrong Ma
- Institute of Crop Sciences, Ningbo Academy of Agricultural Sciences, Ningbo 315000, China
| | - Shirong Zhou
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (S.Z.); (X.W.)
| | - Xiaole Wang
- Institute of Crop Sciences, Ningbo Academy of Agricultural Sciences, Ningbo 315000, China
- Correspondence: (S.Z.); (X.W.)
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26
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Govindan G, Sharma B, Li Y, Armstrong CD, Merum P, Rohila JS, Gregory BD, Sunkar R. mRNA N 6 -methyladenosine is critical for cold tolerance in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1052-1068. [PMID: 35710867 PMCID: PMC9543165 DOI: 10.1111/tpj.15872] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 05/28/2022] [Accepted: 06/13/2022] [Indexed: 05/16/2023]
Abstract
Plants respond to low temperatures by altering the mRNA abundance of thousands of genes contributing to numerous physiological and metabolic processes that allow them to adapt. At the post-transcriptional level, these cold stress-responsive transcripts undergo alternative splicing, microRNA-mediated regulation and alternative polyadenylation, amongst others. Recently, m6 A, m5 C and other mRNA modifications that can affect the regulation and stability of RNA were discovered, thus revealing another layer of post-transcriptional regulation that plays an important role in modulating gene expression. The importance of m6 A in plant growth and development has been appreciated, although its significance under stress conditions is still underexplored. To assess the role of m6 A modifications during cold stress responses, methylated RNA immunoprecipitation sequencing was performed in Arabidopsis seedlings esposed to low temperature stress (4°C) for 24 h. This transcriptome-wide m6 A analysis revealed large-scale shifts in this modification in response to low temperature stress. Because m6 A is known to affect transcript stability/degradation and translation, we investigated these possibilities. Interestingly, we found that cold-enriched m6 A-containing transcripts demonstrated the largest increases in transcript abundance coupled with increased ribosome occupancy under cold stress. The significance of the m6 A epitranscriptome on plant cold tolerance was further assessed using the mta mutant in which the major m6 A methyltransferase gene was mutated. Compared to the wild-type, along with the differences in CBFs and COR gene expression levels, the mta mutant exhibited hypersensitivity to cold treatment as determined by primary root growth, biomass, and reactive oxygen species accumulation. Furthermore, and most importantly, both non-acclimated and cold-acclimated mta mutant demonstrated hypersensitivity to freezing tolerance. Taken together, these findings suggest a critical role for the epitranscriptome in cold tolerance of Arabidopsis.
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Affiliation(s)
- Ganesan Govindan
- Department of Biochemistry and Molecular BiologyOklahoma State UniversityStillwaterOK74078USA
| | - Bishwas Sharma
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPA19104USA
| | - Yong‐Fang Li
- Department of Biochemistry and Molecular BiologyOklahoma State UniversityStillwaterOK74078USA
| | | | - Pandrangaiah Merum
- Department of Biochemistry and Molecular BiologyOklahoma State UniversityStillwaterOK74078USA
| | - Jai S. Rohila
- Dale Bumpers National Rice Research CenterUnited States Department of Agriculture‐Agricultural Research ServicesStuttgartAR72160USA
| | - Brian D. Gregory
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPA19104USA
| | - Ramanjulu Sunkar
- Department of Biochemistry and Molecular BiologyOklahoma State UniversityStillwaterOK74078USA
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27
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Hu J, Cai J, Umme A, Chen Y, Xu T, Kang H. Unique features of mRNA m6A methylomes during expansion of tomato (Solanum lycopersicum) fruits. PLANT PHYSIOLOGY 2022; 188:2215-2227. [PMID: 34730815 PMCID: PMC8968293 DOI: 10.1093/plphys/kiab509] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 10/07/2021] [Indexed: 05/20/2023]
Abstract
N6-methyladenosine (m6A) is the most abundant internal modification in eukaryotic messenger RNA. Although the role of m6A has been demonstrated in many biological processes, including embryonic development, flowering time control, microspore generation, fruit ripening, and stress responses, its contribution to other aspects of plant development still needs to be explored. Herein, we show the potential link between m6A deposition and the expansion of tomato (Solanum lycopersicum) fruits through parallel m6A-immunoprecipitation-sequencing (m6A-seq) and RNA-seq analyses. We found that global m6A levels increased during tomato fruit expansion from immature green to mature green stage. m6A-seq revealed that thousands of protein-coding genes are m6A-modified mainly in the 3'-untranslated regions. m6A-seq and RNA-seq analyses showed a positive association between m6A methylation and mRNA abundance. In particular, a large number of fruit expansion-related genes involved in hormone responses and endoreduplication were m6A modified and expressed more actively than the non-m6A-modified genes, suggesting a potential role of m6A modification in tomato fruit expansion. Importantly, altering m6A levels by direct injection of 3-deazaneplanocin A (DA; m6A writer inhibitor) or meclofenamic acid (MA; m6A eraser inhibitor) into tomato fruits suppressed fruit expansion; however, injection of exogenous DA or MA accelerated or delayed fruit ripening, respectively. Collectively, these results suggest a dynamic role of m6A methylation in the expansion and ripening of tomato fruits.
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Affiliation(s)
| | - Jing Cai
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Korea
| | - Amara Umme
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Korea
| | - Yao Chen
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
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28
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Wang C, Yang J, Song P, Zhang W, Lu Q, Yu Q, Jia G. FIONA1 is an RNA N 6-methyladenosine methyltransferase affecting Arabidopsis photomorphogenesis and flowering. Genome Biol 2022; 23:40. [PMID: 35101091 PMCID: PMC8802475 DOI: 10.1186/s13059-022-02612-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 01/14/2022] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND N6-methyladenosine (m6A) mRNA modification is essential for mammalian and plant viability. The U6 m6A methyltransferases in other species regulate S-adenosylmethionine (SAM) homeostasis through installing m6A in pre-mRNAs of SAM synthetases. However, U6 m6A methyltransferase has not been characterized in Arabidopsis and little is known about its role in regulating photomorphogenesis and flowering. RESULTS Here we characterize that FIONA1 is an Arabidopsis U6 m6A methyltransferase that installs m6A in U6 snRNA and a small subset of poly(A)+ RNA. Disruption of FIONA1 leads to phytochrome signaling-dependent hypocotyl elongation and photoperiod-independent early flowering. Distinct from mammalian METTL16 and worm METT-10, FIONA1 neither installs m6A in the mRNAs of Arabidopsis SAM synthetases nor affects their transcript expression levels under normal or high SAM conditions. We confirm that FIONA1 can methylate plant mRNA m6A motifs in vitro and in vivo. We further show that FIONA1 installs m6A in several phenotypic related transcripts, thereby affecting downstream mRNA stability and regulating phytochrome signaling and floral transition. CONCLUSION FIONA1 is functional as a U6 m6A methyltransferase in Arabidopsis, distinct from mammalian METTL16 and worm METT-10. Our results demonstrate that FIONA1-mediated m6A post-transcriptional regulation is an autonomous regulator for flowering and phytochrome signaling-dependent photomorphogenesis.
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Affiliation(s)
- Chunling Wang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Junbo Yang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Peizhe Song
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Wei Zhang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Qiang Lu
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Qiong Yu
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Guifang Jia
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
- Peking-Tsinghua Center for Life Sciences, Beijing, 100871, China.
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29
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RNA demethylation increases the yield and biomass of rice and potato plants in field trials. Nat Biotechnol 2021; 39:1581-1588. [PMID: 34294912 DOI: 10.1038/s41587-021-00982-9] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 06/11/2021] [Indexed: 02/06/2023]
Abstract
RNA N6-methyladenosine (m6A) modifications are essential in plants. Here, we show that transgenic expression of the human RNA demethylase FTO in rice caused a more than threefold increase in grain yield under greenhouse conditions. In field trials, transgenic expression of FTO in rice and potato caused ~50% increases in yield and biomass. We demonstrate that the presence of FTO stimulates root meristem cell proliferation and tiller bud formation and promotes photosynthetic efficiency and drought tolerance but has no effect on mature cell size, shoot meristem cell proliferation, root diameter, plant height or ploidy. FTO mediates substantial m6A demethylation (around 7% of demethylation in poly(A) RNA and around 35% decrease of m6A in non-ribosomal nuclear RNA) in plant RNA, inducing chromatin openness and transcriptional activation. Therefore, modulation of plant RNA m6A methylation is a promising strategy to dramatically improve plant growth and crop yield.
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30
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Shoaib Y, Hu J, Manduzio S, Kang H. Alpha-ketoglutarate-dependent dioxygenase homolog 10B, an N 6 -methyladenosine mRNA demethylase, plays a role in salt stress and abscisic acid responses in Arabidopsis thaliana. PHYSIOLOGIA PLANTARUM 2021; 173:1078-1089. [PMID: 34309025 DOI: 10.1111/ppl.13505] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 07/12/2021] [Indexed: 06/13/2023]
Abstract
N6 -methyladenosine (m6 A) is an abundant methylation mark in eukaryotic mRNAs. It is installed and removed by methyltransferases ("writers") and demethylases ("erasers"), respectively. A recent study has demonstrated that alpha-ketoglutarate-dependent dioxygenase homolog 10B (ALKBH10B) is an mRNA m6 A eraser affecting floral transition in Arabidopsis thaliana. However, the roles of m6 A eraser proteins, including ALKHB10B, in plant adaptation to abiotic stresses are largely unknown. In this study, we aimed to determine the role of ALKBH10B in the response of A. thaliana to abiotic stresses and abscisic acid (ABA). The m6 A level increased in response to salt stress, and m6 A levels in alkbh10b mutants were higher than those in the wild-type under both normal and salt stress conditions. Germination of alkbh10b mutant seeds was markedly delayed under salt stress but not under dehydration, cold, or ABA conditions. Seedling growth and survival rate of alkbh10b mutants were enhanced under salt stress. Notably, salt-tolerant phenotypes of alkbh10b mutants were correlated with decreased levels of several m6 A-modified genes, including ATAF1, BGLU22, and MYB73, which are negative effectors of salt stress tolerance. In response to ABA, both seedling and root growth of alkbh10b mutants were inhibited via upregulating ABA signaling-related genes, including ABI3 and ABI4. Collectively, these findings indicate that ALKBH10B-mediated m6 A demethylation affects the transcript levels of stress-responsive genes, which are important for seed germination, seedling growth, and survival of Arabidopsis thaliana in response to salt stress or ABA.
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Affiliation(s)
- Yasira Shoaib
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, South Korea
| | - Jianzhong Hu
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, South Korea
| | - Stefano Manduzio
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, South Korea
| | - Hunseung Kang
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, South Korea
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31
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Arribas-Hernández L, Rennie S, Köster T, Porcelli C, Lewinski M, Dr Dorothee Staiger P, Andersson R, Brodersen P. Principles of mRNA targeting via the Arabidopsis m 6A-binding protein ECT2. eLife 2021; 10:72375. [PMID: 34591015 PMCID: PMC8796052 DOI: 10.7554/elife.72375] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 09/25/2021] [Indexed: 11/18/2022] Open
Abstract
Specific recognition of N6-methyladenosine (m6A) in mRNA by RNA-binding proteins containing a YT521-B homology (YTH) domain is important in eukaryotic gene regulation. The Arabidopsis YTH domain protein ECT2 is thought to bind to mRNA at URU(m6A)Y sites, yet RR(m6A)CH is the canonical m6A consensus site in all eukaryotes and ECT2 functions require m6A-binding activity. Here, we apply iCLIP (individual nucleotide resolution crosslinking and immunoprecipitation) and HyperTRIBE (targets of RNA-binding proteins identified by editing) to define high-quality target sets of ECT2 and analyze the patterns of enriched sequence motifs around ECT2 crosslink sites. Our analyses show that ECT2 does in fact bind to RR(m6A)CH. Pyrimidine-rich motifs are enriched around, but not at m6A sites, reflecting a preference for N6-adenosine methylation of RRACH/GGAU islands in pyrimidine-rich regions. Such motifs, particularly oligo-U and UNUNU upstream of m6A sites, are also implicated in ECT2 binding via its intrinsically disordered region (IDR). Finally, URUAY-type motifs are enriched at ECT2 crosslink sites, but their distinct properties suggest function as sites of competition between binding of ECT2 and as yet unidentified RNA-binding proteins. Our study provides coherence between genetic and molecular studies of m6A-YTH function in plants and reveals new insight into the mode of RNA recognition by YTH domain-containing proteins. Genes are strings of genetic code that contain instructions for producing a cell’s proteins. Active genes are copied from DNA into molecules called mRNAs, and mRNA molecules are subsequently translated to create new proteins. However, the number of proteins produced by a cell is not only limited by the number of mRNA molecules produced by copying DNA. Cells use a variety of methods to control the stability of mRNA molecules and their translation efficiency to regulate protein production. One of these methods involves adding a chemical tag, a methyl group, onto mRNA while it is being created. These methyl tags can then be used as docking stations by RNA-binding proteins that help regulate protein translation. Most eukaryotic species – which include animals, plants and fungi – use the same system to add methyl tags to mRNA molecules. One methyl tag in particular, known as m6A, is a well-characterised docking site for a particular type of RNA-binding protein that goes by the name of ECT2 in plants. However, in the flowering plant Arabidopsis thaliana, ECT2 was thought to bind to an mRNA sequence different from the one normally carrying the chemical tag, creating obvious confusion about how the system works in plants. Arribas-Hernández, Rennie et al. investigated this question using advanced large-scale biochemical techniques, and discovered that conventional m6A methyl tags are indeed used by ECT2 in Arabidopsis thaliana. The confusion likely arose because the sequence ECT2 was thought bind is often located in close proximity to the m6A tags, possibly acting as docking stations for proteins that can influence the ability of ECT2 to bind mRNA. Arribas-Hernández, Rennie et al. also uncovered additional mRNA sequences that directly interact with parts of ECT2 previously unknown to participate in mRNA binding. These findings provide new insights into how chemical labels in mRNA control gene activity. They have broad implications that extend beyond plants into other eukaryotic species, including humans. Since this chemical labelling system has a major role in controlling plant growth, these findings could be leveraged in biotechnology applications to improve crop yields and enhance plant-based food production.
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Arribas-Hernández L, Rennie S, Schon M, Porcelli C, Enugutti B, Andersson R, Nodine MD, Brodersen P. The YTHDF proteins ECT2 and ECT3 bind largely overlapping target sets and influence target mRNA abundance, not alternative polyadenylation. eLife 2021; 10:72377. [PMID: 34591013 PMCID: PMC8789314 DOI: 10.7554/elife.72377] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 09/25/2021] [Indexed: 11/18/2022] Open
Abstract
Gene regulation via N6-methyladenosine (m6A) in mRNA involves RNA-binding proteins that recognize m6A via a YT521-B homology (YTH) domain. The plant YTH domain proteins ECT2 and ECT3 act genetically redundantly in stimulating cell proliferation during organogenesis, but several fundamental questions regarding their mode of action remain unclear. Here, we use HyperTRIBE (targets of RNA-binding proteins identified by editing) to show that most ECT2 and ECT3 targets overlap, with only a few examples of preferential targeting by either of the two proteins. HyperTRIBE in different mutant backgrounds also provides direct views of redundant, ectopic, and specific target interactions of the two proteins. We also show that contrary to conclusions of previous reports, ECT2 does not accumulate in the nucleus. Accordingly, inactivation of ECT2, ECT3, and their surrogate ECT4 does not change patterns of polyadenylation site choice in ECT2/3 target mRNAs, but does lead to lower steady-state accumulation of target mRNAs. In addition, mRNA and microRNA expression profiles show indications of stress response activation in ect2/ect3/ect4 mutants, likely via indirect effects. Thus, previous suggestions of control of alternative polyadenylation by ECT2 are not supported by evidence, and ECT2 and ECT3 act largely redundantly to regulate target mRNA, including its abundance, in the cytoplasm.
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Alvarado-Marchena L, Marquez-Molins J, Martinez-Perez M, Aparicio F, Pallás V. Mapping of Functional Subdomains in the atALKBH9B m 6A-Demethylase Required for Its Binding to the Viral RNA and to the Coat Protein of Alfalfa Mosaic Virus. FRONTIERS IN PLANT SCIENCE 2021; 12:701683. [PMID: 34290728 PMCID: PMC8287571 DOI: 10.3389/fpls.2021.701683] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 06/09/2021] [Indexed: 06/01/2023]
Abstract
N 6-methyladenosine (m6A) modification is a dynamically regulated RNA modification that impacts many cellular processes and pathways. This epitranscriptomic methylation relies on the participation of RNA methyltransferases (referred to as "writers") and demethylases (referred to as "erasers"), respectively. We previously demonstrated that the Arabidopsis thaliana protein atALKBH9B showed m6A-demethylase activity and interacted with the coat protein (CP) of alfalfa mosaic virus (AMV), causing a profound impact on the viral infection cycle. To dissect the functional activity of atALKBH9B in AMV infection, we performed a protein-mapping analysis to identify the putative domains required for regulating this process. In this context, the mutational analysis of the protein revealed that the residues between 427 and 467 positions are critical for in vitro binding to the AMV RNA. The atALKBH9B amino acid sequence showed intrinsically disordered regions (IDRs) located at the N-terminal part delimiting the internal AlkB-like domain and at the C-terminal part. We identified an RNA binding domain containing an RGxxxRGG motif that overlaps with the C-terminal IDR. Moreover, bimolecular fluorescent experiments allowed us to determine that residues located between 387 and 427 are critical for the interaction with the AMV CP, which should be critical for modulating the viral infection process. Finally, we observed that atALKBH9B deletions of either N-terminal 20 residues or the C-terminal's last 40 amino acids impede their accumulation in siRNA bodies. The involvement of the regions responsible for RNA and viral CP binding and those required for its localization in stress granules in the viral cycle is discussed.
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Yin S, Ao Q, Tan C, Yang Y. Genome-wide identification and characterization of YTH domain-containing genes, encoding the m 6A readers, and their expression in tomato. PLANT CELL REPORTS 2021; 40:1229-1245. [PMID: 34081180 DOI: 10.1007/s00299-021-02716-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 05/15/2021] [Indexed: 06/12/2023]
Abstract
9 YTH genes in tomato were identified and cloned, and their expression patterns were comprehensively analyzed, which reveal potential multiple roles in development and fruit ripening. N6-methyladenosine (m6A) is an abundant and pervasive post-transcriptional modification in eukaryotic mRNAs. The YTH domain-containing proteins act as m6A readers to read m6A marks and transduce their downstream regulatory effects by altering m6A-mRNA metabolism processes. Identification of YTH proteins is essential for understanding the regulatory mechanisms of m6A in physiological processes, but little is known about YTH proteins in tomato, a model system for fruit development. Here, we report that tomato genomes contain a total of 9 SlYTH genes. While YTH proteins of both tomato and Arabidopsis can be classified into two subfamilies, the member distributions in subfamilies are very different between the two species. Homology modeling exhibited the similar three-dimensional structures of SlYTH proteins to human YTHDF1 or YTHDC1. Multiple hormone-response elements locating on the promoters of SlYTH genes indicate that they are involved in the physiological processes related to phytohormone. SlYTH genes are ubiquitous and spatiotemporal dynamic expression in tomato. Eight SlTYH genes have the strongest expression in stamens among the parts of flowers. Throughout fruit ontogeny, most of the SlYTH genes display obvious high mRNA levels during the developmental phases (4 dpa to mature green); moreover, SlYTH1 and SlYTH2 have absolute predominant expressions demonstrated by RNA-seq. The results lay a foundation for future characterizations on the functions of YTH proteins and m6A regulatory mechanism in tomato.
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Affiliation(s)
- Shuangqin Yin
- Bioengineering College, Chongqing University, Chongqing, 400044, China
| | - Qiujing Ao
- Bioengineering College, Chongqing University, Chongqing, 400044, China
| | - Caiyun Tan
- Bioengineering College, Chongqing University, Chongqing, 400044, China
| | - Yingwu Yang
- Bioengineering College, Chongqing University, Chongqing, 400044, China.
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, Chongqing University, Chongqing, 401331, China.
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Hu J, Cai J, Park SJ, Lee K, Li Y, Chen Y, Yun JY, Xu T, Kang H. N 6 -Methyladenosine mRNA methylation is important for salt stress tolerance in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:1759-1775. [PMID: 33843075 DOI: 10.1111/tpj.15270] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/31/2021] [Accepted: 04/07/2021] [Indexed: 05/16/2023]
Abstract
As the most abundant internal modification of mRNA, N6 -methyladenosine (m6 A) methylation of RNA is emerging as a new layer of epitranscriptomic gene regulation in cellular processes, including embryo development, flowering-time control, microspore generation and fruit ripening, in plants. However, the cellular role of m6 A in plant responses to environmental stimuli remains largely unexplored. In this study, we show that m6 A methylation plays an important role in salt stress tolerance in Arabidopsis. All mutants of m6 A writer components, including MTA, MTB, VIRILIZER (VIR) and HAKAI, displayed salt-sensitive phenotypes in an m6 A-dependent manner. The vir mutant, in which the level of m6 A was most highly reduced, exhibited salt-hypersensitive phenotypes. Analysis of the m6 A methylome in the vir mutant revealed a transcriptome-wide loss of m6 A modification in the 3' untranslated region (3'-UTR). We demonstrated further that VIR-mediated m6 A methylation modulates reactive oxygen species homeostasis by negatively regulating the mRNA stability of several salt stress negative regulators, including ATAF1, GI and GSTU17, through affecting 3'-UTR lengthening linked to alternative polyadenylation. Our results highlight the important role played by epitranscriptomic mRNA methylation in the salt stress response of Arabidopsis and indicate a strong link between m6 A methylation and 3'-UTR length and mRNA stability during stress adaptation.
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Affiliation(s)
- Jianzhong Hu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu Province, 221116, China
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Korea
| | - Jing Cai
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Korea
| | - Su Jung Park
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Korea
| | - Kwanuk Lee
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Korea
| | - Yuxia Li
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu Province, 221116, China
| | - Yao Chen
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu Province, 221116, China
| | - Jae-Young Yun
- Institutes of Green Bio Science & Technology, Seoul National University, Pyeongchang, 25354, Korea
| | - Tao Xu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu Province, 221116, China
| | - Hunseung Kang
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu Province, 221116, China
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Korea
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Song P, Yang J, Wang C, Lu Q, Shi L, Tayier S, Jia G. Arabidopsis N 6-methyladenosine reader CPSF30-L recognizes FUE signals to control polyadenylation site choice in liquid-like nuclear bodies. MOLECULAR PLANT 2021; 14:571-587. [PMID: 33515768 DOI: 10.1016/j.molp.2021.01.014] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 09/10/2020] [Accepted: 12/11/2020] [Indexed: 05/16/2023]
Abstract
The biological functions of the epitranscriptomic modification N6-methyladenosine (m6A) in plants are not fully understood. CPSF30-L is a predominant isoform of the polyadenylation factor CPSF30 and consists of CPSF30-S and an m6A-binding YTH domain. Little is known about the biological roles of CPSF30-L and the molecular mechanism underlying its m6A-binding function in alternative polyadenylation. Here, we characterized CPSF30-L as an Arabidopsis m6A reader whose m6A-binding function is required for the floral transition and abscisic acid (ABA) response. We found that the m6A-binding activity of CPSF30-L enhances the formation of liquid-like nuclear bodies, where CPSF30-L mainly recognizes m6A-modified far-upstream elements to control polyadenylation site choice. Deficiency of CPSF30-L lengthens the 3' untranslated region of three phenotypes-related transcripts, thereby accelerating their mRNA degradation and leading to late flowering and ABA hypersensitivity. Collectively, this study uncovers a new molecular mechanism for m6A-driven phase separation and polyadenylation in plants.
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Affiliation(s)
- Peizhe Song
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Junbo Yang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Chunling Wang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Qiang Lu
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Linqing Shi
- Medical Isotopes Research Center and, Department of Radiation Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Subiding Tayier
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Guifang Jia
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
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Hou Y, Sun J, Wu B, Gao Y, Nie H, Nie Z, Quan S, Wang Y, Cao X, Li S. CPSF30-L-mediated recognition of mRNA m 6A modification controls alternative polyadenylation of nitrate signaling-related gene transcripts in Arabidopsis. MOLECULAR PLANT 2021; 14:688-699. [PMID: 33515769 DOI: 10.1016/j.molp.2021.01.013] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 12/10/2020] [Accepted: 01/21/2021] [Indexed: 05/16/2023]
Abstract
N6-methyladenosine (m6A), a ubiquitous internal modification of eukaryotic mRNAs, plays a vital role in almost every aspect of mRNA metabolism. However, there is little evidence documenting the role of m6A in regulating alternative polyadenylation (APA) in plants. APA is controlled by a large protein-RNA complex with many components, including CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR30 (CPSF30). In Arabidopsis, CPSF30 has two isoforms and the longer isoform (CPSF30-L) contains a YT512-B Homology (YTH) domain, which is unique to plants. In this study, we showed that CPSF30-L YTH domain binds to m6A in vitro. In the cpsf30-2 mutant, the transcripts of many genes including several important nitrate signaling-related genes had shifts in polyadenylation sites that were correlated with m6A peaks, indicating that these gene transcripts carrying m6A tend to be regulated by APA. Wild-type CPSF30-L could rescue the defects in APA and nitrate metabolism in cpsf30-2, but m6A-binding-defective mutants of CPSF30-L could not. Taken together, our results demonstrated that m6A modification regulates APA in Arabidopsis and revealed that the m6A reader CPSF30-L affects nitrate signaling by controlling APA, shedding new light on the roles of the m6A modification during RNA 3'-end processing in nitrate metabolism.
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Affiliation(s)
- Yifeng Hou
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jing Sun
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Baixing Wu
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Yangyang Gao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Hongbo Nie
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Zhentian Nie
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Shuxuan Quan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Yong Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China.
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Beijing 100101, China.
| | - Sisi Li
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.
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Shi R, Ying S, Li Y, Zhu L, Wang X, Jin H. Linking the YTH domain to cancer: the importance of YTH family proteins in epigenetics. Cell Death Dis 2021; 12:346. [PMID: 33795663 PMCID: PMC8016981 DOI: 10.1038/s41419-021-03625-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 03/09/2021] [Accepted: 03/15/2021] [Indexed: 02/06/2023]
Abstract
N6-methyladenosine (m6A), the most prevalent and reversible modification of mRNA in mammalian cells, has recently been extensively studied in epigenetic regulation. YTH family proteins, whose YTH domain can recognize and bind m6A-containing RNA, are the main "readers" of m6A modification. YTH family proteins perform different functions to determine the metabolic fate of m6A-modified RNA. The crystal structure of the YTH domain has been completely resolved, highlighting the important roles of several conserved residues of the YTH domain in the specific recognition of m6A-modified RNAs. Upstream and downstream targets have been successively revealed in different cancer types and the role of YTH family proteins has been emphasized in m6A research. This review describes the regulation of RNAs by YTH family proteins, the structural features of the YTH domain, and the connections of YTH family proteins with human cancers.
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Affiliation(s)
- Rongkai Shi
- grid.13402.340000 0004 1759 700XLaboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang, Sir Run Run Shaw Hospital, Cancer Center, Zhejiang University, Hangzhou, China
| | - Shilong Ying
- grid.13402.340000 0004 1759 700XLaboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang, Sir Run Run Shaw Hospital, Cancer Center, Zhejiang University, Hangzhou, China
| | - Yadan Li
- grid.13402.340000 0004 1759 700XLaboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang, Sir Run Run Shaw Hospital, Cancer Center, Zhejiang University, Hangzhou, China
| | - Liyuan Zhu
- grid.13402.340000 0004 1759 700XLaboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang, Sir Run Run Shaw Hospital, Cancer Center, Zhejiang University, Hangzhou, China
| | - Xian Wang
- grid.13402.340000 0004 1759 700XDepartment of Medical Oncology, Sir Run Run Shaw Hospital, Medical School of Zhejiang University, Hangzhou, China
| | - Hongchuan Jin
- grid.13402.340000 0004 1759 700XLaboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang, Sir Run Run Shaw Hospital, Cancer Center, Zhejiang University, Hangzhou, China
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