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Kumar A, Daripa P, Penumutchu S, Maiti S, Jain N. Thermodynamic insights into N6-methyladenosine-modified ribonucleic acids and their interactions with the RNA recognition motif of heterogeneous nuclear ribonucleoprotein C. Int J Biol Macromol 2025; 312:144210. [PMID: 40373918 DOI: 10.1016/j.ijbiomac.2025.144210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2025] [Revised: 04/14/2025] [Accepted: 05/12/2025] [Indexed: 05/17/2025]
Abstract
N6-methyladenosine (m6A) is a prevalent RNA modification that regulates key functions such as splicing, transport, translation, and stability across various RNA types, including mRNA, tRNA, rRNA, and lncRNA. Transcriptome-wide studies reveal that approximately one-third of mammalian mRNAs carry 3-5 m6A modifications, enriched in the consensus motif RRA*CH. While some studies suggest m6A induces structural changes in RNA to facilitate protein binding through an "m6A switch" mechanism, others propose it primarily primes RNA for enhanced protein interactions, emphasizing the need for further exploration of m6A's role. Here, we investigated how m6A influences the binding of heterogeneous nuclear ribonucleoprotein C (hnRNPC), which recognizes poly (U) tracts via its RNA recognition motif (RRM). Using naturally occurring m6A-modified RNAs, including lncRNA MALAT1, we examined the effects of m6A on RNA folding and protein binding. Biophysical experiments (UV melting, circular dichroism, and molecular dynamics simulations) revealed that m6A subtly alters RNA stability and folding. Binding studies using EMSA, Microscale Thermophoresis (MST), and Isothermal Titration Calorimetry (ITC) showed m6A primes RNA for hnRNPC recognition rather than inducing structural switches. These findings refine our understanding of m6A's role in RNA-protein interactions, highlighting its regulatory importance in RNA metabolism.
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Affiliation(s)
- Ajit Kumar
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Purba Daripa
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Srinivasa Penumutchu
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Souvik Maiti
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Niyati Jain
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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2
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Li Y, Tan P, Liu Q, Sun H, Wang Y, Chen S, Kong W, Sun X, Shao X. Systematic molecular profiling of non-native N 6-substitution effects on m6A binding to the YTH domains of human RNA m6A readers in diabetes. Biophys Chem 2025; 320-321:107417. [PMID: 39987708 DOI: 10.1016/j.bpc.2025.107417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2024] [Revised: 02/11/2025] [Accepted: 02/16/2025] [Indexed: 02/25/2025]
Abstract
The RNA N6-adenosine methylation, resulting in N6-methyl adenosine (m6A), is one of the most important post-transcriptional modification events in the eukaryotic transcriptome, which is dynamically regulated by methyltransferases (writers), recognition proteins (readers) and demethylases (erasers). Human has five m6A readers namely YTHDC1, YTHDC2, YTHDF1, YTHDF2 and YTHDF3 that specifically recognize and bind to the methylated m6A residue of RNA through their YT521-B homology (YTH) domains, which have been involved in the pathogenesis of diabetes mellitus and its diverse complications such as diabetic nephropathy. Instead of the native N6-methylation, we herein attempted to explore the molecular effect of various non-native N6-substitutions on adenosine (A) binding behavior to YTH domains. A systematic interaction profile of 40 reported N6-substituted adenosine (x6A) mononucleotides with 5 human reader YTH domains was created computationally. Heuristic clustering of the profile divided these YTH domains and these x6A mononucleotides into two subfamilies and three classes, respectively; they represent distinct intrinsic interaction modes between the domains and mononucleotides. Statistical survey unraveled that the volume (Vg) and hydrophobicity (Hg) of N6-substituted chemical groups exhibit linear and nonlinear correlations with the binding energy (ΔGttl) of x6A mononucleotides to YTH domains, respectively; N6-substitutions with moderate size and weak polarity are favorable for the x6A binding. From the profile the N6-bromomethyl adenosine (brm6A) was identified as a potent binder of YTHDF2 YTH domain; its affinity was improved significantly by 77.2-fold from A and considerably by 19.5-fold from m6A. Structural modeling observed that the N6-bromomethyl group of brm6A is tightly packed against an aromatic cage defined by the Trp432-Trp486-Trp491 triad of YTHDF2 YTH domain. Electron-correlation analysis revealed that the bromine atom can form geometrically and energetically satisfactory halogen-π interactions with the aromatic cage, thus conferring considerable affinity and specificity to the domain-brm6A interaction.
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Affiliation(s)
- Yuting Li
- Department of Geriatrics, Suzhou Kowloon Hospital, Shanghai Jiaotong University School of Medicine, Suzhou 215028, China
| | - Peng Tan
- Department of Nephrology, Suzhou Kowloon Hospital, Shanghai Jiaotong University School of Medicine, Suzhou 215028, China
| | - Qianpan Liu
- Department of Nephrology, Suzhou Kowloon Hospital, Shanghai Jiaotong University School of Medicine, Suzhou 215028, China
| | - Huaixin Sun
- Department of Nephrology, Suzhou Kowloon Hospital, Shanghai Jiaotong University School of Medicine, Suzhou 215028, China
| | - Yue Wang
- Department of Nephrology, Suzhou Kowloon Hospital, Shanghai Jiaotong University School of Medicine, Suzhou 215028, China
| | - Siyi Chen
- Department of Nephrology, Suzhou Kowloon Hospital, Shanghai Jiaotong University School of Medicine, Suzhou 215028, China
| | - Weixin Kong
- Department of Nephrology, Suzhou Kowloon Hospital, Shanghai Jiaotong University School of Medicine, Suzhou 215028, China
| | - Xiaoyi Sun
- Department of Nephrology, Suzhou Kowloon Hospital, Shanghai Jiaotong University School of Medicine, Suzhou 215028, China
| | - Xiang Shao
- Department of Nephrology, Suzhou Kowloon Hospital, Shanghai Jiaotong University School of Medicine, Suzhou 215028, China; Centralab, Suzhou Kowloon Hospital, Shanghai Jiaotong University School of Medicine, Suzhou 215028, China.
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3
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Widmer J, Vitalis A, Caflisch A. On the specificity of the recognition of m6A-RNA by YTH reader domains. J Biol Chem 2024; 300:107998. [PMID: 39551145 PMCID: PMC11699332 DOI: 10.1016/j.jbc.2024.107998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 10/26/2024] [Accepted: 11/12/2024] [Indexed: 11/19/2024] Open
Abstract
Most processes of life are the result of polyvalent interactions between macromolecules, often of heterogeneous types and sizes. Frequently, the times associated with these interactions are prohibitively long for interrogation using atomistic simulations. Here, we study the recognition of N6-methylated adenine (m6A) in RNA by the reader domain YTHDC1, a prototypical, cognate pair that challenges simulations through its composition and required timescales. Simulations of RNA pentanucleotides in water reveal that the unbound state can impact (un)binding kinetics in a manner that is both model- and sequence-dependent. This is important because there are two contributions to the specificity of the recognition of the Gm6AC motif: from the sequence adjacent to the central adenine and from its methylation. Next, we establish a reductionist model consisting of an RNA trinucleotide binding to the isolated reader domain in high salt. An adaptive sampling protocol allows us to quantitatively study the dissociation of this complex. Through joint analysis of a data set including both the cognate and control sequences (GAC, Am6AA, and AAA), we derive that both contributions to specificity, sequence, and methylation, are significant and in good agreement with experimental numbers. Analysis of the kinetics suggests that flexibility in both the RNA and the YTHDC1 recognition loop leads to many low-populated unbinding pathways. This multiple-pathway mechanism might be dominant for the binding of unstructured polymers, including RNA and peptides, to proteins when their association is driven by polyvalent, electrostatic interactions.
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Affiliation(s)
- Julian Widmer
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Andreas Vitalis
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
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4
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Piomponi V, Krepl M, Sponer J, Bussi G. Molecular Simulations to Investigate the Impact of N6-Methylation in RNA Recognition: Improving Accuracy and Precision of Binding Free Energy Prediction. J Phys Chem B 2024; 128:8896-8907. [PMID: 39240243 DOI: 10.1021/acs.jpcb.4c03397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2024]
Abstract
N6-Methyladenosine (m6A) is a prevalent RNA post-transcriptional modification that plays crucial roles in RNA stability, structural dynamics, and interactions with proteins. The YT521-B (YTH) family of proteins, which are notable m6A readers, functions through its highly conserved YTH domain. Recent structural investigations and molecular dynamics (MD) simulations have shed light on the mechanism of recognition of m6A by the YTHDC1 protein. Despite advancements, using MD to predict the stabilization induced by m6A on the free energy of binding between RNA and YTH proteins remains challenging due to inaccuracy of the employed force field and limited sampling. For instance, simulations often fail to sufficiently capture the hydration dynamics of the binding pocket. This study addresses these challenges through an innovative methodology that integrates metadynamics, alchemical simulations, and force-field refinement. Importantly, our research identifies hydration of the binding pocket as giving only a minor contribution to the binding free energy and emphasizes the critical importance of precisely tuning force-field parameters to experimental data. By employing a fitting strategy built on alchemical calculations, we refine the m6A partial charge parameters, thereby enabling the simultaneous reproduction of N6 methylation on both the protein binding free energy and the thermodynamic stability of nine RNA duplexes. Our findings underscore the sensitivity of binding free energies to partial charges, highlighting the necessity for thorough parametrization and validation against experimental observations across a range of structural contexts.
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Affiliation(s)
- Valerio Piomponi
- Scuola Internazionale Superiore di Studi Avanzati, SISSA, Via Bonomea 265, Trieste 34136, Italy
- Area Science Park, località Padriciano, 99, Trieste 34149, Italy
| | - Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolská 135, Brno 612 00, Czech Republic
| | - Jiri Sponer
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolská 135, Brno 612 00, Czech Republic
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati, SISSA, Via Bonomea 265, Trieste 34136, Italy
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5
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Zálešák F, Nai F, Herok M, Bochenkova E, Bedi RK, Li Y, Errani F, Caflisch A. Structure-Based Design of a Potent and Selective YTHDC1 Ligand. J Med Chem 2024; 67:9516-9535. [PMID: 38787793 PMCID: PMC11181329 DOI: 10.1021/acs.jmedchem.4c00599] [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: 03/13/2024] [Revised: 05/02/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024]
Abstract
N6-Adenosine methylation (m6A) is a prevalent post-transcriptional modification of mRNA, with YTHDC1 being the reader protein responsible for recognizing this modification in the cell nucleus. Here, we present a protein structure-based medicinal chemistry campaign that resulted in the YTHDC1 inhibitor 40, which shows an equilibrium dissociation constant (Kd) of 49 nM. The crystal structure of the complex (1.6 Å resolution) validated the design. Compound 40 is selective against the cytoplasmic m6A-RNA readers YTHDF1-3 and YTHDC2 and shows antiproliferative activity against the acute myeloid leukemia (AML) cell lines THP-1, MOLM-13, and NOMO-1. For the series of compounds that culminated into ligand 40, the good correlation between the affinity in the biochemical assay and antiproliferative activity in the THP-1 cell line provides evidence of YTHDC1 target engagement in the cell. The binding to YTHDC1 in the cell is further supported by the cellular thermal shift assay. Thus, ligand 40 is a tool compound for studying the role of YTHDC1 in AML.
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Affiliation(s)
- František Zálešák
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Francesco Nai
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Marcin Herok
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Elena Bochenkova
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Rajiv K. Bedi
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Yaozong Li
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Francesco Errani
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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6
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Levintov L, Vashisth H. Adenine Methylation Enhances the Conformational Flexibility of an RNA Hairpin Tetraloop. J Phys Chem B 2024; 128:3157-3166. [PMID: 38535997 PMCID: PMC11000223 DOI: 10.1021/acs.jpcb.4c00522] [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: 01/25/2024] [Revised: 03/10/2024] [Accepted: 03/14/2024] [Indexed: 04/04/2024]
Abstract
The N6-methyladenosine modification is one of the most abundant post-transcriptional modifications in ribonucleic acid (RNA) molecules. Using molecular dynamics simulations and alchemical free-energy calculations, we studied the structural and energetic implications of incorporating this modification in an adenine mononucleotide and an RNA hairpin structure. At the mononucleotide level, we found that the syn configuration is more favorable than the anti configuration by 2.05 ± 0.15 kcal/mol. The unfavorable effect of methylation was due to the steric overlap between the methyl group and a nitrogen atom in the purine ring. We then probed the effect of methylation in an RNA hairpin structure containing an AUCG tetraloop, which is recognized by a "reader" protein (YTHDC1) to promote transcriptional silencing of long noncoding RNAs. While methylation had no significant conformational effect on the hairpin stem, the methylated tetraloop showed enhanced conformational flexibility compared to the unmethylated tetraloop. The increased flexibility was associated with the outward flipping of two bases (A6 and U7) which formed stacking interactions with each other and with the C8 and G9 bases in the tetraloop, leading to a conformation similar to that in the RNA/reader protein complex. Therefore, methylation-induced conformational flexibility likely facilitates RNA recognition by the reader protein.
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Affiliation(s)
- Lev Levintov
- Department of Chemical Engineering
and Bioengineering, University of New Hampshire, Durham, New Hampshire 03824, United States
| | - Harish Vashisth
- Department of Chemical Engineering
and Bioengineering, University of New Hampshire, Durham, New Hampshire 03824, United States
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7
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Liu R, Zhao E, Yu H, Yuan C, Abbas MN, Cui H. Methylation across the central dogma in health and diseases: new therapeutic strategies. Signal Transduct Target Ther 2023; 8:310. [PMID: 37620312 PMCID: PMC10449936 DOI: 10.1038/s41392-023-01528-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 08/26/2023] Open
Abstract
The proper transfer of genetic information from DNA to RNA to protein is essential for cell-fate control, development, and health. Methylation of DNA, RNAs, histones, and non-histone proteins is a reversible post-synthesis modification that finetunes gene expression and function in diverse physiological processes. Aberrant methylation caused by genetic mutations or environmental stimuli promotes various diseases and accelerates aging, necessitating the development of therapies to correct the disease-driver methylation imbalance. In this Review, we summarize the operating system of methylation across the central dogma, which includes writers, erasers, readers, and reader-independent outputs. We then discuss how dysregulation of the system contributes to neurological disorders, cancer, and aging. Current small-molecule compounds that target the modifiers show modest success in certain cancers. The methylome-wide action and lack of specificity lead to undesirable biological effects and cytotoxicity, limiting their therapeutic application, especially for diseases with a monogenic cause or different directions of methylation changes. Emerging tools capable of site-specific methylation manipulation hold great promise to solve this dilemma. With the refinement of delivery vehicles, these new tools are well positioned to advance the basic research and clinical translation of the methylation field.
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Affiliation(s)
- Ruochen Liu
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400715, China
- Jinfeng Laboratory, Chongqing, 401329, China
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Chongqing, 400716, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, 400715, China
| | - Erhu Zhao
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400715, China
- Jinfeng Laboratory, Chongqing, 401329, China
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Chongqing, 400716, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, 400715, China
| | - Huijuan Yu
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400715, China
| | - Chaoyu Yuan
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400715, China
| | - Muhammad Nadeem Abbas
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400715, China
- Jinfeng Laboratory, Chongqing, 401329, China
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Chongqing, 400716, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, 400715, China
| | - Hongjuan Cui
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400715, China.
- Jinfeng Laboratory, Chongqing, 401329, China.
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Chongqing, 400716, China.
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, 400715, China.
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8
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Bedi R, Huang D, Li Y, Caflisch A. Structure-Based Design of Inhibitors of the m 6A-RNA Writer Enzyme METTL3. ACS BIO & MED CHEM AU 2023; 3:359-370. [PMID: 37599794 PMCID: PMC10436262 DOI: 10.1021/acsbiomedchemau.3c00023] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/31/2023] [Accepted: 05/31/2023] [Indexed: 08/22/2023]
Abstract
Methyltransferase-like 3 (METTL3) and METTL14 form a heterodimeric complex that catalyzes the most abundant internal mRNA modification, N6-methyladenosine (m6A). METTL3 is the catalytic subunit that binds the co-substrate S-adenosyl methionine (SAM), while METTL14 is involved in mRNA binding. The m6A modification provides post-transcriptional level control over gene expression as it affects almost all stages of the mRNA life cycle, including splicing, nuclear export, translation, and decay. There is increasing evidence for an oncogenic role of METTL3 in acute myeloid leukemia. Here, we use structural and dynamic details of the catalytic subunit METTL3 for developing small-molecule inhibitors that compete with SAM. Starting from a hit identified by high-throughput docking, protein crystallography and molecular dynamics simulations were employed to guide the optimization of inhibitory activity. The potency was successfully improved by 8000-fold as measured by a homogeneous time-resolved fluorescence assay. The optimized compound is selective against the off-targets RNA methyltransferases METTL1 and METTL16.
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Affiliation(s)
- Rajiv
Kumar Bedi
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Danzhi Huang
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Yaozong Li
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
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9
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Miller LG, Demny M, Tamamis P, Contreras LM. Characterization of epitranscriptome reader proteins experimentally and in silico: Current knowledge and future perspectives beyond the YTH domain. Comput Struct Biotechnol J 2023; 21:3541-3556. [PMID: 37501707 PMCID: PMC10371769 DOI: 10.1016/j.csbj.2023.06.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/23/2023] [Accepted: 06/27/2023] [Indexed: 07/29/2023] Open
Abstract
To date, over 150 chemical modifications to the four canonical RNA bases have been discovered, known collectively as the epitranscriptome. Many of these modifications have been implicated in a variety of cellular processes and disease states. Additional work has been done to identify proteins known as "readers" that selectively interact with RNAs that contain specific chemical modifications. Protein interactomes with N6-methyladenosine (m6A), N1-methyladenosine (m1A), N5-methylcytosine (m5C), and 8-oxo-7,8-dihydroguanosine (8-oxoG) have been determined, mainly through experimental advances in proteomics techniques. However, relatively few proteins have been confirmed to bind directly to RNA containing these modifications. Furthermore, for many of these protein readers, the exact binding mechanisms as well as the exclusivity for recognition of modified RNA species remain elusive, leading to questions regarding their roles within different cellular processes. In the case of the YT-521B homology (YTH) family of proteins, both experimental and in silico techniques have been leveraged to provide valuable biophysical insights into the mechanisms of m6A recognition at atomic resolution. To date, the YTH family is one of the best characterized classes of readers. Here, we review current knowledge about epitranscriptome recognition of the YTH domain proteins from previously published experimental and computational studies. We additionally outline knowledge gaps for proteins beyond the well-studied human YTH domains and the current in silico techniques and resources that can enable investigation of protein interactions with modified RNA outside of the YTH-m6A context.
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Affiliation(s)
- Lucas G. Miller
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Madeline Demny
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | - Phanourios Tamamis
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
- Department of Materials Science & Engineering, Texas A&M University, College Station, TX, USA
| | - Lydia M. Contreras
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
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10
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Ma S, Barr T, Yu J. Recent Advances of RNA m 6A Modifications in Cancer Immunoediting and Immunotherapy. Cancer Treat Res 2023; 190:49-94. [PMID: 38112999 DOI: 10.1007/978-3-031-45654-1_3] [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] [Indexed: 12/21/2023]
Abstract
Cancer immunotherapy, which modulates immune responses against tumors using immune-checkpoint inhibitors or adoptive cell transfer, has emerged as a novel and promising therapy for tumors. However, only a minority of patients demonstrate durable responses, while the majority of patients are resistant to immunotherapy. The immune system can paradoxically constrain and promote tumor development and progression. This process is referred to as cancer immunoediting. The mechanisms of resistance to immunotherapy seem to be that cancer cells undergo immunoediting to evade recognition and elimination by the immune system. RNA modifications, specifically N6-methyladenosine (m6A) methylation, have emerged as a key regulator of various post-transcriptional gene regulatory processes, such as RNA export, splicing, stability, and degradation, which play unappreciated roles in various physiological and pathological processes, including immune system development and cancer pathogenesis. Therefore, a deeper understanding of the mechanisms by which RNA modifications impact the cancer immunoediting process can provide insight into the mechanisms of resistance to immunotherapies and the strategies that can be used to overcome such resistance. In this chapter, we briefly introduce the background of cancer immunoediting and immunotherapy. We also review and discuss the roles and mechanisms of RNA m6A modifications in fine-tuning the innate and adaptive immune responses, as well as in regulating tumor escape from immunosurveillance. Finally, we summarize the current strategies targeting m6A regulators for cancer immunotherapy.
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Affiliation(s)
- Shoubao Ma
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Los Angeles, CA, 91010, USA
- Hematologic Malignancies and Stem Cell Transplantation Institute, City of Hope National Medical Center, Los Angeles, CA, 91010, USA
| | - Tasha Barr
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Los Angeles, CA, 91010, USA
- Hematologic Malignancies and Stem Cell Transplantation Institute, City of Hope National Medical Center, Los Angeles, CA, 91010, USA
| | - Jianhua Yu
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Los Angeles, CA, 91010, USA.
- Hematologic Malignancies and Stem Cell Transplantation Institute, City of Hope National Medical Center, Los Angeles, CA, 91010, USA.
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope, Los Angeles, CA, 91010, USA.
- Comprehensive Cancer Center, City of Hope, Los Angeles, CA, 91010, USA.
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11
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Interaction preferences between protein side chains and key epigenetic modifications 5-methylcytosine, 5-hydroxymethycytosine and N 6-methyladenine. Sci Rep 2022; 12:19583. [PMID: 36380112 PMCID: PMC9666514 DOI: 10.1038/s41598-022-23585-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 11/02/2022] [Indexed: 11/16/2022] Open
Abstract
Covalent modifications of standard DNA/RNA nucleobases affect epigenetic regulation of gene expression by modulating interactions between nucleic acids and protein readers. We derive here the absolute binding free energies and analyze the binding modalities between key modified nucleobases 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC) and N6-methyladenine (m6A) and all non-prolyl/non-glycyl protein side chains using molecular dynamics simulations and umbrella sampling in both water and methanol, the latter mimicking the low dielectric environment at the dehydrated nucleic-acid/protein interfaces. We verify the derived affinities by comparing against a comprehensive set of high-resolution structures of nucleic-protein complexes involving 5mC. Our analysis identifies protein side chains that are highly tuned for detecting cytosine methylation as a function of the environment and can thus serve as microscopic readers of epigenetic marks. Conversely, we show that the relative ordering of sidechain affinities for 5hmC and m6A does not differ significantly from those for their precursor bases, cytosine and adenine, respectively, especially in the low dielectric environment. For those two modified bases, the effect is more nuanced and manifests itself primarily at the level of absolute changes in the binding free energy. Our results contribute towards establishing a quantitative foundation for understanding, predicting and modulating the interactions between modified nucleic acids and proteins at the atomistic level.
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12
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Piomponi V, Fröhlking T, Bernetti M, Bussi G. Molecular Simulations Matching Denaturation Experiments for N 6-Methyladenosine. ACS CENTRAL SCIENCE 2022; 8:1218-1228. [PMID: 36032773 PMCID: PMC9413829 DOI: 10.1021/acscentsci.2c00565] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Indexed: 06/15/2023]
Abstract
Post-transcriptional modifications are crucial for RNA function and can affect its structure and dynamics. Force-field-based classical molecular dynamics simulations are a fundamental tool to characterize biomolecular dynamics, and their application to RNA is flourishing. Here, we show that the set of force-field parameters for N6-methyladenosine (m6A) developed for the commonly used AMBER force field does not reproduce duplex denaturation experiments and, specifically, cannot be used to describe both paired and unpaired states. Then, we use reweighting techniques to derive new parameters matching available experimental data. The resulting force field can be used to properly describe paired and unpaired m6A in both syn and anti conformation, which thus opens the way to the use of molecular simulations to investigate the effects of N6 methylations on RNA structural dynamics.
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13
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Nai F, Nachawati R, Zálešák F, Wang X, Li Y, Caflisch A. Fragment Ligands of the m 6A-RNA Reader YTHDF2. ACS Med Chem Lett 2022; 13:1500-1509. [PMID: 36110386 PMCID: PMC9466600 DOI: 10.1021/acsmedchemlett.2c00303] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/11/2022] [Indexed: 12/24/2022] Open
Affiliation(s)
- Francesco Nai
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Raed Nachawati
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - František Zálešák
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Xiang Wang
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Yaozong Li
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
- Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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14
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Zhou W, Han Z, Wu Z, Gong W, Yang S, Chen L, Li C. Specific recognition between
YTHDF3
and
m
6
A
‐modified
RNA
: An all‐atom molecular dynamics simulation study. Proteins 2022; 90:1965-1972. [DOI: 10.1002/prot.26389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 05/10/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Wenxue Zhou
- Faculty of Environmental and Life Sciences Beijing University of Technology Beijing China
| | - Zhongjie Han
- Faculty of Environmental and Life Sciences Beijing University of Technology Beijing China
| | - Zhixiang Wu
- Faculty of Environmental and Life Sciences Beijing University of Technology Beijing China
| | - Weikang Gong
- Faculty of Environmental and Life Sciences Beijing University of Technology Beijing China
| | - Shuang Yang
- Faculty of Environmental and Life Sciences Beijing University of Technology Beijing China
| | - Lei Chen
- Faculty of Environmental and Life Sciences Beijing University of Technology Beijing China
| | - Chunhua Li
- Faculty of Environmental and Life Sciences Beijing University of Technology Beijing China
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15
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Cancer epitranscriptomics in a nutshell. Curr Opin Genet Dev 2022; 75:101924. [PMID: 35679814 DOI: 10.1016/j.gde.2022.101924] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/29/2022] [Accepted: 05/03/2022] [Indexed: 11/22/2022]
Abstract
Remarkable technological progress has led to breakthrough discoveries in epitranscriptomics, reshaping our understanding of modifications decorating RNA. The past decade has seen a tremendous endeavor to describe the nature, functions, and biological roles of messenger RNA (mRNA) modifications, positioning epitranscriptomics as a crucial pillar in tumor biology. Like DNA and histone modifications, mRNA marks have been increasingly linked to cancer pathogenesis. Here, we summarize the latest research in cancer epitranscriptomics with emphasis on N6-methyladenosine, untangling its contribution to five prime oncogenic features: tumor growth, activating invasion and metastasis, stemness, metabolic reprogramming, and tumor microenvironment. We discuss mRNA-modifying enzymes, their impact on biological processes, and contribution to cancer hallmarks. We spotlight epitranscriptomics as a promising bonanza for forthcoming targeting approaches in cancer therapy.
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16
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Zhang R, Zhang Y, Guo F, Li S, Cui H. RNA N6-Methyladenosine Modifications and Its Roles in Alzheimer's Disease. Front Cell Neurosci 2022; 16:820378. [PMID: 35401117 PMCID: PMC8989074 DOI: 10.3389/fncel.2022.820378] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 02/28/2022] [Indexed: 11/13/2022] Open
Abstract
The importance of epitranscriptomics in regulating gene expression has received widespread attention. Recently, RNA methylation modifications, particularly N6-methyladenosine (m6A), have received marked attention. m6A, the most common and abundant type of eukaryotic methylation modification in RNAs, is a dynamic reversible modification that regulates nuclear splicing, stability, translation, and subcellular localization of RNAs. These processes are involved in the occurrence and development of many diseases. An increasing number of studies have focused on the role of m6A modification in Alzheimer's disease, which is the most common neurodegenerative disease. This review focuses on the general features, mechanisms, and functions of m6A methylation modification and its role in Alzheimer's disease.
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Affiliation(s)
- Runjiao Zhang
- Department of Anatomy, Hebei Medical University, Shijiazhuang, China
- Neuroscience Research Center, Hebei Medical University, Shijiazhuang, China
| | - Yizhou Zhang
- Department of Anatomy, Hebei Medical University, Shijiazhuang, China
- Neuroscience Research Center, Hebei Medical University, Shijiazhuang, China
- Hebei Key Laboratory of Neurodegenerative Disease Mechanism, Shijiazhuang, China
| | - Fangzhen Guo
- Department of Anatomy, Hebei Medical University, Shijiazhuang, China
- Neuroscience Research Center, Hebei Medical University, Shijiazhuang, China
| | - Sha Li
- Department of Anatomy, Hebei Medical University, Shijiazhuang, China
- Neuroscience Research Center, Hebei Medical University, Shijiazhuang, China
- Hebei Key Laboratory of Neurodegenerative Disease Mechanism, Shijiazhuang, China
| | - Huixian Cui
- Department of Anatomy, Hebei Medical University, Shijiazhuang, China
- Neuroscience Research Center, Hebei Medical University, Shijiazhuang, China
- Hebei Key Laboratory of Neurodegenerative Disease Mechanism, Shijiazhuang, China
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17
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Xiao Q, Lei L, Ren J, Peng M, Jing Y, Jiang X, Huang J, Tao Y, Lin C, Yang J, Sun M, Tang L, Wei X, Yang Z, Zhang L. Mutant NPM1-Regulated FTO-Mediated m 6A Demethylation Promotes Leukemic Cell Survival via PDGFRB/ERK Signaling Axis. Front Oncol 2022; 12:817584. [PMID: 35211409 PMCID: PMC8862181 DOI: 10.3389/fonc.2022.817584] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 01/17/2022] [Indexed: 12/12/2022] Open
Abstract
Acute myeloid leukemia (AML) with nucleophosmin 1 (NPM1) mutations exhibits distinct biological and clinical features, accounting for approximately one-third of AML. Recently, the N6-methyladenosine (m6A) RNA modification has emerged as a new epigenetic modification to contribute to tumorigenesis and development. However, there is limited knowledge on the role of m6A modifications in NPM1-mutated AML. In this study, the decreased m6A level was first detected and high expression of fat mass and obesity-associated protein (FTO) was responsible for the m6A suppression in NPM1-mutated AML. FTO upregulation was partially induced by NPM1 mutation type A (NPM1-mA) through impeding the proteasome pathway. Importantly, FTO promoted leukemic cell survival by facilitating cell cycle and inhibiting cell apoptosis. Mechanistic investigations demonstrated that FTO depended on its m6A RNA demethylase activity to activate PDGFRB/ERK signaling axis. Our findings indicate that FTO-mediated m6A demethylation plays an oncogenic role in NPM1-mutated AML and provide a new layer of epigenetic insight for future treatments of this distinctly leukemic entity.
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Affiliation(s)
- Qiaoling Xiao
- Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Li Lei
- Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Jun Ren
- Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Meixi Peng
- Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Yipei Jing
- Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Xueke Jiang
- Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Junpeng Huang
- Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Yonghong Tao
- Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Can Lin
- Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Jing Yang
- Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Minghui Sun
- Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Lisha Tang
- Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Xingyu Wei
- Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Zailin Yang
- Hematology Oncology Center, Chongqing University Cancer Hospital, Chongqing, China
| | - Ling Zhang
- Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing, China
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18
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Jones AN, Tikhaia E, Mourão A, Sattler M. Structural effects of m6A modification of the Xist A-repeat AUCG tetraloop and its recognition by YTHDC1. Nucleic Acids Res 2022; 50:2350-2362. [PMID: 35166835 PMCID: PMC8887474 DOI: 10.1093/nar/gkac080] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 12/28/2021] [Accepted: 02/11/2022] [Indexed: 12/12/2022] Open
Abstract
The A-repeat region of the lncRNA Xist is critical for X inactivation and harbors several N6-methyladenosine (m6A) modifications. How the m6A modification affects the conformation of the conserved AUCG tetraloop hairpin of the A-repeats and how it can be recognized by the YTHDC1 reader protein is unknown. Here, we report the NMR solution structure of the (m6A)UCG hairpin, which reveals that the m6A base extends 5′ stacking of the A-form helical stem, resembling the unmethylated AUCG tetraloop. A crystal structure of YTHDC1 bound to the (m6A)UCG tetraloop shows that the (m6A)UC nucleotides are recognized by the YTH domain of YTHDC1 in a single-stranded conformation. The m6A base inserts into the aromatic cage and the U and C bases interact with a flanking charged surface region, resembling the recognition of single-stranded m6A RNA ligands. Notably, NMR and fluorescence quenching experiments show that the binding requires local unfolding of the upper stem region of the (m6A)UCG hairpin. Our data show that m6A can be readily accommodated in hairpin loop regions, but recognition by YTH readers requires local unfolding of flanking stem regions. This suggests how m6A modifications may regulate lncRNA function by modulating RNA structure.
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Affiliation(s)
- Alisha N Jones
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85747, Garching, Germany
| | - Ekaterina Tikhaia
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85747, Garching, Germany
| | - André Mourão
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85747, Garching, Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85747, Garching, Germany
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19
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Krepl M, Damberger FF, von Schroetter C, Theler D, Pokorná P, Allain FHT, Šponer J. Recognition of N6-Methyladenosine by the YTHDC1 YTH Domain Studied by Molecular Dynamics and NMR Spectroscopy: The Role of Hydration. J Phys Chem B 2021; 125:7691-7705. [PMID: 34258996 DOI: 10.1021/acs.jpcb.1c03541] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The YTH domain of YTHDC1 belongs to a class of protein "readers", recognizing the N6-methyladenosine (m6A) chemical modification in mRNA. Static ensemble-averaged structures revealed details of N6-methyl recognition via a conserved aromatic cage. Here, we performed molecular dynamics (MD) simulations along with nuclear magnetic resonance (NMR) and isothermal titration calorimetry (ITC) to examine how dynamics and solvent interactions contribute to the m6A recognition and negative selectivity toward an unmethylated substrate. The structured water molecules surrounding the bound RNA and the methylated substrate's ability to exclude bulk water molecules contribute to the YTH domain's preference for m6A. Intrusions of bulk water deep into the binding pocket disrupt binding of unmethylated adenosine. The YTHDC1's preference for the 5'-Gm6A-3' motif is partially facilitated by a network of water-mediated interactions between the 2-amino group of the guanosine and residues in the m6A binding pocket. The 5'-Im6A-3' (where I is inosine) motif can be recognized too, but disruption of the water network lowers affinity. The D479A mutant also disrupts the water network and destabilizes m6A binding. Our interdisciplinary study of the YTHDC1 protein-RNA complex reveals an unusual physical mechanism by which solvent interactions contribute toward m6A recognition.
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Affiliation(s)
- Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Fred Franz Damberger
- Department of Biology, Institute of Biochemistry, ETH Zürich, 8093 Zürich, Switzerland
| | | | - Dominik Theler
- Department of Biology, Institute of Biochemistry, ETH Zürich, 8093 Zürich, Switzerland
| | - Pavlína Pokorná
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Frédéric H-T Allain
- Department of Biology, Institute of Biochemistry, ETH Zürich, 8093 Zürich, Switzerland
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Olomouc 783 71, Czech Republic
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