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For: Koh CWQ, Goh YT, Goh WSS. Atlas of quantitative single-base-resolution N6-methyl-adenine methylomes. Nat Commun 2019;10:5636. [PMID: 31822664 DOI: 10.1038/s41467-019-13561-z] [Citation(s) in RCA: 132] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 11/12/2019] [Indexed: 01/14/2023]  Open
Number Cited by Other Article(s)
1
Huang H, Zhou F, Jia J, Zhang H. DTC-m6Am: A Framework for Recognizing N6,2'-O-dimethyladenosine Sites in Unbalanced Classification Patterns Based on DenseNet and Attention Mechanisms. FRONT BIOSCI-LANDMRK 2025;30:36603. [PMID: 40302345 DOI: 10.31083/fbl36603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2024] [Revised: 03/12/2025] [Accepted: 03/25/2025] [Indexed: 05/02/2025]
2
Spangenberg J, Mündnich S, Busch A, Pastore S, Wierczeiko A, Goettsch W, Dietrich V, Pryszcz LP, Cruciani S, Novoa EM, Joshi K, Perera R, Di Giorgio S, Arrubarrena P, Tellioglu I, Poon CL, Wan YK, Göke J, Hildebrandt A, Dieterich C, Helm M, Marz M, Gerber S, Alagna N. The RMaP challenge of predicting RNA modifications by nanopore sequencing. Commun Chem 2025;8:115. [PMID: 40221591 PMCID: PMC11993749 DOI: 10.1038/s42004-025-01507-0] [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: 10/10/2024] [Accepted: 03/24/2025] [Indexed: 04/14/2025]  Open
3
Chen Y, Davidson NM, Wan YK, Yao F, Su Y, Gamaarachchi H, Sim A, Patel H, Low HM, Hendra C, Wratten L, Hakkaart C, Sawyer C, Iakovleva V, Lee PL, Xin L, Ng HEV, Loo JM, Ong X, Ng HQA, Wang J, Koh WQC, Poon SYP, Stanojevic D, Tran HD, Lim KHE, Toh SY, Ewels PA, Ng HH, Iyer NG, Thiery A, Chng WJ, Chen L, DasGupta R, Sikic M, Chan YS, Tan BOP, Wan Y, Tam WL, Yu Q, Khor CC, Wüstefeld T, Lezhava A, Pratanwanich PN, Love MI, Goh WSS, Ng SB, Oshlack A, Göke J. A systematic benchmark of Nanopore long-read RNA sequencing for transcript-level analysis in human cell lines. Nat Methods 2025;22:801-812. [PMID: 40082608 PMCID: PMC11978509 DOI: 10.1038/s41592-025-02623-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 02/04/2025] [Indexed: 03/16/2025]
4
Liu JF, Hawley BR, Nicholson LS, Jaffrey SR. Decoding m6Am by simultaneous transcription-start mapping and methylation quantification. eLife 2025;13:RP104139. [PMID: 40162895 PMCID: PMC11957539 DOI: 10.7554/elife.104139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2025]  Open
5
Guo W, Ren Z, Huang X, Liu J, Shao J, Ma X, Wei C, Cun Y, He J, Zhang J, Wu Z, Guo Y, Zhang Z, Feng Z, He J, Wang J. Single-molecule m6A detection empowered by endogenous labeling unveils complexities across RNA isoforms. Mol Cell 2025;85:1233-1246.e7. [PMID: 39922195 DOI: 10.1016/j.molcel.2025.01.014] [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: 02/05/2024] [Revised: 12/26/2024] [Accepted: 01/15/2025] [Indexed: 02/10/2025]
6
Verhamme R, Jansens RJJ, Liu J, Van Raemdonck F, Van Waesberghe C, Nicholson L, Jaffrey SR, Favoreel HW. The pseudorabies virus UL13 protein kinase triggers phosphorylation of the RNA demethylase FTO, which is associated with FTO-dependent suppression of interferon-stimulated gene expression. J Virol 2025;99:e0201924. [PMID: 39791911 PMCID: PMC11852732 DOI: 10.1128/jvi.02019-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2024] [Accepted: 12/11/2024] [Indexed: 01/12/2025]  Open
7
Liu JF, Hawley BR, Nicholson LS, Jaffrey SR. Decoding m6Am by simultaneous transcription-start mapping and methylation quantification. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.10.16.618717. [PMID: 39677659 PMCID: PMC11642800 DOI: 10.1101/2024.10.16.618717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2024]
8
Li P, Lin Y, Ma H, Zhang J, Zhang Q, Yan R, Fan Y. Epigenetic regulation in female reproduction: the impact of m6A on maternal-fetal health. Cell Death Discov 2025;11:43. [PMID: 39904996 PMCID: PMC11794895 DOI: 10.1038/s41420-025-02324-z] [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: 09/02/2024] [Revised: 01/09/2025] [Accepted: 01/24/2025] [Indexed: 02/06/2025]  Open
9
Liu C, Liang H, Wan AH, Xiao M, Sun L, Yu Y, Yan S, Deng Y, Liu R, Fang J, Wang Z, He W, Wan G. Decoding the m6A epitranscriptomic landscape for biotechnological applications using a direct RNA sequencing approach. Nat Commun 2025;16:798. [PMID: 39824841 PMCID: PMC11742432 DOI: 10.1038/s41467-025-56173-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 01/09/2025] [Indexed: 01/20/2025]  Open
10
Diensthuber G, Novoa EM. Charting the epitranscriptomic landscape across RNA biotypes using native RNA nanopore sequencing. Mol Cell 2025;85:276-289. [PMID: 39824168 DOI: 10.1016/j.molcel.2024.12.014] [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: 09/10/2024] [Revised: 12/04/2024] [Accepted: 12/11/2024] [Indexed: 01/20/2025]
11
Cui X, Li H, Huang X, Xue T, Wang S, Zhu X, Jing X. N6-Methyladenosine Modification on the Function of Female Reproductive Development and Related Diseases. Immun Inflamm Dis 2024;12:e70089. [PMID: 39660878 PMCID: PMC11632877 DOI: 10.1002/iid3.70089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2024] [Revised: 10/17/2024] [Accepted: 11/20/2024] [Indexed: 12/12/2024]  Open
12
Teng H, Stoiber M, Bar-Joseph Z, Kingsford C. Detecting m6A RNA modification from nanopore sequencing using a semisupervised learning framework. Genome Res 2024;34:1987-1999. [PMID: 39406497 DOI: 10.1101/gr.278960.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 10/03/2024] [Indexed: 10/23/2024]
13
Li Q, Liu J, Guo L, Zhang Y, Chen Y, Liu H, Cheng H, Deng L, Qiu J, Zhang K, Goh WSS, Wang Y, Peng Q. Decoding the interplay between m6A modification and stress granule stability by live-cell imaging. SCIENCE ADVANCES 2024;10:eadp5689. [PMID: 39546601 PMCID: PMC11566999 DOI: 10.1126/sciadv.adp5689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 10/16/2024] [Indexed: 11/17/2024]
14
An H, Hong Y, Goh YT, Koh CWQ, Kanwal S, Zhang Y, Lu Z, Yap PML, Neo SP, Wong CM, Wong AST, Yu Y, Ho JSY, Gunaratne J, Goh WSS. m6Am sequesters PCF11 to suppress premature termination and drive neuroblastoma differentiation. Mol Cell 2024;84:4142-4157.e14. [PMID: 39481383 DOI: 10.1016/j.molcel.2024.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 08/08/2024] [Accepted: 10/01/2024] [Indexed: 11/02/2024]
15
Fang X, Lu Z, Wang Y, Zhao R, Mo J, Yang W, Sun M, Zhou X, Weng X. Exonuclease-assisted enrichment and base resolution analysis of pseudouridine in single-stranded RNA. Chem Sci 2024:d4sc03576c. [PMID: 39479159 PMCID: PMC11515940 DOI: 10.1039/d4sc03576c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Accepted: 10/20/2024] [Indexed: 11/02/2024]  Open
16
Yu B, Nagae G, Midorikawa Y, Tatsuno K, Dasgupta B, Aburatani H, Ueda H. m6ATM: a deep learning framework for demystifying the m6A epitranscriptome with Nanopore long-read RNA-seq data. Brief Bioinform 2024;25:bbae529. [PMID: 39438075 PMCID: PMC11495873 DOI: 10.1093/bib/bbae529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 09/16/2024] [Accepted: 10/07/2024] [Indexed: 10/25/2024]  Open
17
YuYan, Yuan E. Regulatory effect of N6-methyladenosine on tumor angiogenesis. Front Immunol 2024;15:1453774. [PMID: 39295872 PMCID: PMC11408240 DOI: 10.3389/fimmu.2024.1453774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Accepted: 08/19/2024] [Indexed: 09/21/2024]  Open
18
Cao Y, Jia M, Duan C, Yang Z, Cheng B, Wang R. The m6A regulators in prostate cancer: molecular basis and clinical perspective. Front Pharmacol 2024;15:1448872. [PMID: 39268470 PMCID: PMC11391310 DOI: 10.3389/fphar.2024.1448872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Accepted: 08/14/2024] [Indexed: 09/15/2024]  Open
19
Jin H, Shi Z, Zhou T, Xie S. Regulation of m6Am RNA modification and its implications in human diseases. J Mol Cell Biol 2024;16:mjae012. [PMID: 38509021 PMCID: PMC11345611 DOI: 10.1093/jmcb/mjae012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 03/06/2024] [Accepted: 03/19/2024] [Indexed: 03/22/2024]  Open
20
Wang Z, Fang Y, Liu Z, Hao N, Zhang HH, Sun X, Que J, Ding H. Adapting nanopore sequencing basecalling models for modification detection via incremental learning and anomaly detection. Nat Commun 2024;15:7148. [PMID: 39169028 PMCID: PMC11339354 DOI: 10.1038/s41467-024-51639-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 08/12/2024] [Indexed: 08/23/2024]  Open
21
Wang K, Wang Y, Li Y, Fang B, Li B, Cheng W, Wang K, Yang S. The potential of RNA methylation in the treatment of cardiovascular diseases. iScience 2024;27:110524. [PMID: 39165846 PMCID: PMC11334793 DOI: 10.1016/j.isci.2024.110524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2024]  Open
22
Yang Y, Lu Y, Wang Y, Wen X, Qi C, Piao W, Jin H. Current progress in strategies to profile transcriptomic m6A modifications. Front Cell Dev Biol 2024;12:1392159. [PMID: 39055651 PMCID: PMC11269109 DOI: 10.3389/fcell.2024.1392159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 06/18/2024] [Indexed: 07/27/2024]  Open
23
Zheng Y, Lin S, Chen M, Xu L, Huang H. Regulation of N6-methyladenosine modification in erythropoiesis and thalassemia. Clin Genet 2024;106:3-12. [PMID: 38488342 DOI: 10.1111/cge.14518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/21/2024] [Accepted: 02/23/2024] [Indexed: 06/04/2024]
24
XIONG J, FENG T, YUAN BF. [Advances in mapping analysis of ribonucleic acid modifications through sequencing]. Se Pu 2024;42:632-645. [PMID: 38966972 PMCID: PMC11224946 DOI: 10.3724/sp.j.1123.2023.12025] [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: 12/20/2023] [Indexed: 07/06/2024]  Open
25
Relier S, Schiffers S, Beiki H, Oberdoerffer S. Enhanced ac4C detection in RNA via chemical reduction and cDNA synthesis with modified dNTPs. RNA (NEW YORK, N.Y.) 2024;30:938-953. [PMID: 38697668 PMCID: PMC11182010 DOI: 10.1261/rna.079863.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 04/04/2024] [Indexed: 05/05/2024]
26
Xue H, Ma Y, Guan K, Zhou Y, Liu Y, Cao F, Kang X. The role of m6A methylation in targeted therapy resistance in lung cancer. Am J Cancer Res 2024;14:2994-3009. [PMID: 39005690 PMCID: PMC11236795 DOI: 10.62347/lxos2662] [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: 01/18/2024] [Accepted: 05/28/2024] [Indexed: 07/16/2024]  Open
27
Ni P, Xu J, Zhong Z, Luo F, Wang J. RNA m6A detection using raw current signals and basecalling errors from Nanopore direct RNA sequencing reads. Bioinformatics 2024;40:btae375. [PMID: 38889266 PMCID: PMC11211211 DOI: 10.1093/bioinformatics/btae375] [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: 01/26/2024] [Revised: 05/28/2024] [Accepted: 06/16/2024] [Indexed: 06/20/2024]  Open
28
Knight HM, Demirbugen Öz M, PerezGrovas-Saltijeral A. Dysregulation of RNA modification systems in clinical populations with neurocognitive disorders. Neural Regen Res 2024;19:1256-1261. [PMID: 37905873 PMCID: PMC11467953 DOI: 10.4103/1673-5374.385858] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/05/2023] [Accepted: 08/10/2023] [Indexed: 11/02/2023]  Open
29
Wu Y, Shao W, Yan M, Wang Y, Xu P, Huang G, Li X, Gregory BD, Yang J, Wang H, Yu X. Transfer learning enables identification of multiple types of RNA modifications using nanopore direct RNA sequencing. Nat Commun 2024;15:4049. [PMID: 38744925 PMCID: PMC11094168 DOI: 10.1038/s41467-024-48437-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 04/26/2024] [Indexed: 05/16/2024]  Open
30
Acera Mateos P, J Sethi A, Ravindran A, Srivastava A, Woodward K, Mahmud S, Kanchi M, Guarnacci M, Xu J, W S Yuen Z, Zhou Y, Sneddon A, Hamilton W, Gao J, M Starrs L, Hayashi R, Wickramasinghe V, Zarnack K, Preiss T, Burgio G, Dehorter N, E Shirokikh N, Eyras E. Prediction of m6A and m5C at single-molecule resolution reveals a transcriptome-wide co-occurrence of RNA modifications. Nat Commun 2024;15:3899. [PMID: 38724548 PMCID: PMC11082244 DOI: 10.1038/s41467-024-47953-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 04/15/2024] [Indexed: 05/12/2024]  Open
31
Pang J, Kuang TD, Yu XY, Novák P, Long Y, Liu M, Deng WQ, Zhu X, Yin K. N6-methyladenosine in myeloid cells: a novel regulatory factor for inflammation-related diseases. J Physiol Biochem 2024;80:249-260. [PMID: 38158555 DOI: 10.1007/s13105-023-01002-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 12/04/2023] [Indexed: 01/03/2024]
32
Chan A, Naarmann-de Vries IS, Scheitl CPM, Höbartner C, Dieterich C. Detecting m6A at single-molecular resolution via direct RNA sequencing and realistic training data. Nat Commun 2024;15:3323. [PMID: 38637518 PMCID: PMC11026524 DOI: 10.1038/s41467-024-47661-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 04/05/2024] [Indexed: 04/20/2024]  Open
33
Andersson D, Kebede FT, Escobar M, Österlund T, Ståhlberg A. Principles of digital sequencing using unique molecular identifiers. Mol Aspects Med 2024;96:101253. [PMID: 38367531 DOI: 10.1016/j.mam.2024.101253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/26/2024] [Accepted: 02/03/2024] [Indexed: 02/19/2024]
34
Liu WW, Zheng SQ, Li T, Fei YF, Wang C, Zhang S, Wang F, Jiang GM, Wang H. RNA modifications in cellular metabolism: implications for metabolism-targeted therapy and immunotherapy. Signal Transduct Target Ther 2024;9:70. [PMID: 38531882 DOI: 10.1038/s41392-024-01777-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 02/08/2024] [Accepted: 02/19/2024] [Indexed: 03/28/2024]  Open
35
Warminski M, Trepkowska E, Smietanski M, Sikorski PJ, Baranowski MR, Bednarczyk M, Kedzierska H, Majewski B, Mamot A, Papiernik D, Popielec A, Serwa RA, Shimanski BA, Sklepkiewicz P, Sklucka M, Sokolowska O, Spiewla T, Toczydlowska-Socha D, Warminska Z, Wolosewicz K, Zuberek J, Mugridge JS, Nowis D, Golab J, Jemielity J, Kowalska J. Trinucleotide mRNA Cap Analogue N6-Benzylated at the Site of Posttranscriptional m6Am Mark Facilitates mRNA Purification and Confers Superior Translational Properties In Vitro and In Vivo. J Am Chem Soc 2024;146:8149-8163. [PMID: 38442005 PMCID: PMC10979456 DOI: 10.1021/jacs.3c12629] [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: 11/10/2023] [Revised: 02/12/2024] [Accepted: 02/12/2024] [Indexed: 03/07/2024]
36
Goh WSS, Kuang Y. Heterogeneity of chemical modifications on RNA. Biophys Rev 2024;16:79-87. [PMID: 38495447 PMCID: PMC10937866 DOI: 10.1007/s12551-023-01128-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 08/27/2023] [Indexed: 03/19/2024]  Open
37
Liang Z, Ye H, Ma J, Wei Z, Wang Y, Zhang Y, Huang D, Song B, Meng J, Rigden DJ, Chen K. m6A-Atlas v2.0: updated resources for unraveling the N6-methyladenosine (m6A) epitranscriptome among multiple species. Nucleic Acids Res 2024;52:D194-D202. [PMID: 37587690 PMCID: PMC10768109 DOI: 10.1093/nar/gkad691] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/02/2023] [Accepted: 08/10/2023] [Indexed: 08/18/2023]  Open
38
Wang Z, Fang Y, Liu Z, Hao N, Zhang HH, Sun X, Que J, Ding H. Adapting Nanopore Sequencing Basecalling Models for Modification Detection via Incremental Learning and Anomaly Detection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.19.572449. [PMID: 38187611 PMCID: PMC10769248 DOI: 10.1101/2023.12.19.572431] [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: 02/23/2024]
39
Bi CF, Liu J, Hu XD, Yang LS, Zhang JF. Novel insights into the regulatory role of N6-methyladenosine methylation modified autophagy in sepsis. Aging (Albany NY) 2023;15:15676-15700. [PMID: 38112620 PMCID: PMC10781468 DOI: 10.18632/aging.205312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 10/23/2023] [Indexed: 12/21/2023]
40
Ren J, Chen X, Zhang Z, Shi H, Wu S. DPred_3S: identifying dihydrouridine (D) modification on three species epitranscriptome based on multiple sequence-derived features. Front Genet 2023;14:1334132. [PMID: 38169665 PMCID: PMC10758487 DOI: 10.3389/fgene.2023.1334132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 11/29/2023] [Indexed: 01/05/2024]  Open
41
Benak D, Kolar F, Zhang L, Devaux Y, Hlavackova M. RNA modification m6Am: the role in cardiac biology. Epigenetics 2023;18:2218771. [PMID: 37331009 DOI: 10.1080/15592294.2023.2218771] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 05/19/2023] [Accepted: 05/23/2023] [Indexed: 06/20/2023]  Open
42
Zhang M, Xiao Y, Jiang Z, Yi C. Quantifying m6A and Ψ Modifications in the Transcriptome via Chemical-Assisted Approaches. Acc Chem Res 2023;56:2980-2991. [PMID: 37851547 DOI: 10.1021/acs.accounts.3c00436] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
43
Jia J, Wei Z, Sun M. EMDL_m6Am: identifying N6,2'-O-dimethyladenosine sites based on stacking ensemble deep learning. BMC Bioinformatics 2023;24:397. [PMID: 37880673 PMCID: PMC10598967 DOI: 10.1186/s12859-023-05543-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 10/20/2023] [Indexed: 10/27/2023]  Open
44
Wu Y, Pu X, Wu S, Zhang Y, Fu S, Tang H, Wang X, Xu M. PCIF1, the only methyltransferase of N6,2-O-dimethyladenosine. Cancer Cell Int 2023;23:226. [PMID: 37779183 PMCID: PMC10544176 DOI: 10.1186/s12935-023-03066-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 09/14/2023] [Indexed: 10/03/2023]  Open
45
Liu J, Huang T, Yao J, Zhao T, Zhang Y, Zhang R. Epitranscriptomic subtyping, visualization, and denoising by global motif visualization. Nat Commun 2023;14:5944. [PMID: 37741827 PMCID: PMC10517956 DOI: 10.1038/s41467-023-41653-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 09/13/2023] [Indexed: 09/25/2023]  Open
46
Breger K, Kunkler CN, O'Leary NJ, Hulewicz JP, Brown JA. Ghost authors revealed: The structure and function of human N6 -methyladenosine RNA methyltransferases. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023;15:e1810. [PMID: 37674370 PMCID: PMC10915109 DOI: 10.1002/wrna.1810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/14/2023] [Accepted: 07/15/2023] [Indexed: 09/08/2023]
47
Li K, Peng J, Yi C. Sequencing methods and functional decoding of mRNA modifications. FUNDAMENTAL RESEARCH 2023;3:738-748. [PMID: 38933299 PMCID: PMC11197720 DOI: 10.1016/j.fmre.2023.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 04/27/2023] [Accepted: 05/07/2023] [Indexed: 06/28/2024]  Open
48
Zhao Y, Luo Q, Wang W, Geng S, Sun Y, Xu T. METTL16, an evolutionarily conserved m6A methyltransferase member, inhibits the antiviral immune response of miiuy croaker (Miichthys miiuy). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023;145:104713. [PMID: 37085020 DOI: 10.1016/j.dci.2023.104713] [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: 01/29/2023] [Revised: 04/17/2023] [Accepted: 04/17/2023] [Indexed: 05/03/2023]
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Deng X, Qing Y, Horne D, Huang H, Chen J. The roles and implications of RNA m6A modification in cancer. Nat Rev Clin Oncol 2023;20:507-526. [PMID: 37221357 DOI: 10.1038/s41571-023-00774-x] [Citation(s) in RCA: 161] [Impact Index Per Article: 80.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2023] [Indexed: 05/25/2023]
50
Flamand MN, Tegowski M, Meyer KD. The Proteins of mRNA Modification: Writers, Readers, and Erasers. Annu Rev Biochem 2023;92:145-173. [PMID: 37068770 PMCID: PMC10443600 DOI: 10.1146/annurev-biochem-052521-035330] [Citation(s) in RCA: 82] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
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