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For: Hendra C, Pratanwanich PN, Wan YK, Goh WSS, Thiery A, Göke J. Detection of m6A from direct RNA sequencing using a multiple instance learning framework. Nat Methods 2022;19:1590-1598. [PMID: 36357692 PMCID: PMC9718678 DOI: 10.1038/s41592-022-01666-1] [Citation(s) in RCA: 109] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 09/27/2022] [Indexed: 11/12/2022]
Number Cited by Other Article(s)
1
Li Y, Xue J, Ma Y, Ye K, Zhao X, Ge F, Zheng F, Liu L, Gao X, Wang D, Xia Q. The complex roles of m 6 A modifications in neural stem cell proliferation, differentiation, and self-renewal and implications for memory and neurodegenerative diseases. Neural Regen Res 2025;20:1582-1598. [PMID: 38845217 PMCID: PMC11688559 DOI: 10.4103/nrr.nrr-d-23-01872] [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: 11/13/2023] [Revised: 02/19/2024] [Accepted: 03/25/2024] [Indexed: 08/07/2024]  Open
2
Kim Y, Saville L, O'Neill K, Garant JM, Liu Y, Haile-Merhu S, Ghashghaei M, Hoang QA, Louwagie A, Park YP, Jones SJM, Vu LP. Nanopore direct RNA sequencing of human transcriptomes reveals the complexity of mRNA modifications and crosstalk between regulatory features. CELL GENOMICS 2025:100872. [PMID: 40359935 DOI: 10.1016/j.xgen.2025.100872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 01/20/2025] [Accepted: 04/09/2025] [Indexed: 05/15/2025]
3
Shi C, Yang D, Ma X, Chen Y, Hou P, Pan L, Li M, Wang P. Quantitative and Multiplexing Analysis of MicroRNAs by Direct Full-Length Sequencing in Nanopores. J Am Chem Soc 2025;147:15614-15624. [PMID: 40293972 PMCID: PMC12063164 DOI: 10.1021/jacs.5c02808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2025] [Revised: 04/18/2025] [Accepted: 04/21/2025] [Indexed: 04/30/2025]
4
Roy P, Gujarati S, Gupta P, Gupta I, Mahapatra T, Gupta D, Kochar SK, Kochar DK, Das A. A tale of two parasites: a glimpse into the RNA methylome of patient-derived Plasmodium falciparum and Plasmodium vivax isolates. Malar J 2025;24:139. [PMID: 40316999 PMCID: PMC12046715 DOI: 10.1186/s12936-025-05376-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2025] [Accepted: 04/17/2025] [Indexed: 05/04/2025]  Open
5
Fan Q, Zhao X, Li J, Liu R, Liu M, Feng Q, Long Y, Fu Y, Zhai J, Pan Q, Li Y. De novo non-canonical nanopore basecalling enables private communication using heavily-modified DNA data at single-molecule level. Nat Commun 2025;16:4099. [PMID: 40316536 PMCID: PMC12048662 DOI: 10.1038/s41467-025-59357-2] [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: 08/06/2024] [Accepted: 04/16/2025] [Indexed: 05/04/2025]  Open
6
Wu Y, Shao W, Liu S, Wang L, Xu P, Zhang X, Song H, Li X, Wang J, Yu X. Simultaneous profiling of ac4C and m5C modifications from nanopore direct RNA sequencing. Int J Biol Macromol 2025;305:140863. [PMID: 39954891 DOI: 10.1016/j.ijbiomac.2025.140863] [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: 11/25/2024] [Revised: 01/20/2025] [Accepted: 02/08/2025] [Indexed: 02/17/2025]
7
Yen YP, Lung TH, Liau ES, Wu CC, Huang GL, Hsu FY, Chang M, Yang ZD, Huang CY, Zheng Z, Zhao W, Hung JH, He C, Nie Q, Chen JA. The motor neuron m6A repertoire governs neuronal homeostasis and FTO inhibition mitigates ALS symptom manifestation. Nat Commun 2025;16:4063. [PMID: 40307231 PMCID: PMC12043976 DOI: 10.1038/s41467-025-59117-2] [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: 03/27/2024] [Accepted: 04/10/2025] [Indexed: 05/02/2025]  Open
8
Park D, Cenik C. Long-read RNA sequencing reveals allele-specific N 6-methyladenosine modifications. Genome Res 2025;35:999-1011. [PMID: 39472020 PMCID: PMC12047277 DOI: 10.1101/gr.279270.124] [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: 03/14/2024] [Accepted: 10/23/2024] [Indexed: 11/06/2024]
9
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
10
Qiu X, Gao Q, Wang J, Zhang Z, Tao L. The microbiota-m6A-metabolism axis: Implications for therapeutic strategies in gastrointestinal cancers. Biochim Biophys Acta Rev Cancer 2025;1880:189317. [PMID: 40222422 DOI: 10.1016/j.bbcan.2025.189317] [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: 09/11/2024] [Revised: 04/06/2025] [Accepted: 04/06/2025] [Indexed: 04/15/2025]
11
Kovaka S, Hook PW, Jenike KM, Shivakumar V, Morina LB, Razaghi R, Timp W, Schatz MC. Uncalled4 improves nanopore DNA and RNA modification detection via fast and accurate signal alignment. Nat Methods 2025;22:681-691. [PMID: 40155722 PMCID: PMC11978507 DOI: 10.1038/s41592-025-02631-4] [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: 03/15/2024] [Accepted: 02/16/2025] [Indexed: 04/01/2025]
12
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]
13
Samarakoon H, Wan YK, Parameswaran S, Göke J, Gamaarachchi H, Deveson IW. Leveraging basecaller's move table to generate a lightweight k-mer model for nanopore sequencing analysis. Bioinformatics 2025;41:btaf111. [PMID: 40085000 PMCID: PMC11964489 DOI: 10.1093/bioinformatics/btaf111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Revised: 01/28/2025] [Accepted: 03/11/2025] [Indexed: 03/16/2025]  Open
14
Monzó C, Liu T, Conesa A. Transcriptomics in the era of long-read sequencing. Nat Rev Genet 2025:10.1038/s41576-025-00828-z. [PMID: 40155769 DOI: 10.1038/s41576-025-00828-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2025] [Indexed: 04/01/2025]
15
Song J, Lin LA, Tang C, Chen C, Yang Q, Zhang D, Zhao Y, Wei HC, Linghu K, Xu Z, Chen T, He Z, Liu D, Zhong Y, Zhu W, Zeng W, Chen L, Song G, Chen M, Jiang J, Zhou J, Wang J, Chen B, Ying B, Wang Y, Geng J, Lin JW, Chen L. DEMINERS enables clinical metagenomics and comparative transcriptomic analysis by increasing throughput and accuracy of nanopore direct RNA sequencing. Genome Biol 2025;26:76. [PMID: 40155949 PMCID: PMC11954306 DOI: 10.1186/s13059-025-03536-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2024] [Accepted: 03/10/2025] [Indexed: 04/01/2025]  Open
16
Leitner M, Murigneux V, Etebari K, Asgari S. Wolbachia elevates host methyltransferase expression and alters the m6A methylation landscape in Aedes aegypti mosquito cells. BMC Microbiol 2025;25:164. [PMID: 40128692 PMCID: PMC11934717 DOI: 10.1186/s12866-025-03898-5] [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: 10/10/2024] [Accepted: 03/17/2025] [Indexed: 03/26/2025]  Open
17
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]
18
Riquelme-Barrios S, Vásquez-Camus L, Cusack S, Burdack K, Petrov D, Yeşiltaç-Tosun GN, Kaiser S, Giehr P, Jung K. Direct RNA sequencing of the Escherichia coli epitranscriptome uncovers alterations under heat stress. Nucleic Acids Res 2025;53:gkaf175. [PMID: 40114376 PMCID: PMC11925731 DOI: 10.1093/nar/gkaf175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Revised: 01/21/2025] [Accepted: 03/03/2025] [Indexed: 03/22/2025]  Open
19
Verstraten R, Cetraro P, Fitzpatrick AH, Alwie Y, Frommeyer YN, Loliashvili E, Stein SC, Häussler S, Ouwendijk WJ, Depledge DP. Defining expansions and perturbations to the RNA polymerase III transcriptome and epitranscriptome by modified direct RNA nanopore sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.07.641986. [PMID: 40161704 PMCID: PMC11952314 DOI: 10.1101/2025.03.07.641986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 04/02/2025]
20
Ament IH, DeBruyne N, Wang F, Lin L. Long-read RNA sequencing: A transformative technology for exploring transcriptome complexity in human diseases. Mol Ther 2025;33:883-894. [PMID: 39563027 PMCID: PMC11897757 DOI: 10.1016/j.ymthe.2024.11.025] [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: 08/29/2024] [Revised: 10/30/2024] [Accepted: 11/15/2024] [Indexed: 11/21/2024]  Open
21
Angelo M, Zhang W, Vilseck J, Aoki S. In silico λ-dynamics predicts protein binding specificities to modified RNAs. Nucleic Acids Res 2025;53:gkaf166. [PMID: 40066880 PMCID: PMC11894534 DOI: 10.1093/nar/gkaf166] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 02/19/2025] [Accepted: 02/20/2025] [Indexed: 03/15/2025]  Open
22
Cruciani S, Delgado-Tejedor A, Pryszcz LP, Medina R, Llovera L, Novoa EM. De novo basecalling of RNA modifications at single molecule and nucleotide resolution. Genome Biol 2025;26:38. [PMID: 40001217 PMCID: PMC11853310 DOI: 10.1186/s13059-025-03498-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2024] [Accepted: 02/07/2025] [Indexed: 02/27/2025]  Open
23
Zou Y, Ahsan MU, Chan J, Meng W, Gao SJ, Huang Y, Wang K. A Comparative Evaluation of Computational Models for RNA modification detection using Nanopore sequencing with RNA004 Chemistry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.03.636352. [PMID: 39975272 PMCID: PMC11838592 DOI: 10.1101/2025.02.03.636352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2025]
24
Pilala KM, Panoutsopoulou K, Papadimitriou MA, Soureas K, Scorilas A, Avgeris M. Exploring the methyl-verse: Dynamic interplay of epigenome and m6A epitranscriptome. Mol Ther 2025;33:447-464. [PMID: 39659016 PMCID: PMC11852398 DOI: 10.1016/j.ymthe.2024.12.003] [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: 07/23/2024] [Revised: 11/19/2024] [Accepted: 12/05/2024] [Indexed: 12/12/2024]  Open
25
Li Z, Lao Y, Yan R, Li F, Guan X, Dong Z. N6-methyladenosine in inflammatory diseases: Important actors and regulatory targets. Gene 2025;936:149125. [PMID: 39613051 DOI: 10.1016/j.gene.2024.149125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2024] [Revised: 11/17/2024] [Accepted: 11/25/2024] [Indexed: 12/01/2024]
26
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
27
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
28
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]
29
Vujaklija I, Biđin S, Volarić M, Bakić S, Li Z, Foo R, Liu J, Šikić M. Detecting a wide range of epitranscriptomic modifications using a nanopore-sequencing-based computational approach with 1D score-clustering. Nucleic Acids Res 2025;53:gkae1168. [PMID: 39658045 PMCID: PMC11724293 DOI: 10.1093/nar/gkae1168] [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: 01/28/2024] [Revised: 10/30/2024] [Accepted: 11/22/2024] [Indexed: 12/12/2024]  Open
30
Mitsuhashi H, Lin R, Chawla A, Mechawar N, Nagy C, Turecki G. Altered m6A RNA methylation profiles in depression implicate the dysregulation of discrete cellular functions in males and females. iScience 2024;27:111316. [PMID: 39650737 PMCID: PMC11625292 DOI: 10.1016/j.isci.2024.111316] [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: 05/22/2024] [Revised: 09/03/2024] [Accepted: 10/30/2024] [Indexed: 12/11/2024]  Open
31
Wu K, Li Y, Yi Y, Yu Y, Wang Y, Zhang L, Cao Q, Chen K. The detection, function, and therapeutic potential of RNA 2'-O-methylation. THE INNOVATION LIFE 2024;3:100112. [PMID: 40206865 PMCID: PMC11981644 DOI: 10.59717/j.xinn-life.2024.100112] [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: 04/11/2025]
32
Zhou Y, Ćorović M, Hoch-Kraft P, Meiser N, Mesitov M, Körtel N, Back H, Naarmann-de Vries IS, Katti K, Obrdlík A, Busch A, Dieterich C, Vaňáčová Š, Hengesbach M, Zarnack K, König J. m6A sites in the coding region trigger translation-dependent mRNA decay. Mol Cell 2024;84:4576-4593.e12. [PMID: 39577428 DOI: 10.1016/j.molcel.2024.10.033] [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: 12/15/2023] [Revised: 09/19/2024] [Accepted: 10/24/2024] [Indexed: 11/24/2024]
33
Huang S, Wylder AC, Pan T. Simultaneous nanopore profiling of mRNA m6A and pseudouridine reveals translation coordination. Nat Biotechnol 2024;42:1831-1835. [PMID: 38321115 PMCID: PMC11300707 DOI: 10.1038/s41587-024-02135-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 01/10/2024] [Indexed: 02/08/2024]
34
Liang Q, Zhang J, Lam HM, Chan TF. Nanopore direct RNA sequencing reveals N6-methyladenosine and polyadenylation landscapes on long non-coding RNAs in Arabidopsis thaliana. BMC PLANT BIOLOGY 2024;24:1126. [PMID: 39592939 PMCID: PMC11590578 DOI: 10.1186/s12870-024-05845-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2024] [Accepted: 11/18/2024] [Indexed: 11/28/2024]
35
McCormick CA, Meseonznik M, Qiu Y, Fanari O, Thomas M, Liu Y, Bloch D, Klink IN, Jain M, Wanunu M, Rouhanifard SH. mRNA psi profiling using nanopore DRS reveals cell type-specific pseudouridylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.08.593203. [PMID: 38766185 PMCID: PMC11100687 DOI: 10.1101/2024.05.08.593203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
36
Diensthuber G, Pryszcz LP, Llovera L, Lucas MC, Delgado-Tejedor A, Cruciani S, Roignant JY, Begik O, Novoa EM. Enhanced detection of RNA modifications and read mapping with high-accuracy nanopore RNA basecalling models. Genome Res 2024;34:1865-1877. [PMID: 39271295 PMCID: PMC11610583 DOI: 10.1101/gr.278849.123] [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: 12/12/2023] [Accepted: 09/10/2024] [Indexed: 09/15/2024]
37
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]
38
Zhu XT, Sanz-Jimenez P, Ning XT, Tahir Ul Qamar M, Chen LL. Direct RNA sequencing in plants: Practical applications and future perspectives. PLANT COMMUNICATIONS 2024;5:101064. [PMID: 39155503 PMCID: PMC11589328 DOI: 10.1016/j.xplc.2024.101064] [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: 05/13/2024] [Revised: 07/17/2024] [Accepted: 08/14/2024] [Indexed: 08/20/2024]
39
Chang KJ, Shiau LY, Lin SC, Cheong HP, Wang CY, Ma C, Liang YW, Yang YP, Ko PS, Hsu CH, Chiou SH. N6-methyladenosine and its epitranscriptomic effects on hematopoietic stem cell regulation and leukemogenesis. Mol Med 2024;30:196. [PMID: 39497033 PMCID: PMC11536562 DOI: 10.1186/s10020-024-00965-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: 08/26/2024] [Accepted: 10/20/2024] [Indexed: 11/06/2024]  Open
40
Li W, Huang Y, Yuan H, Han J, Li Z, Tong A, Li Y, Li H, Liu Y, Jia L, Wang X, Li J, Zhang B, Li L. Characterizing transcripts of HIV-1 different substrains using direct RNA sequencing. Heliyon 2024;10:e39474. [PMID: 39512311 PMCID: PMC11541491 DOI: 10.1016/j.heliyon.2024.e39474] [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: 05/26/2024] [Revised: 10/07/2024] [Accepted: 10/15/2024] [Indexed: 11/15/2024]  Open
41
Shaw E, Thomas N, Jones J, Abu-Shumays R, Vaaler A, Akeson M, Koutmou K, Jain M, Garcia D. Combining Nanopore direct RNA sequencing with genetics and mass spectrometry for analysis of T-loop base modifications across 42 yeast tRNA isoacceptors. Nucleic Acids Res 2024;52:12074-12092. [PMID: 39340295 PMCID: PMC11514469 DOI: 10.1093/nar/gkae796] [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: 11/13/2023] [Revised: 08/28/2024] [Accepted: 09/05/2024] [Indexed: 09/30/2024]  Open
42
Xu Z, Zheng X, Fan J, Jiao Y, Huang S, Xie Y, Xu S, Lu Y, Liu A, Liu R, Yang Y, Luo GZ, Pan T, Wang X. Microbiome-induced reprogramming in post-transcriptional landscape using nanopore direct RNA sequencing. Cell Rep 2024;43:114798. [PMID: 39365698 DOI: 10.1016/j.celrep.2024.114798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 08/10/2024] [Accepted: 09/10/2024] [Indexed: 10/06/2024]  Open
43
Zhang L, Chen Z, Sun G, Li C, Wu P, Xu W, Zhu H, Zhang Z, Tang Y, Li Y, Li Y, Xu S, Li H, Chen M, Xiao F, Zhang Y, Zhang W. Dynamic landscape of m6A modifications and related post-transcriptional events in muscle-invasive bladder cancer. J Transl Med 2024;22:912. [PMID: 39380003 PMCID: PMC11460118 DOI: 10.1186/s12967-024-05701-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: 08/05/2024] [Accepted: 09/23/2024] [Indexed: 10/10/2024]  Open
44
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
45
Cheng Y, Xu SM, Santucci K, Lindner G, Janitz M. Machine learning and related approaches in transcriptomics. Biochem Biophys Res Commun 2024;724:150225. [PMID: 38852503 DOI: 10.1016/j.bbrc.2024.150225] [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: 02/25/2024] [Revised: 05/18/2024] [Accepted: 06/03/2024] [Indexed: 06/11/2024]
46
Park D, Cenik C. Long-read RNA sequencing reveals allele-specific N6-methyladenosine modifications. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.08.602538. [PMID: 39026828 PMCID: PMC11257478 DOI: 10.1101/2024.07.08.602538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
47
Xu Y, Liu W, Ren L. Role of m6A RNA Methylation in Ischemic Stroke. Mol Neurobiol 2024;61:6997-7008. [PMID: 38363537 DOI: 10.1007/s12035-024-04029-3] [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: 11/04/2023] [Accepted: 02/09/2024] [Indexed: 02/17/2024]
48
Martinek V, Martin J, Belair C, Payea M, Malla S, Alexiou P, Maragkakis M. Deep learning and direct sequencing of labeled RNA captures transcriptome dynamics. NAR Genom Bioinform 2024;6:lqae116. [PMID: 39211330 PMCID: PMC11358824 DOI: 10.1093/nargab/lqae116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 07/29/2024] [Accepted: 08/19/2024] [Indexed: 09/04/2024]  Open
49
Tan L, Guo Z, Shao Y, Ye L, Wang M, Deng X, Chen S, Li R. Analysis of bacterial transcriptome and epitranscriptome using nanopore direct RNA sequencing. Nucleic Acids Res 2024;52:8746-8762. [PMID: 39011882 PMCID: PMC11347139 DOI: 10.1093/nar/gkae601] [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: 01/10/2024] [Accepted: 06/28/2024] [Indexed: 07/17/2024]  Open
50
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
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