相似文献
1
Simultaneous nanopore profiling of mRNA mA and pseudouridine reveals translation coordination.
Nat Biotechnol. 2024 Dec;42(12):1831-1835. doi: 10.1038/s41587-024-02135-0. Epub 2024 Feb 6.
2
Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling.
Genome Biol. 2021 Dec 6;22(1):330. doi: 10.1186/s13059-021-02557-y.
3
Quantitative profiling of pseudouridylation dynamics in native RNAs with nanopore sequencing.
Nat Biotechnol. 2021 Oct;39(10):1278-1291. doi: 10.1038/s41587-021-00915-6. Epub 2021 May 13.
4
Absolute quantitative and base-resolution sequencing reveals comprehensive landscape of pseudouridine across the human transcriptome.
Nat Methods. 2024 Nov;21(11):2024-2033. doi: 10.1038/s41592-024-02439-8. Epub 2024 Sep 30.
5
Analysis of bacterial transcriptome and epitranscriptome using nanopore direct RNA sequencing.
Nucleic Acids Res. 2024 Aug 27;52(15):8746-8762. doi: 10.1093/nar/gkae601.
6
Penguin: A tool for predicting pseudouridine sites in direct RNA nanopore sequencing data.
Methods. 2022 Jul;203:478-487. doi: 10.1016/j.ymeth.2022.02.005. Epub 2022 Feb 16.
7
NanoMUD: Profiling of pseudouridine and N1-methylpseudouridine using Oxford Nanopore direct RNA sequencing.
Int J Biol Macromol. 2024 Jun;270(Pt 2):132433. doi: 10.1016/j.ijbiomac.2024.132433. Epub 2024 May 15.
8
Nanopore signal deviations from pseudouridine modifications in RNA are sequence-specific: quantification requires dedicated synthetic controls.
Sci Rep. 2024 Sep 28;14(1):22457. doi: 10.1038/s41598-024-72994-9.
9
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 Oct 28;52(19):12074-12092. doi: 10.1093/nar/gkae796.
10
m6ATM: a deep learning framework for demystifying the m6A epitranscriptome with Nanopore long-read RNA-seq data.
Brief Bioinform. 2024 Sep 23;25(6). doi: 10.1093/bib/bbae529.
引用本文的文献
1
Analysis of the mRNA modification machinery alterations in breast cancer through the SCAN-B cohort.
NAR Cancer. 2025 Sep 3;7(3):zcaf027. doi: 10.1093/narcan/zcaf027. eCollection 2025 Sep.
2
DNA-encoded library screening uncovers potent DNMT2 inhibitors targeting a cryptic allosteric binding site.
iScience. 2025 Aug 5;28(9):113300. doi: 10.1016/j.isci.2025.113300. eCollection 2025 Sep 19.
3
Uncovering the Epitranscriptome: A Review on mRNA Modifications and Emerging Frontiers.
Genes (Basel). 2025 Aug 12;16(8):951. doi: 10.3390/genes16080951.
4
ModiDeC: a multi-RNA modification classifier for direct nanopore sequencing.
Nucleic Acids Res. 2025 Jul 19;53(14). doi: 10.1093/nar/gkaf673.
5
Pseudouridine reprogramming in the human T cell epitranscriptome: from primary to immortalized states.
RNA. 2025 Jul 9. doi: 10.1261/rna.080633.125.
6
Functions and therapeutic applications of pseudouridylation.
Nat Rev Mol Cell Biol. 2025 May 20. doi: 10.1038/s41580-025-00852-1.
7
Nanopore direct RNA sequencing of human transcriptomes reveals the complexity of mRNA modifications and crosstalk between regulatory features.
Cell Genom. 2025 Jun 11;5(6):100872. doi: 10.1016/j.xgen.2025.100872. Epub 2025 May 12.
8
The RMaP challenge of predicting RNA modifications by nanopore sequencing.
Commun Chem. 2025 Apr 12;8(1):115. doi: 10.1038/s42004-025-01507-0.
9
The detection, function, and therapeutic potential of RNA 2'-O-methylation.
Innov Life. 2025;3(1). doi: 10.59717/j.xinn-life.2024.100112. Epub 2024 Dec 17.
10
Defining expansions and perturbations to the RNA polymerase III transcriptome and epitranscriptome by modified direct RNA nanopore sequencing.
bioRxiv. 2025 Mar 12:2025.03.07.641986. doi: 10.1101/2025.03.07.641986.
本文引用的文献
1
Systematic comparison of tools used for mA mapping from nanopore direct RNA sequencing.
Nat Commun. 2023 Apr 5;14(1):1906. doi: 10.1038/s41467-023-37596-5.
2
Identifying RNA Modifications by Direct RNA Sequencing Reveals Complexity of Epitranscriptomic Dynamics in Rice.
Genomics Proteomics Bioinformatics. 2023 Aug;21(4):788-804. doi: 10.1016/j.gpb.2023.02.002. Epub 2023 Feb 11.
3
Semi-quantitative detection of pseudouridine modifications and type I/II hypermodifications in human mRNAs using direct long-read sequencing.
Nat Commun. 2023 Jan 19;14(1):334. doi: 10.1038/s41467-023-35858-w.
4
Transcriptome-wide profiling and quantification of N-methyladenosine by enzyme-assisted adenosine deamination.
Nat Biotechnol. 2023 Jul;41(7):993-1003. doi: 10.1038/s41587-022-01587-6. Epub 2023 Jan 2.
5
Detection of m6A from direct RNA sequencing using a multiple instance learning framework.
Nat Methods. 2022 Dec;19(12):1590-1598. doi: 10.1038/s41592-022-01666-1. Epub 2022 Nov 10.
6
Absolute quantification of single-base mA methylation in the mammalian transcriptome using GLORI.
Nat Biotechnol. 2023 Mar;41(3):355-366. doi: 10.1038/s41587-022-01487-9. Epub 2022 Oct 27.
7
Quantitative sequencing using BID-seq uncovers abundant pseudouridines in mammalian mRNA at base resolution.
Nat Biotechnol. 2023 Mar;41(3):344-354. doi: 10.1038/s41587-022-01505-w. Epub 2022 Oct 27.
8
Chemical Probe-Based Nanopore Sequencing to Selectively Assess the RNA Modifications.
ACS Chem Biol. 2022 Oct 21;17(10):2704-2709. doi: 10.1021/acschembio.2c00221. Epub 2022 Oct 3.
9
RNA modification mapping with JACUSA2.
Genome Biol. 2022 May 16;23(1):115. doi: 10.1186/s13059-022-02676-0.
10
An informatics approach to distinguish RNA modifications in nanopore direct RNA sequencing.
Genomics. 2022 May;114(3):110372. doi: 10.1016/j.ygeno.2022.110372. Epub 2022 Apr 20.
Zotero 插件