{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T17:21:30Z","timestamp":1788801690941,"version":"build-2803163510"},"reference-count":160,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2025,12,10]],"date-time":"2025-12-10T00:00:00Z","timestamp":1765324800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Institute of General Medical Sciences of the National Institutes of Health","award":["R44GM137636"],"award-info":[{"award-number":["R44GM137636"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Life"],"abstract":"<jats:p>RNA modifications are essential regulators of gene expression and cellular function, modulating RNA stability, splicing, translation, and localization. Dysregulation of these modifications has been linked to cancer, neurodegenerative disorders, viral infections, and other diseases. Precise quantification and mapping of RNA modifications are crucial for understanding their biological roles. This review summarizes current and emerging methodologies for RNA modification analysis, including mass spectrometry, antibody-based and non-antibody-based approaches, PCR- and NMR-based detection, chemical- and enzyme-assisted sequencing, and nanopore direct RNA sequencing. We also highlight advanced techniques for single-cell and single-molecule imaging, enabling the study of modification dynamics and cellular heterogeneity. The advantages, limitations, and challenges of each method are discussed, providing a framework for selecting appropriate analytical strategies. Future perspectives emphasize high-throughput, multiplexed, and single-cell approaches, integrating multiple technologies to decode the epitranscriptome. These approaches form a robust toolkit for uncovering RNA modification functions, discovering biomarkers, and developing novel therapeutic strategies.<\/jats:p>","DOI":"10.3390\/life15121888","type":"journal-article","created":{"date-parts":[[2025,12,10]],"date-time":"2025-12-10T12:20:57Z","timestamp":1765369257000},"page":"1888","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Advances in Quantitative Techniques for Mapping RNA Modifications"],"prefix":"10.3390","volume":"15","author":[{"given":"Ling","family":"Tian","sequence":"first","affiliation":[{"name":"Mediomics, LLC, 5445 Highland Park Drive, Saint Louis, MO 63110, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bharathi","family":"Vallabhaneni","sequence":"additional","affiliation":[{"name":"Mediomics, LLC, 5445 Highland Park Drive, Saint Louis, MO 63110, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yie-Hwa","family":"Chang","sequence":"additional","affiliation":[{"name":"Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, MO 63104, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,12,10]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1016\/S0021-9258(18)70770-9","article-title":"Ribonucleic acids from yeast which contain a fifth nucleotide","volume":"227","author":"Davis","year":"1957","journal-title":"J. Biol. Chem."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"D239","DOI":"10.1093\/nar\/gkad1083","article-title":"MODOMICS: A database of RNA modifications and related information. 2023 update","volume":"52","author":"Cappannini","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Arzumanian, V.A., Dolgalev, G.V., Kurbatov, I.Y., Kiseleva, O.I., and Poverennaya, E.V. (2022). Epitranscriptome: Review of Top 25 Most-Studied RNA Modifications. Int. J. Mol. Sci., 23.","DOI":"10.3390\/ijms232213851"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"343154","DOI":"10.1016\/j.aca.2024.343154","article-title":"A review of advances in analytical strategies for RNA methylation","volume":"1333","author":"Sun","year":"2025","journal-title":"Anal. Chim. Acta"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1601","DOI":"10.1038\/s12276-022-00821-0","article-title":"Detection technologies for RNA modifications","volume":"54","author":"Zhang","year":"2022","journal-title":"Exp. Mol. Med."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"117606","DOI":"10.1016\/j.trac.2024.117606","article-title":"Quantification and mapping of RNA modifications","volume":"172","author":"Xiong","year":"2024","journal-title":"TrAC Trends Anal. Chem."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1146\/annurev-anchem-061622-125954","article-title":"Analysis of RNA and Its Modifications","volume":"17","author":"Herbert","year":"2024","journal-title":"Annu. Rev. Anal. Chem."},{"key":"ref_8","unstructured":"National Academies of Sciences, Engineering, and Medicine (2024). Charting a Future for Sequencing RNA and Its Modifications: A New Era for Biology and Medicine, The National Academies Press."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"3971","DOI":"10.1073\/pnas.71.10.3971","article-title":"Identification of methylated nucleosides in messenger RNA from Novikoff hepatoma cells","volume":"71","author":"Desrosiers","year":"1974","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1016\/0304-3835(92)90296-8","article-title":"Monitoring of urinary excretion of modified nucleosides in cancer patients using a set of six monoclonal antibodies","volume":"61","author":"Reynaud","year":"1992","journal-title":"Cancer Lett."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1387","DOI":"10.1016\/j.molp.2017.09.013","article-title":"5-Methylcytosine RNA Methylation in Arabidopsis Thaliana","volume":"10","author":"Cui","year":"2017","journal-title":"Mol. Plant"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"546","DOI":"10.1016\/j.brainres.2016.04.055","article-title":"5-Hydroxymethylcytosine is detected in RNA from mouse brain tissues","volume":"1642","author":"Miao","year":"2016","journal-title":"Brain Res."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"282","DOI":"10.1126\/science.aac5253","article-title":"Transcriptome-wide distribution and function of RNA hydroxymethylcytosine","volume":"351","author":"Delatte","year":"2016","journal-title":"Science"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"4","DOI":"10.21769\/BioProtoc.2095","article-title":"Dot blot analysis of N6-methyladenosine RNA modification levels","volume":"7","author":"Shen","year":"2017","journal-title":"Bio-Protocol"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1007\/978-1-4939-8808-2_20","article-title":"Dot Blot Analysis for Measuring Global N(6)-Methyladenosine Modification of RNA","volume":"1870","author":"Nagarajan","year":"2019","journal-title":"Methods Mol. Biol."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Mishima, E., Jinno, D., Akiyama, Y., Itoh, K., Nankumo, S., Shima, H., Kikuchi, K., Takeuchi, Y., Elkordy, A., and Suzuki, T. (2015). Immuno-Northern Blotting: Detection of RNA Modifications by Using Antibodies against Modified Nucleosides. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0143756"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1016\/0009-8981(91)90103-J","article-title":"An enzyme-linked immunosorbent assay (ELISA) for the detection and quantitation of the tumor marker 1-methylinosine in human urine","volume":"199","author":"Trewyn","year":"1991","journal-title":"Clin. Chim. Acta"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"705","DOI":"10.1261\/rna.079554.122","article-title":"m6A-ELISA, a simple method for quantifying N6-methyladenosine from mRNA populations","volume":"29","author":"Ensinck","year":"2023","journal-title":"RNA"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1038\/nature11112","article-title":"Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq","volume":"485","author":"Dominissini","year":"2012","journal-title":"Nature"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1635","DOI":"10.1016\/j.cell.2012.05.003","article-title":"Comprehensive analysis of mRNA methylation reveals enrichment in 3\u2032 UTRs and near stop codons","volume":"149","author":"Meyer","year":"2012","journal-title":"Cell"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"2037","DOI":"10.1101\/gad.269415.115","article-title":"A majority of m6A residues are in the last exons, allowing the potential for 3\u2032 UTR regulation","volume":"29","author":"Ke","year":"2015","journal-title":"Genes Dev."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"767","DOI":"10.1038\/nmeth.3453","article-title":"Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome","volume":"12","author":"Linder","year":"2015","journal-title":"Nat. Methods"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1016\/j.molcel.2019.06.006","article-title":"Identification of the m6Am Methyltransferase PCIF1 Reveals the Location and Functions of m6Am in the Transcriptome","volume":"75","author":"Boulias","year":"2019","journal-title":"Mol. Cell."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1038\/nchembio.2040","article-title":"Transcriptome-wide mapping reveals reversible and dynamic N1-methyladenosine methylome","volume":"12","author":"Li","year":"2016","journal-title":"Nat. Chem. Biol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"993","DOI":"10.1016\/j.molcel.2017.10.019","article-title":"Base-Resolution Mapping Reveals Distinct m1A Methylome in Nuclear- and Mitochondrial-Encoded Transcripts","volume":"68","author":"Li","year":"2017","journal-title":"Mol. Cell."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"441","DOI":"10.1038\/nature16998","article-title":"The dynamic N(1)-methyladenosine methylome in eukaryotic messenger RNA","volume":"530","author":"Dominissini","year":"2016","journal-title":"Nature"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1872","DOI":"10.1016\/j.cell.2018.10.030","article-title":"Acetylation of cytidine in mRNA promotes translation efficiency","volume":"175","author":"Arango","year":"2018","journal-title":"Cell"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"927","DOI":"10.1038\/s41422-019-0230-z","article-title":"Dynamic methylome of internal mRNA N7-methylguanosine and its regulatory role in translation","volume":"29","author":"Malbec","year":"2019","journal-title":"Cell Res."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"5126","DOI":"10.1038\/s41467-019-13146-w","article-title":"Antibody cross-reactivity accounts for widespread appearance of m1A in 5\u2032UTRs","volume":"10","author":"Grozhik","year":"2019","journal-title":"Nat. Commun."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"591","DOI":"10.1038\/s41587-023-01831-7","article-title":"Single-cell m6A mapping in vivo using picoMeRIP\u2013seq","volume":"42","author":"Li","year":"2023","journal-title":"Nat. Biotechnol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"22646","DOI":"10.1002\/anie.202109118","article-title":"Single-cell imaging of m6A modified RNA using m6A-specific in situ hybridization mediated proximity ligation assay (m6AISH-PLA)","volume":"60","author":"Ren","year":"2021","journal-title":"Angew. Chem. Int. Ed. Engl."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"958","DOI":"10.1038\/s41467-025-56331-w","article-title":"Multichrome encoding-based multiplexed, spatially resolved imaging reveals single-cell RNA epigenetic modifications heterogeneity","volume":"16","author":"Mao","year":"2025","journal-title":"Nat. Commun."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"4577","DOI":"10.1093\/nar\/21.19.4577","article-title":"A novel method for the determination of post-transcriptional modification in RNA by mass spectrometry","volume":"21","author":"Kowalak","year":"1993","journal-title":"Nucleic Acids Res."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1039\/C5AN01797A","article-title":"Mass spectrometry of modified RNAs: Recent developments (Minireview)","volume":"141","author":"Wetzel","year":"2015","journal-title":"Analyst"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"1152","DOI":"10.1080\/15476286.2015.1076612","article-title":"Variable presence of 5-methylcytosine in commercial RNA and DNA","volume":"12","author":"Schmid","year":"2015","journal-title":"RNA Biol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"e142","DOI":"10.1093\/nar\/gku733","article-title":"Absolute and relative quantification of RNA modifications via biosynthetic isotopomers","volume":"42","author":"Kellner","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"108522","DOI":"10.1016\/j.cclet.2023.108522","article-title":"Adolescent alcohol exposure changes RNA modifications in adult brain by mass spectrometry-based comprehensive profiling analysis","volume":"35","author":"Chen","year":"2024","journal-title":"Chin. Chem. Lett."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"109259","DOI":"10.1016\/j.cclet.2023.109259","article-title":"Chronic sleep deprivation induces alterations in DNA and RNA modifications by liquid chromatography-mass spectrometry analysis","volume":"35","author":"Feng","year":"2024","journal-title":"Chin. Chem. Lett."},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Baek, A., Rayhan, A., Lee, G.E., Golconda, S., Yu, H., Kim, S., Limbach, P.A., Addepalli, B., and Kim, S. (2024). Mapping m6A sites on HIV-1 RNA using oligonucleotide LC-MS\/MS. Methods Protoc., 7.","DOI":"10.3390\/mps7010007"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"514","DOI":"10.1261\/rna.080324.124","article-title":"Global analysis by LC-MS\/MS of N6-methyladenosine and inosine in mRNA reveals complex incidence","volume":"31","author":"Stejskal","year":"2025","journal-title":"RNA"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"e1663","DOI":"10.1002\/wrna.1663","article-title":"Detecting the epitranscriptome","volume":"12","author":"Sarkar","year":"2021","journal-title":"Wiley Interdiscip. Rev. RNA"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"13958","DOI":"10.1021\/acs.analchem.2c03172","article-title":"Higher-energy collisional dissociation mass spectral networks for the rapid, semi-automated characterization of known and unknown ribonucleoside modifications","volume":"94","author":"Jora","year":"2022","journal-title":"Anal. Chem."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"3516","DOI":"10.1039\/c3cc49114e","article-title":"Profiling of RNA modifications by multiplexed stable isotope labelling","volume":"50","author":"Kellner","year":"2014","journal-title":"Chem. Commun."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"828","DOI":"10.1038\/nprot.2014.047","article-title":"Quantitative analysis of tRNA modifications by HPLC-coupled mass spectrometry","volume":"9","author":"Su","year":"2014","journal-title":"Nat. Protoc."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"1363","DOI":"10.1007\/s13361-011-0137-5","article-title":"Mass spectrometry-based quantification of pseudouridine in RNA","volume":"22","author":"Addepalli","year":"2011","journal-title":"J. Am. Soc. Mass. Spectrom."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"27564","DOI":"10.1038\/s41598-024-78734-3","article-title":"Quantitative detection of pseudouridine in RNA by mass spectrometry","volume":"14","author":"Hermon","year":"2024","journal-title":"Sci. Rep."},{"key":"ref_47","first-page":"13304","article-title":"Quantification of 2\u2032-O-methylcytidine in tRNA using LC-MS\/MS","volume":"89","author":"Heiss","year":"2017","journal-title":"Anal. Chem."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"2671","DOI":"10.1038\/s41596-023-00857-0","article-title":"A systems-level mass spectrometry-based technique for accurate and sensitive quantification of the RNA cap epitranscriptome","volume":"18","author":"Wang","year":"2023","journal-title":"Nat. Protoc."},{"key":"ref_49","first-page":"852","article-title":"Quantification of N4-acetylcytidine in tRNA by LC-MS\/MS","volume":"26","author":"Bessler","year":"2020","journal-title":"RNA"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1080\/10408363.2021.1958743","article-title":"Quantifying RNA modifications by mass spectrometry: A novel source of biomarkers in oncology","volume":"59","author":"Amalric","year":"2022","journal-title":"Crit. Rev. Clin. Lab. Sci."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"105058","DOI":"10.1016\/j.nbd.2020.105058","article-title":"Small RNA modifications in Alzheimer\u2019s disease","volume":"145","author":"Zhang","year":"2020","journal-title":"Neurobiol. Dis."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"404","DOI":"10.1038\/s41422-020-00465-7","article-title":"The m6A methylome of SARS-CoV-2 in host cells","volume":"31","author":"Liu","year":"2021","journal-title":"Cell Res."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"eadn9519","DOI":"10.1126\/sciadv.adn9519","article-title":"Epitranscriptomic m5C methylation of SARS-CoV-2 RNA regulates viral replication and the virulence of progeny viruses in the new infection","volume":"10","author":"Wang","year":"2024","journal-title":"Sci. Adv."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"1361","DOI":"10.1261\/rna.049429.114","article-title":"Profiling ribonucleotide modifications at full-transcriptome level: A step toward MS-based epitranscriptomics","volume":"21","author":"Rose","year":"2015","journal-title":"RNA"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"1745","DOI":"10.1007\/s13361-018-1999-6","article-title":"Differentiating positional isomers of nucleoside modifications by higher-energy collisional dissociation mass spectrometry (HCD MS)","volume":"29","author":"Jora","year":"2018","journal-title":"J. Am. Soc. Mass. Spectrom."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1016\/0958-1669(95)80015-8","article-title":"Characterization of oligonucleotides and nucleic acids by mass spectrometry","volume":"6","author":"Limbach","year":"1995","journal-title":"Curr. Opin. Biotechnol."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"918","DOI":"10.1016\/j.jasms.2010.02.025","article-title":"Top-down mass spectrometry for sequencing of larger (up to 61 nt) RNA by CAD and EDD","volume":"21","author":"Taucher","year":"2010","journal-title":"J. Am. Soc. Mass. Spectrom."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"890","DOI":"10.1016\/j.jasms.2009.12.007","article-title":"Top-down tandem mass spectrometry of tRNA via ion trap collision-induced dissociation","volume":"21","author":"Huang","year":"2010","journal-title":"J. Am. Soc. Mass. Spectrom."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"11289","DOI":"10.1002\/anie.201206232","article-title":"Characterization of modified RNA by top-down mass spectrometry","volume":"51","author":"Taucher","year":"2012","journal-title":"Angew. Chem. Int. Ed. Engl."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"4309","DOI":"10.1002\/anie.201914275","article-title":"Radical transfer dissociation for de novo characterization of modified ribonucleic acids by mass spectrometry","volume":"59","author":"Calderisi","year":"2020","journal-title":"Angew. Chem. Int. Ed. Engl."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"4436","DOI":"10.1021\/acs.analchem.9b05388","article-title":"Ribonucleic acid sequence characterization by negative electron transfer dissociation mass spectrometry","volume":"92","author":"Quan","year":"2020","journal-title":"Anal. Chem."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"6474","DOI":"10.1021\/ac901216n","article-title":"A fast capillary electrophoresis method for separation and quantification of modified nucleosides in urinary samples","volume":"81","author":"Jiang","year":"2009","journal-title":"Anal. Chem."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"7777","DOI":"10.1021\/acs.analchem.6b01796","article-title":"Analysis of trinitrophenylated adenosine and inosine by capillary electrophoresis and gamma-cyclodextrin-enhanced fluorescence detection","volume":"88","author":"Stephen","year":"2016","journal-title":"Anal. Chem."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"7595","DOI":"10.1039\/C9CC03195B","article-title":"Ultrasensitive and simultaneous determination of RNA modified nucleotides by sheathless interfaced capillary electrophoresis-tandem mass spectrometry","volume":"55","author":"Yu","year":"2019","journal-title":"Chem. Commun."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"5645","DOI":"10.1093\/nar\/9.21.5645","article-title":"Primary and secondary structure of U2 snRNA","volume":"9","author":"Reddy","year":"1981","journal-title":"Nucleic Acids Res."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1016\/0076-6879(87)55026-1","article-title":"Analysis of modified nucleosides and nucleotide sequence of tRNA","volume":"155","author":"Kuchino","year":"1987","journal-title":"Methods Enzymol."},{"key":"ref_67","doi-asserted-by":"crossref","unstructured":"Grosjean, H., and Benne, R. (1998). RNA-modifying and RNA-editing enzymes: Methods for their identification. Modification and Editing of RNA, ASM Press.","DOI":"10.1128\/9781555818296"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1261\/rna.7110804","article-title":"Detection and quantitation of RNA base modifications","volume":"10","author":"Zhao","year":"2004","journal-title":"RNA"},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"1848","DOI":"10.1261\/rna.041178.113","article-title":"Probing N6-methyladenosine RNA modification status at single nucleotide resolution in mRNA and long noncoding RNA","volume":"19","author":"Liu","year":"2013","journal-title":"RNA"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"3354","DOI":"10.1039\/C7SC05233B","article-title":"Identification of a selective DNA ligase for accurate recognition and ultrasensitive quantification of N6-methyladenosine in RNA","volume":"9","author":"Liu","year":"2018","journal-title":"Chem. Sci."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"15995","DOI":"10.1002\/anie.201807942","article-title":"An elongation- and ligation-based qPCR amplification method for radiolabeling-free detection of locus-specific N6-methyladenosine","volume":"57","author":"Xiao","year":"2018","journal-title":"Angew. Chem. Int. Ed."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"2612","DOI":"10.1021\/acs.analchem.9b04454","article-title":"Quantification and single-base resolution analysis of N1-methyladenosine in mRNA by ligation-assisted differentiation","volume":"92","author":"Ding","year":"2020","journal-title":"Anal. Chem."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"e157","DOI":"10.1093\/nar\/gks698","article-title":"RTL-P: A sensitive approach for detecting sites of 2\u2032-O-methylation in RNA molecules","volume":"40","author":"Dong","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"3495","DOI":"10.1093\/nar\/gkw200","article-title":"Direct quantification of RNA 2\u2032-O-methylation by PCR with an engineered DNA polymerase","volume":"44","author":"Aschenbrenner","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"14878","DOI":"10.1002\/anie.201708276","article-title":"A radiolabeling-free qPCR method for pseudouridine detection","volume":"56","author":"Lei","year":"2017","journal-title":"Angew. Chem. Int. Ed."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/S0006-291X(71)80150-X","article-title":"NMR studies of organic solvent denatured yeast phenylalanyl transfer RNA at 220 MHz","volume":"44","author":"Crawford","year":"1971","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1016\/S0006-291X(74)80168-3","article-title":"NMR study on the methyl and methylene proton resonances of tRNA Phe yeast","volume":"59","author":"Kan","year":"1974","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"3373","DOI":"10.1038\/s41467-019-11356-w","article-title":"Time-resolved NMR monitoring of tRNA maturation","volume":"10","author":"Barraud","year":"2019","journal-title":"Nat. Commun."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1080\/10409238.2021.1887807","article-title":"Instrumental analysis of RNA modifications","volume":"56","author":"Ammann","year":"2021","journal-title":"Crit. Rev. Biochem. Mol. Biol."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1111\/j.1432-1033.1993.tb18154.x","article-title":"A modified uridine in the first position of the anticodon of a minor species of arginine tRNA, the argU gene product, from Escherichia coli","volume":"216","author":"Sakamoto","year":"1993","journal-title":"Eur. J. Biochem."},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1016\/S0022-2836(03)00760-5","article-title":"The tRNA-like domains of E. coli and A. aeolicus transfer-messenger RNA: Structural and functional studies","volume":"331","author":"Gaudin","year":"2003","journal-title":"J. Mol. Biol."},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"2387","DOI":"10.1093\/nar\/gkp1189","article-title":"The ribosome assembly factor Nep1 responsible for Bowen-Conradi syndrome is a pseudouridine-N1-specific methyltransferase","volume":"38","author":"Wurm","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"572","DOI":"10.4161\/rna.24327","article-title":"RNA-methyltransferase TrmA is a dual-specific enzyme responsible for C5-methylation of uridine in both tmRNA and tRNA","volume":"10","author":"Fabret","year":"2013","journal-title":"RNA Biol."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"803","DOI":"10.1038\/nsmb.3270","article-title":"m(1)A and m(1)G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs","volume":"23","author":"Zhou","year":"2016","journal-title":"Nat. Struct. Mol. Biol."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"19988","DOI":"10.1021\/jacs.9b10939","article-title":"NMR chemical exchange measurements reveal that N6-methyladenosine slows RNA annealing","volume":"141","author":"Shi","year":"2019","journal-title":"J. Am. Chem. Soc."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"2350","DOI":"10.1093\/nar\/gkac080","article-title":"Structural effects of m6A modification of the Xist A-repeat AUCG tetraloop and its recognition by YTHDC1","volume":"50","author":"Jones","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"822","DOI":"10.1016\/j.jmb.2015.08.021","article-title":"N(6)-methyladenosine modification in a long noncoding RNA hairpin predisposes its conformation to protein binding","volume":"428","author":"Zhou","year":"2016","journal-title":"J. Mol. Biol."},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"4223","DOI":"10.1021\/bi00231a017","article-title":"1H-15N NMR studies of Escherichia coli tRNA(Phe) from hisT mutants: A structural role for pseudouridine","volume":"30","author":"Davis","year":"1991","journal-title":"Biochemistry"},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"4960","DOI":"10.1039\/C5OB00164A","article-title":"Contribution of dihydrouridine in folding of the D-arm in tRNA","volume":"13","author":"Dyubankova","year":"2015","journal-title":"Org. Biomol. Chem."},{"key":"ref_90","doi-asserted-by":"crossref","unstructured":"Sa\u011flam, B., Akku\u015f, O., Ak\u00e7a\u00f6z-Alasar, A., Ceylan, \u00c7., G\u00fcler, G., and Akg\u00fcl, B. (2024). An Investigation of RNA Methylations with Biophysical Approaches in a Cervical Cancer Cell Model. Cells, 13.","DOI":"10.3390\/cells13221832"},{"key":"ref_91","doi-asserted-by":"crossref","unstructured":"Motorin, Y., and Marchand, V. (2021). Analysis of RNA modifications by second- and third-generation deep sequencing: 2020 update. Genes, 12.","DOI":"10.3390\/genes12020278"},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1002\/1873-3468.15052","article-title":"High-throughput detection of RNA modifications at single base resolution","volume":"599","author":"Ron","year":"2025","journal-title":"FEBS Lett."},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1126\/science.1207018","article-title":"Widespread RNA and DNA sequence differences in the human transcriptome","volume":"333","author":"Li","year":"2011","journal-title":"Science"},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1101\/gr.124107.111","article-title":"Accurate identification of A-to-I RNA editing in human by transcriptome sequencing","volume":"22","author":"Bahn","year":"2012","journal-title":"Genome Res."},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1038\/nbt.2122","article-title":"Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome","volume":"30","author":"Peng","year":"2012","journal-title":"Nat. Biotechnol."},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"1433","DOI":"10.1093\/nar\/gkw810","article-title":"High-throughput single-base resolution mapping of RNA 2\u2032-O-methylated residues","volume":"45","author":"Incarnato","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref_97","doi-asserted-by":"crossref","unstructured":"Bartoli, K.M., Schaening, C., Carlile, T.M., and Gilbert, W.V. (2018). Conserved Methyltransferase Spb1 Targets mRNAs for Regulated Modification with 2\u2019-O-Methyl Ribose. bioRxiv.","DOI":"10.1101\/271916"},{"key":"ref_98","first-page":"408053","article-title":"Use of specific chemical reagents for detection of modified nucleotides in RNA","volume":"2011","author":"Helm","year":"2011","journal-title":"J. Nucleic Acids"},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"e126","DOI":"10.1093\/nar\/gkz736","article-title":"Detection of internal N7-methylguanosine (m7G) RNA modifications by mutational profiling sequencing","volume":"47","author":"Enroth","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"1278","DOI":"10.1016\/j.molcel.2019.03.040","article-title":"METTL1 promotes Let-7 microRNA processing via m7G methylation","volume":"74","author":"Pandolfini","year":"2019","journal-title":"Mol. Cell"},{"key":"ref_101","doi-asserted-by":"crossref","first-page":"3306","DOI":"10.1021\/acschembio.2c00792","article-title":"m(7)G-quant-seq: Quantitative detection of RNA internal N(7)-methylguanosine","volume":"17","author":"Zhang","year":"2022","journal-title":"ACS Chem. Biol."},{"key":"ref_102","doi-asserted-by":"crossref","first-page":"638","DOI":"10.1038\/s41586-020-2418-2","article-title":"Dynamic RNA acetylation revealed by quantitative cross-evolutionary mapping","volume":"583","author":"Thomas","year":"2020","journal-title":"Nature"},{"key":"ref_103","doi-asserted-by":"crossref","first-page":"2286","DOI":"10.1038\/s41596-021-00501-9","article-title":"Quantitative nucleotide resolution profiling of RNA cytidine acetylation by ac4C-seq","volume":"16","author":"Schwartz","year":"2021","journal-title":"Nat. Protoc."},{"key":"ref_104","doi-asserted-by":"crossref","first-page":"2024","DOI":"10.1038\/s41592-024-02439-8","article-title":"Absolute quantitative and base-resolution sequencing reveals comprehensive landscape of pseudouridine across the human transcriptome","volume":"21","author":"Xu","year":"2024","journal-title":"Nat. Methods"},{"key":"ref_105","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1038\/nature13802","article-title":"Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells","volume":"515","author":"Carlile","year":"2014","journal-title":"Nature"},{"key":"ref_106","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1016\/j.cell.2014.08.028","article-title":"Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA","volume":"159","author":"Schwartz","year":"2014","journal-title":"Cell"},{"key":"ref_107","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1038\/s41587-022-01487-9","article-title":"Absolute quantification of single-base m6A methylation in the mammalian transcriptome using GLORI","volume":"41","author":"Liu","year":"2022","journal-title":"Nat. Biotechnol."},{"key":"ref_108","doi-asserted-by":"crossref","first-page":"1252","DOI":"10.1038\/s41596-023-00937-1","article-title":"GLORI for absolute quantification of transcriptome-wide m6A at single-base resolution","volume":"19","author":"Shen","year":"2024","journal-title":"Nat. Protoc."},{"key":"ref_109","doi-asserted-by":"crossref","first-page":"522","DOI":"10.1101\/gr.162537.113","article-title":"A biochemical landscape of A-to-I RNA editing in the human brain transcriptome","volume":"24","author":"Sakurai","year":"2014","journal-title":"Genome Res."},{"key":"ref_110","doi-asserted-by":"crossref","first-page":"451","DOI":"10.1002\/anie.201408362","article-title":"Profiling of ribose methylations in RNA by high-throughput sequencing","volume":"54","author":"Birkedal","year":"2015","journal-title":"Angew. Chem. Int. Ed. Engl."},{"key":"ref_111","doi-asserted-by":"crossref","first-page":"e135","DOI":"10.1093\/nar\/gkw547","article-title":"Illumina-based RiboMethSeq approach for mapping of 2\u2032-O-Me residues in RNA","volume":"44","author":"Marchand","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_112","doi-asserted-by":"crossref","first-page":"695","DOI":"10.1038\/nmeth.4294","article-title":"Nm-seq maps 2\u2032-O-methylation sites in human mRNA with base precision","volume":"14","author":"Dai","year":"2017","journal-title":"Nat. Methods"},{"key":"ref_113","doi-asserted-by":"crossref","first-page":"1303","DOI":"10.1261\/rna.061549.117","article-title":"High-throughput and site-specific identification of 2\u2032-O-methylation sites using ribose oxidation sequencing (RibOxi-seq)","volume":"23","author":"Zhu","year":"2017","journal-title":"RNA"},{"key":"ref_114","doi-asserted-by":"crossref","first-page":"16785","DOI":"10.1002\/anie.201810946","article-title":"AlkAniline-Seq: Profiling of m7G and m3C RNA modifications at single nucleotide resolution","volume":"57","author":"Marchand","year":"2018","journal-title":"Angew. Chem. Int. Ed. Engl."},{"key":"ref_115","doi-asserted-by":"crossref","first-page":"e110","DOI":"10.1093\/nar\/gkaa769","article-title":"HydraPsiSeq: A method for systematic and quantitative mapping of pseudouridines in RNA","volume":"48","author":"Marchand","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"ref_116","doi-asserted-by":"crossref","first-page":"e12","DOI":"10.1093\/nar\/gkn954","article-title":"RNA cytosine methylation analysis by bisulfite sequencing","volume":"37","author":"Schaefer","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"ref_117","doi-asserted-by":"crossref","first-page":"1559","DOI":"10.1038\/s41587-023-02034-w","article-title":"Ultrafast bisulfite sequencing detection of 5-methylcytosine in DNA and RNA","volume":"42","author":"Dai","year":"2024","journal-title":"Nat. Biotechnol."},{"key":"ref_118","doi-asserted-by":"crossref","first-page":"e23","DOI":"10.1093\/nar\/gkaa1173","article-title":"NOseq: Amplicon sequencing evaluation method for RNA m6A sites after chemical deamination","volume":"49","author":"Werner","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref_119","doi-asserted-by":"crossref","first-page":"12149","DOI":"10.1039\/D2SC03181G","article-title":"Transcriptome-wide profiling of N(6)-methyladenosine via a selective chemical labeling method","volume":"13","author":"Xie","year":"2022","journal-title":"Chem. Sci."},{"key":"ref_120","doi-asserted-by":"crossref","first-page":"887","DOI":"10.1038\/s41589-020-0526-9","article-title":"A metabolic labeling method detects m6A transcriptome-wide at single base resolution","volume":"16","author":"Shu","year":"2020","journal-title":"Nat. Chem. Biol."},{"key":"ref_121","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1038\/s41422-023-00836-w","article-title":"Nm-Mut-seq: A base-resolution quantitative method for mapping transcriptome-wide 2\u2032-methylation","volume":"33","author":"Chen","year":"2023","journal-title":"Cell Res."},{"key":"ref_122","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1261\/rna.036202.112","article-title":"Transcriptome-wide identification of A > I RNA editing sites by inosine specific cleavage","volume":"19","author":"Cattenoz","year":"2013","journal-title":"RNA"},{"key":"ref_123","doi-asserted-by":"crossref","first-page":"8740","DOI":"10.1021\/acs.analchem.2c01226","article-title":"Single-base resolution detection of adenosine-to-inosine RNA editing by endonuclease-mediated sequencing","volume":"94","author":"Chen","year":"2022","journal-title":"Anal. Chem."},{"key":"ref_124","doi-asserted-by":"crossref","first-page":"5241","DOI":"10.1021\/jacs.9b13406","article-title":"Selective enrichment of A-to-I edited transcripts from cellular RNA using endonuclease V","volume":"142","author":"Knutson","year":"2020","journal-title":"J. Am. Chem. Soc."},{"key":"ref_125","doi-asserted-by":"crossref","first-page":"e87","DOI":"10.1093\/nar\/gkad604","article-title":"Transcriptome-wide profiling of A-to-I RNA editing by Slic-seq","volume":"51","author":"Wei","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"ref_126","doi-asserted-by":"crossref","first-page":"1275","DOI":"10.1038\/s41592-019-0570-0","article-title":"DART-seq: An antibody-free method for global m6A detection","volume":"16","author":"Meyer","year":"2019","journal-title":"Nat. Methods"},{"key":"ref_127","doi-asserted-by":"crossref","first-page":"868","DOI":"10.1016\/j.molcel.2021.12.038","article-title":"scDART-seq reveals distinct m6A signatures and mRNA methylation heterogeneity in single cells","volume":"82","author":"Tegowski","year":"2022","journal-title":"Mol. Cell"},{"key":"ref_128","doi-asserted-by":"crossref","first-page":"993","DOI":"10.1038\/s41587-022-01587-6","article-title":"Transcriptome-wide profiling and quantification of N6-methyladenosine by enzyme-assisted adenosine deamination","volume":"41","author":"Xiao","year":"2023","journal-title":"Nat. Biotechnol."},{"key":"ref_129","doi-asserted-by":"crossref","first-page":"10588","DOI":"10.1021\/acs.analchem.3c00502","article-title":"Single-base resolution detection of N6-methyladenosine in RNA by adenosine deamination sequencing","volume":"95","author":"Shao","year":"2023","journal-title":"Anal. Chem."},{"key":"ref_130","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1038\/nmeth.4577","article-title":"Highly parallel direct RNA sequencing on an array of nanopores","volume":"15","author":"Garalde","year":"2018","journal-title":"Nat. Methods"},{"key":"ref_131","doi-asserted-by":"crossref","first-page":"e7","DOI":"10.1093\/nar\/gkaa620","article-title":"Decoding the epitranscriptional landscape from native RNA sequences","volume":"49","author":"Jenjaroenpun","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref_132","doi-asserted-by":"crossref","first-page":"4079","DOI":"10.1038\/s41467-019-11713-9","article-title":"Accurate detection of m6A RNA modifications in native RNA sequences","volume":"10","author":"Liu","year":"2019","journal-title":"Nat. Commun."},{"key":"ref_133","doi-asserted-by":"crossref","first-page":"e49658","DOI":"10.7554\/eLife.49658","article-title":"Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification","volume":"9","author":"Parker","year":"2020","journal-title":"Elife"},{"key":"ref_134","doi-asserted-by":"crossref","unstructured":"Smith, A.M., Jain, M., Mulroney, L., Garalde, D.R., and Akeson, M. (2019). Reading canonical and modified nucleobases in 16S ribosomal RNA using nanopore native RNA sequencing. PLoS ONE, 14.","DOI":"10.1371\/journal.pone.0216709"},{"key":"ref_135","doi-asserted-by":"crossref","first-page":"1278","DOI":"10.1038\/s41587-021-00915-6","article-title":"Quantitative profiling of pseudouridylation dynamics in native RNAs with nanopore sequencing","volume":"39","author":"Begik","year":"2021","journal-title":"Nat. Biotechnol."},{"key":"ref_136","doi-asserted-by":"crossref","first-page":"7198","DOI":"10.1038\/s41467-021-27393-3","article-title":"RNA modifications detection by comparative nanopore direct RNA sequencing","volume":"12","author":"Leger","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_137","doi-asserted-by":"crossref","first-page":"1348","DOI":"10.1038\/s41587-021-01108-x","article-title":"Nanopore sequencing technology, bioinformatics and applications","volume":"39","author":"Wang","year":"2021","journal-title":"Nat. Biotechnol."},{"key":"ref_138","doi-asserted-by":"crossref","first-page":"608","DOI":"10.1038\/s41587-023-01801-z","article-title":"Spatial imaging of glycoRNA in single cells with ARPLA","volume":"42","author":"Ma","year":"2024","journal-title":"Nat. Biotechnol."},{"key":"ref_139","doi-asserted-by":"crossref","first-page":"e101","DOI":"10.1093\/nar\/gkad787","article-title":"In situ visualization of m6A sites in cellular mRNAs","volume":"51","author":"Sheehan","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"ref_140","doi-asserted-by":"crossref","first-page":"1394","DOI":"10.1038\/s41587-021-00949-w","article-title":"Identification of differential RNA modifications from nanopore direct RNA sequencing with xPore","volume":"39","author":"Pratanwanich","year":"2021","journal-title":"Nat. Biotechnol."},{"key":"ref_141","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1007\/978-1-0716-1374-0_3","article-title":"EpiNano: Detection of m6A RNA Modifications Using Oxford Nanopore Direct RNA Sequencing","volume":"2298","author":"Liu","year":"2021","journal-title":"Methods Mol. Biol."},{"key":"ref_142","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1186\/s13059-022-02676-0","article-title":"RNA modification mapping with JACUSA2","volume":"23","author":"Piechotta","year":"2022","journal-title":"Genome Biol."},{"key":"ref_143","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1080\/15476286.2021.1978215","article-title":"Computational methods for RNA modification detection from nanopore direct RNA sequencing data","volume":"18","author":"Furlan","year":"2021","journal-title":"RNA Biol."},{"key":"ref_144","doi-asserted-by":"crossref","first-page":"4049","DOI":"10.1038\/s41467-024-48437-4","article-title":"Transfer learning enables identification of multiple types of RNA modifications using nanopore direct RNA sequencing","volume":"15","author":"Wu","year":"2024","journal-title":"Nat. Commun."},{"key":"ref_145","doi-asserted-by":"crossref","first-page":"gkaf673","DOI":"10.1093\/nar\/gkaf673","article-title":"ModiDeC: A multi-RNA modification classifier for direct nanopore sequencing","volume":"53","author":"Alagna","year":"2025","journal-title":"Nucleic Acids Res."},{"key":"ref_146","doi-asserted-by":"crossref","unstructured":"Lin, Z., Bao, X., Zhang, L., Huang, Y., Li, H., Liu, W., Ren, J., Zuo, Z., and Hu, K. (2025). RMPore: A comprehensive database of single-molecule RNA modifications detected by Nanopore direct RNA sequencing. Nucleic Acids Res., gkaf1144.","DOI":"10.1093\/nar\/gkaf1144"},{"key":"ref_147","doi-asserted-by":"crossref","first-page":"3121","DOI":"10.1021\/acs.accounts.3c00402","article-title":"Pitfalls in RNA modification quantification using nucleoside mass spectrometry","volume":"56","author":"Ammann","year":"2023","journal-title":"Acc. Chem. Res."},{"key":"ref_148","doi-asserted-by":"crossref","first-page":"gkaf895","DOI":"10.1093\/nar\/gkaf895","article-title":"Toward standardized epitranscriptome analytics: An inter-laboratory comparison of mass spectrometric detection and quantification of modified ribonucleosides in human RNA","volume":"53","author":"Hengesbach","year":"2025","journal-title":"Nucleic Acids Res."},{"key":"ref_149","doi-asserted-by":"crossref","first-page":"280","DOI":"10.1016\/j.bbagrm.2018.10.012","article-title":"Detection of ribonucleoside modifications by liquid chromatography coupled with mass spectrometry","volume":"1862","author":"Jora","year":"2019","journal-title":"Biochim. Biophys. Acta Gene Regul. Mech."},{"key":"ref_150","doi-asserted-by":"crossref","first-page":"1749","DOI":"10.1093\/clinchem\/43.9.1749","article-title":"Advanced multiplexed analysis with the FlowMetrix system","volume":"43","author":"Fulton","year":"1997","journal-title":"Clin. Chem."},{"key":"ref_151","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1016\/j.cccn.2005.06.023","article-title":"Applications of Luminex xMAP technology for rapid, high-throughput multiplexed nucleic acid detection","volume":"363","author":"Dunbar","year":"2006","journal-title":"Clin. Chim. Acta"},{"key":"ref_152","doi-asserted-by":"crossref","first-page":"5152","DOI":"10.1021\/ac8004154","article-title":"Molecular pincers: Antibody-based homogeneous protein sensors","volume":"80","author":"Heyduk","year":"2008","journal-title":"Anal. Chem."},{"key":"ref_153","doi-asserted-by":"crossref","first-page":"472","DOI":"10.1038\/nature24482","article-title":"Visualization of chemical modifications in the human 80S ribosome structure","volume":"551","author":"Natchiar","year":"2017","journal-title":"Nature"},{"key":"ref_154","doi-asserted-by":"crossref","first-page":"58","DOI":"10.1038\/s41392-022-00916-0","article-title":"Cryo-EM advances in RNA structure determination","volume":"7","author":"Ma","year":"2022","journal-title":"Sig. Transduct. Target. Ther."},{"key":"ref_155","doi-asserted-by":"crossref","first-page":"4043","DOI":"10.1093\/nar\/gkad194","article-title":"Cryo-EM reconstruction of the human 40S ribosomal subunit at 2.15 \u00c5 resolution","volume":"51","author":"Pellegrino","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"ref_156","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1002\/cbdv.200900177","article-title":"Crystallographic studies of chemically modified nucleic acids: A backward glance","volume":"7","author":"Egli","year":"2010","journal-title":"Chem. Biodivers."},{"key":"ref_157","doi-asserted-by":"crossref","unstructured":"Jackson, R.W., Smathers, C.M., and Robart, A.R. (2023). General strategies for RNA X-ray crystallography. Molecules, 28.","DOI":"10.3390\/molecules28052111"},{"key":"ref_158","doi-asserted-by":"crossref","first-page":"1019","DOI":"10.1126\/science.aaq0180","article-title":"RNA editing with CRISPR-Cas13","volume":"358","author":"Cox","year":"2017","journal-title":"Science"},{"key":"ref_159","doi-asserted-by":"crossref","first-page":"1431","DOI":"10.1038\/s41587-020-0572-6","article-title":"Programmable m6A modification of cellular RNAs with a Cas13-directed methyltransferase","volume":"38","author":"Wilson","year":"2020","journal-title":"Nat. Biotechnol."},{"key":"ref_160","doi-asserted-by":"crossref","first-page":"2468","DOI":"10.1021\/acs.analchem.9b03797","article-title":"RCasFISH: CRISPR\/dCas9-mediated in situ imaging of mRNA transcripts in fixed cells and tissues","volume":"92","author":"Wang","year":"2020","journal-title":"Anal. Chem."}],"container-title":["Life"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2075-1729\/15\/12\/1888\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,12,10]],"date-time":"2025-12-10T12:38:48Z","timestamp":1765370328000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2075-1729\/15\/12\/1888"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,12,10]]},"references-count":160,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["life15121888"],"URL":"https:\/\/doi.org\/10.3390\/life15121888","relation":{},"ISSN":["2075-1729"],"issn-type":[{"value":"2075-1729","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,12,10]]}}}