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For: Ryvkin P, Leung YY, Silverman IM, Childress M, Valladares O, Dragomir I, Gregory BD, Wang LS. HAMR: high-throughput annotation of modified ribonucleotides. RNA 2013;19:1684-92. [PMID: 24149843 PMCID: PMC3884653 DOI: 10.1261/rna.036806.112] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 08/23/2013] [Indexed: 05/17/2023]
Number Cited by Other Article(s)
51
Analysis of tRNA-derived RNA fragments (tRFs) in Cryptococcus spp.: RNAi-independent generation and possible compensatory effects in a RNAi-deficient genotype. Fungal Biol 2021;125:389-399. [PMID: 33910680 DOI: 10.1016/j.funbio.2020.12.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 11/30/2020] [Accepted: 12/18/2020] [Indexed: 01/03/2023]
52
The epitranscriptome beyond m6A. Nat Rev Genet 2020;22:119-131. [PMID: 33188361 DOI: 10.1038/s41576-020-00295-8] [Citation(s) in RCA: 433] [Impact Index Per Article: 86.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/06/2020] [Indexed: 12/21/2022]
53
Kristen M, Plehn J, Marchand V, Friedland K, Motorin Y, Helm M, Werner S. Manganese Ions Individually Alter the Reverse Transcription Signature of Modified Ribonucleosides. Genes (Basel) 2020;11:genes11080950. [PMID: 32824672 PMCID: PMC7466121 DOI: 10.3390/genes11080950] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/10/2020] [Accepted: 08/12/2020] [Indexed: 12/17/2022]  Open
54
Wang J, Toffano-Nioche C, Lorieux F, Gautheret D, Lehmann J. Accurate characterization of Escherichia coli tRNA modifications with a simple method of deep-sequencing library preparation. RNA Biol 2020;18:33-46. [PMID: 32618488 DOI: 10.1080/15476286.2020.1790871] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]  Open
55
Mathlin J, Le Pera L, Colombo T. A Census and Categorization Method of Epitranscriptomic Marks. Int J Mol Sci 2020;21:ijms21134684. [PMID: 32630140 PMCID: PMC7370119 DOI: 10.3390/ijms21134684] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 06/26/2020] [Accepted: 06/27/2020] [Indexed: 12/21/2022]  Open
56
Liu L, Song B, Ma J, Song Y, Zhang SY, Tang Y, Wu X, Wei Z, Chen K, Su J, Rong R, Lu Z, de Magalhães JP, Rigden DJ, Zhang L, Zhang SW, Huang Y, Lei X, Liu H, Meng J. Bioinformatics approaches for deciphering the epitranscriptome: Recent progress and emerging topics. Comput Struct Biotechnol J 2020;18:1587-1604. [PMID: 32670500 PMCID: PMC7334300 DOI: 10.1016/j.csbj.2020.06.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 06/02/2020] [Accepted: 06/07/2020] [Indexed: 12/13/2022]  Open
57
Kimura S, Dedon PC, Waldor MK. Comparative tRNA sequencing and RNA mass spectrometry for surveying tRNA modifications. Nat Chem Biol 2020;16:964-972. [PMID: 32514182 DOI: 10.1038/s41589-020-0558-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 04/22/2020] [Indexed: 12/12/2022]
58
Ma X, Si F, Liu X, Luan W. PRMdb: A Repository of Predicted RNA Modifications in Plants. PLANT & CELL PHYSIOLOGY 2020;61:1213-1222. [PMID: 32542382 DOI: 10.1093/pcp/pcaa042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 03/28/2020] [Indexed: 06/11/2023]
59
Liu Q, Gregory RI. RNAmod: an integrated system for the annotation of mRNA modifications. Nucleic Acids Res 2020;47:W548-W555. [PMID: 31147718 PMCID: PMC6602476 DOI: 10.1093/nar/gkz479] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 05/02/2019] [Accepted: 05/17/2019] [Indexed: 01/13/2023]  Open
60
Werner S, Schmidt L, Marchand V, Kemmer T, Falschlunger C, Sednev MV, Bec G, Ennifar E, Höbartner C, Micura R, Motorin Y, Hildebrandt A, Helm M. Machine learning of reverse transcription signatures of variegated polymerases allows mapping and discrimination of methylated purines in limited transcriptomes. Nucleic Acids Res 2020;48:3734-3746. [PMID: 32095818 PMCID: PMC7144921 DOI: 10.1093/nar/gkaa113] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 02/10/2020] [Accepted: 02/19/2020] [Indexed: 12/23/2022]  Open
61
Guo Q, Ng PQ, Shi S, Fan D, Li J, Zhao J, Wang H, David R, Mittal P, Do T, Bock R, Zhao M, Zhou W, Searle I. Arabidopsis TRM5 encodes a nuclear-localised bifunctional tRNA guanine and inosine-N1-methyltransferase that is important for growth. PLoS One 2019;14:e0225064. [PMID: 31756231 PMCID: PMC6874348 DOI: 10.1371/journal.pone.0225064] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 10/28/2019] [Indexed: 12/30/2022]  Open
62
Grozhik AV, Olarerin-George AO, Sindelar M, Li X, Gross SS, Jaffrey SR. Antibody cross-reactivity accounts for widespread appearance of m1A in 5'UTRs. Nat Commun 2019;10:5126. [PMID: 31719534 PMCID: PMC6851129 DOI: 10.1038/s41467-019-13146-w] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 10/10/2019] [Indexed: 11/30/2022]  Open
63
Schmidt L, Werner S, Kemmer T, Niebler S, Kristen M, Ayadi L, Johe P, Marchand V, Schirmeister T, Motorin Y, Hildebrandt A, Schmidt B, Helm M. Graphical Workflow System for Modification Calling by Machine Learning of Reverse Transcription Signatures. Front Genet 2019;10:876. [PMID: 31608115 PMCID: PMC6774277 DOI: 10.3389/fgene.2019.00876] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 08/21/2019] [Indexed: 01/28/2023]  Open
64
Qi C, Ding J, Yuan B, Feng Y. Analytical methods for locating modifications in nucleic acids. CHINESE CHEM LETT 2019. [DOI: 10.1016/j.cclet.2019.02.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
65
Linder B, Jaffrey SR. Discovering and Mapping the Modified Nucleotides That Comprise the Epitranscriptome of mRNA. Cold Spring Harb Perspect Biol 2019;11:11/6/a032201. [PMID: 31160350 DOI: 10.1101/cshperspect.a032201] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
66
Vandivier LE, Anderson ZD, Gregory BD. HAMR: High-Throughput Annotation of Modified Ribonucleotides. Methods Mol Biol 2019;1870:51-67. [PMID: 30539546 DOI: 10.1007/978-1-4939-8808-2_4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
67
Mongan NP, Emes RD, Archer N. Detection and analysis of RNA methylation. F1000Res 2019;8:F1000 Faculty Rev-559. [PMID: 31069058 PMCID: PMC6489984 DOI: 10.12688/f1000research.17956.1] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/15/2019] [Indexed: 12/13/2022]  Open
68
Torres AG, Reina O, Stephan-Otto Attolini C, Ribas de Pouplana L. Differential expression of human tRNA genes drives the abundance of tRNA-derived fragments. Proc Natl Acad Sci U S A 2019;116:8451-8456. [PMID: 30962382 PMCID: PMC6486751 DOI: 10.1073/pnas.1821120116] [Citation(s) in RCA: 131] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]  Open
69
Nucleotide resolution sequencing of N4-acetylcytidine in RNA. Methods Enzymol 2019;621:31-51. [PMID: 31128786 DOI: 10.1016/bs.mie.2019.02.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
70
Saleembhasha A, Mishra S. Novel molecules lncRNAs, tRFs and circRNAs deciphered from next-generation sequencing/RNA sequencing: computational databases and tools. Brief Funct Genomics 2019. [PMID: 28637169 DOI: 10.1093/bfgp/elx013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]  Open
71
Motorin Y, Helm M. Methods for RNA Modification Mapping Using Deep Sequencing: Established and New Emerging Technologies. Genes (Basel) 2019;10:genes10010035. [PMID: 30634534 PMCID: PMC6356707 DOI: 10.3390/genes10010035] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 01/03/2019] [Accepted: 01/04/2019] [Indexed: 12/17/2022]  Open
72
Hoffmann A, Fallmann J, Vilardo E, Mörl M, Stadler PF, Amman F. Accurate mapping of tRNA reads. Bioinformatics 2019;34:1116-1124. [PMID: 29228294 DOI: 10.1093/bioinformatics/btx756] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 12/07/2017] [Indexed: 11/12/2022]  Open
73
Vandivier LE, Gregory BD. New insights into the plant epitranscriptome. JOURNAL OF EXPERIMENTAL BOTANY 2018;69:4659-4665. [PMID: 30020491 DOI: 10.1093/jxb/ery262] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 07/09/2018] [Indexed: 06/08/2023]
74
Chen B, Yuan BF, Feng YQ. Analytical Methods for Deciphering RNA Modifications. Anal Chem 2018;91:743-756. [DOI: 10.1021/acs.analchem.8b04078] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
75
Wu DC, Yao J, Ho KS, Lambowitz AM, Wilke CO. Limitations of alignment-free tools in total RNA-seq quantification. BMC Genomics 2018;19:510. [PMID: 29969991 PMCID: PMC6042521 DOI: 10.1186/s12864-018-4869-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 06/14/2018] [Indexed: 11/11/2022]  Open
76
Shi J, Ko EA, Sanders KM, Chen Q, Zhou T. SPORTS1.0: A Tool for Annotating and Profiling Non-coding RNAs Optimized for rRNA- and tRNA-derived Small RNAs. GENOMICS, PROTEOMICS & BIOINFORMATICS 2018;16:144-151. [PMID: 29730207 PMCID: PMC6112344 DOI: 10.1016/j.gpb.2018.04.004] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Revised: 03/25/2018] [Accepted: 04/07/2018] [Indexed: 01/07/2023]
77
In Silico Identification of RNA Modifications from High-Throughput Sequencing Data Using HAMR. Methods Mol Biol 2018;1562:211-229. [PMID: 28349463 DOI: 10.1007/978-1-4939-6807-7_14] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
78
Pan T. Modifications and functional genomics of human transfer RNA. Cell Res 2018;28:395-404. [PMID: 29463900 PMCID: PMC5939049 DOI: 10.1038/s41422-018-0013-y] [Citation(s) in RCA: 268] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 12/27/2017] [Indexed: 11/18/2022]  Open
79
Aschenbrenner J, Werner S, Marchand V, Adam M, Motorin Y, Helm M, Marx A. Engineering of a DNA Polymerase for Direct m6 A Sequencing. Angew Chem Int Ed Engl 2018;57:417-421. [PMID: 29115744 PMCID: PMC5768020 DOI: 10.1002/anie.201710209] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Indexed: 12/16/2022]
80
Thompson A, Zielezinski A, Plewka P, Szymanski M, Nuc P, Szweykowska-Kulinska Z, Jarmolowski A, Karlowski WM. tRex: A Web Portal for Exploration of tRNA-Derived Fragments in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2018;59:e1. [PMID: 29145635 DOI: 10.1093/pcp/pcx173] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 11/13/2017] [Indexed: 06/07/2023]
81
Aschenbrenner J, Werner S, Marchand V, Adam M, Motorin Y, Helm M, Marx A. Entwicklung einer DNA-Polymerase für die direkte m6A-Sequenzierung. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201710209] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
82
Jonkhout N, Tran J, Smith MA, Schonrock N, Mattick JS, Novoa EM. The RNA modification landscape in human disease. RNA (NEW YORK, N.Y.) 2017;23:1754-1769. [PMID: 28855326 PMCID: PMC5688997 DOI: 10.1261/rna.063503.117] [Citation(s) in RCA: 409] [Impact Index Per Article: 51.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
83
Chen X, Sun YZ, Liu H, Zhang L, Li JQ, Meng J. RNA methylation and diseases: experimental results, databases, Web servers and computational models. Brief Bioinform 2017;20:896-917. [DOI: 10.1093/bib/bbx142] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 09/12/2017] [Indexed: 12/15/2022]  Open
84
Marín M, Fernández-Calero T, Ehrlich R. Protein folding and tRNA biology. Biophys Rev 2017;9:573-588. [PMID: 28944442 PMCID: PMC5662057 DOI: 10.1007/s12551-017-0322-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 08/28/2017] [Indexed: 12/14/2022]  Open
85
Alenko A, Fleming AM, Burrows CJ. Reverse Transcription Past Products of Guanine Oxidation in RNA Leads to Insertion of A and C opposite 8-Oxo-7,8-dihydroguanine and A and G opposite 5-Guanidinohydantoin and Spiroiminodihydantoin Diastereomers. Biochemistry 2017;56:5053-5064. [PMID: 28845978 DOI: 10.1021/acs.biochem.7b00730] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
86
Wulff TF, Argüello RJ, Molina Jordàn M, Roura Frigolé H, Hauquier G, Filonava L, Camacho N, Gatti E, Pierre P, Ribas de Pouplana L, Torres AG. Detection of a Subset of Posttranscriptional Transfer RNA Modifications in Vivo with a Restriction Fragment Length Polymorphism-Based Method. Biochemistry 2017;56:4029-4038. [PMID: 28703578 DOI: 10.1021/acs.biochem.7b00324] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
87
Foley SW, Kramer MC, Gregory BD. RNA structure, binding, and coordination in Arabidopsis. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017;8. [PMID: 28660659 DOI: 10.1002/wrna.1426] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 03/08/2017] [Accepted: 04/13/2017] [Indexed: 11/05/2022]
88
Detecting RNA modifications in the epitranscriptome: predict and validate. Nat Rev Genet 2017;18:275-291. [DOI: 10.1038/nrg.2016.169] [Citation(s) in RCA: 379] [Impact Index Per Article: 47.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
89
Krogh N, Birkedal U, Nielsen H. RiboMeth-seq: Profiling of 2'-O-Me in RNA. Methods Mol Biol 2017;1562:189-209. [PMID: 28349462 DOI: 10.1007/978-1-4939-6807-7_13] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
90
Vandivier LE, Gregory BD. Reading the Epitranscriptome. RNA MODIFICATION 2017;41:269-298. [DOI: 10.1016/bs.enz.2017.03.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
91
Orioli A. tRNA biology in the omics era: Stress signalling dynamics and cancer progression. Bioessays 2016;39. [PMID: 28026052 DOI: 10.1002/bies.201600158] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
92
CoverageAnalyzer (CAn): A Tool for Inspection of Modification Signatures in RNA Sequencing Profiles. Biomolecules 2016;6:biom6040042. [PMID: 27834909 PMCID: PMC5197952 DOI: 10.3390/biom6040042] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 10/20/2016] [Accepted: 10/21/2016] [Indexed: 12/23/2022]  Open
93
Clark WC, Evans ME, Dominissini D, Zheng G, Pan T. tRNA base methylation identification and quantification via high-throughput sequencing. RNA (NEW YORK, N.Y.) 2016;22:1771-1784. [PMID: 27613580 PMCID: PMC5066629 DOI: 10.1261/rna.056531.116] [Citation(s) in RCA: 160] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 08/12/2016] [Indexed: 05/03/2023]
94
Schwartz S, Motorin Y. Next-generation sequencing technologies for detection of modified nucleotides in RNAs. RNA Biol 2016;14:1124-1137. [PMID: 27791472 PMCID: PMC5699547 DOI: 10.1080/15476286.2016.1251543] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]  Open
95
Burgess A, David R, Searle IR. Deciphering the epitranscriptome: A green perspective. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2016;58:822-835. [PMID: 27172004 PMCID: PMC5094531 DOI: 10.1111/jipb.12483] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 05/10/2016] [Indexed: 05/13/2023]
96
Mansur F, Ivshina M, Gu W, Schaevitz L, Stackpole E, Gujja S, Edwards YJK, Richter JD. Gld2-catalyzed 3' monoadenylation of miRNAs in the hippocampus has no detectable effect on their stability or on animal behavior. RNA (NEW YORK, N.Y.) 2016;22:1492-9. [PMID: 27495319 PMCID: PMC5029448 DOI: 10.1261/rna.056937.116] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 06/30/2016] [Indexed: 05/20/2023]
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Veneziano D, Di Bella S, Nigita G, Laganà A, Ferro A, Croce CM. Noncoding RNA: Current Deep Sequencing Data Analysis Approaches and Challenges. Hum Mutat 2016;37:1283-1298. [PMID: 27516218 DOI: 10.1002/humu.23066] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 08/09/2016] [Indexed: 02/06/2023]
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Tserovski L, Helm M. Diastereoselectivity of 5-Methyluridine Osmylation Is Inverted inside an RNA Chain. Bioconjug Chem 2016;27:2188-97. [PMID: 27540864 DOI: 10.1021/acs.bioconjchem.6b00403] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Arimbasseri AG, Iben J, Wei FY, Rijal K, Tomizawa K, Hafner M, Maraia RJ. Evolving specificity of tRNA 3-methyl-cytidine-32 (m3C32) modification: a subset of tRNAsSer requires N6-isopentenylation of A37. RNA (NEW YORK, N.Y.) 2016;22:1400-10. [PMID: 27354703 PMCID: PMC4986895 DOI: 10.1261/rna.056259.116] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Accepted: 05/24/2016] [Indexed: 05/10/2023]
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Tserovski L, Marchand V, Hauenschild R, Blanloeil-Oillo F, Helm M, Motorin Y. High-throughput sequencing for 1-methyladenosine (m(1)A) mapping in RNA. Methods 2016;107:110-21. [PMID: 26922842 DOI: 10.1016/j.ymeth.2016.02.012] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 02/22/2016] [Accepted: 02/22/2016] [Indexed: 01/28/2023]  Open
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