Newest publications of the TRR319
Nunes IV, Breitenbach L, Pawusch S, Eigenbrod T, Ananth S, Schad P, Fackler OT, Butter F, Dalpke AH, Chen LS. Bacterial RNA sensing by TLR8 requires RNase 6 processing and is inhibited by RNA 2’O-methylation. EMBO Rep. 2024 Oct 3. doi: 10.1038/s44319-024-00281-9. Epub ahead of print. PMID: 39363059.
Meidner JL, Frey AF, Zimmermann RA, Sabin MO, Nidoieva Z, Weldert AC, Hoba SN, Krone MW, Barthels F. Nanomole Scale Screening of Fluorescent RNA-Methyltransferase Probes Enables the Discovery of METTL1 Inhibitors. Angew Chem Int Ed Engl. 2024 Aug 15:e202403792. doi: 10.1002/anie.202403792. Epub ahead of print. PMID: 39145518.
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 Sep 13:gr.278849.123. doi: 10.1101/gr.278849.123. Epub ahead of print. PMID: 39271295.
Koch J, Lyko F. Refining the role of N6-methyladenosine in cancer. Curr Opin Genet Dev. 2024 Oct;88:102242. doi: 10.1016/j.gde.2024.102242. Epub 2024 Aug 6. PMID: 39111230.
Bessler L, Sirleaf J, Kampf CJ, Frankowska K, Leszczyńska G, Opatz T, Helm M. Esterification of Cyclic N6-Threonylcarbamoyladenosine During RNA Sample Preparation. ChemMedChem. 2024 Jul 2;19(13):e202400115. doi: 10.1002/cmdc.202400115. Epub 2024 May 26. PMID: 38630955.
Toubdji S, Thullier Q, Kilz LM, Marchand V, Yuan Y, Sudol C, Goyenvalle C, Jean-Jean O, Rose S, Douthwaite S, Hardy L, Baharoglu Z, de Crécy-Lagard V, Helm M, Motorin Y, Hamdane D, Brégeon D. Exploring a unique class of flavoenzymes: Identification and biochemical characterization of ribosomal RNA dihydrouridine synthase. Proc Natl Acad Sci U S A. 2024 Aug 6;121(32):e2401981121. doi: 10.1073/pnas.2401981121. Epub 2024 Jul 30. PMID: 39078675; PMCID: PMC11317573.
Helm M, Winz ML. Nascent mRNA damage: depot and disposal. Signal Transduct Target Ther. 2024 Aug 9;9(1):198. doi: 10.1038/s41392-024-01900-6. PMID: 39117645; PMCID: PMC11310187.
Kristen M, Lander M, Kilz ML, Gleue L, Jörg M, Bregeon B, Hamdane D, Marchand V, Motorin Y, Friedland K, Helm M. DORQ-seq: high-throughput quantification of femtomol tRNA pools by combination of cDNA hybridization and Deep sequencing. Nucleic Acids Res. 2024 Sep 11:gkae765. doi: 10.1093/nar/gkae765. Epub ahead of print. PMID: 39258547.
Guillen-Angel M, Roignant JY. Exploring pseudouridylation: dysregulation in disease and therapeutic potential. Curr Opin Genet Dev. 2024 Jun 3;87:102210. doi: 10.1016/j.gde.2024.102210. Epub ahead of print. PMID: 38833893.
Becker MA, Meiser N, Schmidt-Dengler M, Richter C, Wacker A, Schwalbe H, Hengesbach M. m6A methylation of transcription leader sequence impacts discontinuous transcription of subgenomic mRNAs. Chemistry. 2024 May 24:e202401897. doi: 10.1002/chem.202401897. Epub ahead of print. PMID: 38785102.
Schmidt B, Hildebrandt A. From GPUs to AI and quantum: three waves of acceleration in bioinformatics. Drug Discov Today. 2024 Jun;29(6):103990. doi: 10.1016/j.drudis.2024.103990. Epub 2024 Apr 23. PMID: 38663581.
Sudol C, Kilz LM, Marchand V, Thullier Q, Guérineau V, Goyenvalle C, Faivre B, Toubdji S, Lombard M, Jean-Jean O, de Crécy-Lagard V, Helm M, Motorin Y, Brégeon D, Hamdane D. Functional redundancy in tRNA dihydrouridylation. Nucleic Acids Res. 2024 Jun 10;52(10):5880-5894. doi: 10.1093/nar/gkae325. PMID: 38682613; PMCID: PMC11162810.
Görlitz K, Bessler L, Helm M, Schaffrath R, Klassen R. Fluoropyrimidines trigger decay of hypomodified tRNA in yeast. Nucleic Acids Res. 2024 Jun 10;52(10):5841-5851. doi: 10.1093/nar/gkae341. PMID: 38716877; PMCID: PMC11162795.
Wolfram-Schauerte M, Pozhydaieva N, Grawenhoff J, Welp LM, Silbern, I, Wulf A, Billau FA, Glatter T, Urlaub H, Jäschke A, Höfer K . A viral ADP-ribosyltransferase attaches RNA chains to host proteins. Nature 620, 1054–1062 (2023). https://doi.org/10.1038/s41586-023-06429-2
Espadas G, Llovera L, Ollivier A, Tuorto F, Novoa EM, Sabidó E. Spectral libraries from nucleobases and deoxyribonucleosides facilitate the identification of ribonucleosides by nano-flow liquid chromatography-tandem mass spectrometry. Rapid Commun Mass Spectrom. 2024 Jul 15;38(13):e9759. doi: 10.1002/rcm.9759. PMID: 38680121.
Magg V, Manetto A, Kopp K, Wu CC, Naghizadeh M, Lindner D, Eke L, Welsch J, Kallenberger SM, Schott J, Haucke V, Locker N, Stoecklin G, Ruggieri A. Turnover of PPP1R15A mRNA encoding GADD34 controls responsiveness and adaptation to cellular stress. Cell Rep. 2024 Apr 23;43(4):114069. doi: 10.1016/j.celrep.2024.114069. Epub 2024 Apr 10. PMID: 38602876.
Lorenzo JP, Molla L, Amro EM, Ibarra IL, Ruf S, Neber C, Gkougkousis C, Ridani J, Subramani PG, Boulais J, Harjanto D, Vonica A, Di Noia JM, Dieterich C, Zaugg JB, Papavasiliou FN. APOBEC2 safeguards skeletal muscle cell fate through binding chromatin and regulating transcription of non-muscle genes during myoblast differentiation. Proc Natl Acad Sci U S A. 2024 Apr 23;121(17):e2312330121. doi: 10.1073/pnas.2312330121. Epub 2024 Apr 16. PMID: 38625936; PMCID: PMC11047093.
Sklias A, Cruciani S, Marchand V, Spagnuolo M, Lavergne G, Bourguignon V, Brambilla A, Dreos R, Marygold SJ, Novoa EM, Motorin Y, Roignant JY. Comprehensive map of ribosomal 2′-O-methylation and C/D box snoRNAs in Drosophila melanogaster. Nucleic Acids Res. 2024 Feb 28:gkae139. doi: 10.1093/nar/gkae139. Epub ahead of print. PMID: 38416577
Boulet M, Gilbert G, Renaud Y, Schmidt-Dengler M, Plantié E, Bertrand R, Nan X, Jurkowski T, Helm M, Vandel L, Waltzer L. Adenine methylation is very scarce in the Drosophila genome and not erased by the ten-eleven translocation dioxygenase. Elife. 2023 Dec 21;12:RP91655. doi: 10.7554/eLife.91655. PMID: 38126351; PMCID: PMC10735219.
Jörg M, Plehn JE, Kristen M, Lander M, Walz L, Lietz C, Wijns J, Pichot F, Rojas-Charry L, Wirtz Martin KM, Ruffini N, Kreim N, Gerber S, Motorin Y, Endres K, Rossmanith W, Methner A, Helm M, Friedland K. N1-methylation of adenosine (m1A) in ND5 mRNA leads to complex I dysfunction in Alzheimer’s disease. Mol Psychiatry. 2024 Jan 29. doi: 10.1038/s41380-024-02421-y. Epub ahead of print. PMID: 38287100.
Bessler L, Groß J, Kampf CJ, Opatz T, Helm M. Reversible oxidative dimerization of 4-thiouridines in tRNA isolates. RSC Chem Biol. 2024 Feb 1;5(3):216-224. doi: 10.1039/d3cb00221g. PMID: 38456039; PMCID: PMC10915967.
Gerber, J.L., Morales Guzmán, S.I., Worf, L. Hubbe, P., Kopp, J. and Peschek, J. Structural and mechanistic insights into activation of the human RNA ligase RTCB by Archease. Nat Commun 15, 2378 (2024). https://doi.org/10.1038/s41467-024-46568-2.
Delaunay S, Helm M, Frye M. RNA modifications in physiology and disease: towards clinical applications. Nat Rev Genet. 2024 Feb;25(2):104-122. doi: 10.1038/s41576-023-00645-2. Epub 2023 Sep 15. PMID: 37714958
Wei G, Russo S, Tuorto F. Lost in translation: How neurons cope with tRNA decoding. Bioessays. 2024 Jul 11:e2400107. doi: 10.1002/bies.202400107. Epub ahead of print. PMID: 38990077.
Chan A, Naarmann-de Vries IS, Scheitl CPM, Höbartner C, Dieterich C. Detecting m6A at single-molecular resolution via direct RNA sequencing and realistic training data. Nat Commun. 2024 Apr 18;15(1):3323. doi: 10.1038/s41467-024-47661-2. PMID: 38637518; PMCID: PMC11026524.
A continuously updated publication list can be found here.
Chronologically ordered publication list of the TRR319
-2023-
Podvalnaya N, Bronkhorst AW, Lichtenberger R, Hellmann S, Nischwitz E, Falk T, Karaulanov E, Butter F, Falk S, Ketting RF. piRNA processing by a trimeric Schlafen-domain nuclease. Nature. 2023 Oct;622(7982):402-409. doi: 10.1038/s41586-023-06588-2. Epub 2023 Sep 27. PMID: 37758951; PMCID: PMC10567574.
Motorin Y, Helm M. General Principles and Limitations for Detection of RNA Modifications by Sequencing. Acc Chem Res. 2023 Dec 8. doi: 10.1021/acs.accounts.3c00529. Epub ahead of print. PMID: 38065564.
Helm M, Bohnsack MT, Carell T, Dalpke A, Entian KD, Ehrenhofer-Murray A, Ficner R, Hammann C, Höbartner C, Jäschke A, Jeltsch A, Kaiser S, Klassen R, Leidel SA, Marx A, Mörl M, Meier JC, Meister G, Rentmeister A, Rodnina M, Roignant JY, Schaffrath R, Stadler P, Stafforst T. Experience with German Research Consortia in the Field of Chemical Biology of Native Nucleic Acid Modifications. ACS Chem Biol. 2023 Nov 14. doi: 10.1021/acschembio.3c00586. Epub ahead of print. PMID: 37962075.
Sung HM, Schott J, Boss P, Lehmann JA, Hardt MR, Lindner D, Messens J, Bogeski I, Ohler U, Stoecklin G. Stress-induced nuclear speckle reorganization is linked to activation of immediate early gene splicing. J Cell Biol. 2023 Dec 4;222(12):e202111151. doi: 10.1083/jcb.202111151. Epub 2023 Nov 13. PMID: 37956386; PMCID: PMC10641589.
Sun Y, Piechotta M, Naarmann-de Vries I, Dieterich C, Ehrenhofer-Murray AE. Detection of queuosine and queuosine precursors in tRNAs by direct RNA sequencing. Nucleic Acids Res. 2023 Nov 10;51(20):11197-11212. doi: 10.1093/nar/gkad826. PMID: 37811872; PMCID: PMC10639084.
Möhler M, Jäschke A. Future Perspectives for the Identification and Sequencing of Nicotinamide Adenine Dinucleotide-Capped RNAs. Acc Chem Res. 2023 Nov 7;56(21):3000-3009. doi: 10.1021/acs.accounts.3c00446. Epub 2023 Oct 18. PMID: 37852615; PMCID: PMC10634297.
Kallert E, Behrendt M, Frey A, Kersten C, Barthels F. Non-covalent dyes in microscale thermophoresis for studying RNA ligand interactions and modifications. Chem. Sci., 2023, 14, 9827-9837. DOI: 10.1039/D3SC02993J
Naarmann-de Vries IS, Gjerga E, Gandor CLA, Dieterich C. Adaptive Sampling for Nanopore direct RNA sequencing. RNA. 2023 Sep 6:rna.079727.123. doi: 10.1261/rna.079727.123. Epub ahead of print. PMID: 37673469
Trendel J, Boileau E, Jochem M, Dieterich C, Krijgsveld J. PEPseq quantifies transcriptome-wide changes in protein occupancy and reveals selective translational repression after translational stress. Nucleic Acids Res. 2023 Aug 11;51(14):e79. doi: 10.1093/nar/gkad557. PMID: 37395449; PMCID: PMC10415142
Iyer KV, Müller M, Tittel LS, Winz ML. Molecular Highway Patrol for Ribosome Collisions. Chembiochem. 2023 Jun 29:e202300264. doi: 10.1002/cbic.202300264. Epub ahead of print. PMID: 37382189.
Cirzi C, Dyckow J, Legrand C, Schott J, Guo W, Perez Hernandez D, Hisaoka M, Parlato R, Pitzer C, van der Hoeven F, Dittmar G, Helm M, Stoecklin G, Schirmer L, Lyko F, Tuorto F. Queuosine-tRNA promotes sex-dependent learning and memory formation by maintaining codon-biased translation elongation speed. EMBO J. 2023 Aug 23:e112507. doi: 10.15252/embj.2022112507. Epub ahead of print. PMID: 37609797.
Mattioli F, Worpenberg L, Li CT, Ibrahim N, Naz S, Sharif S, Firouzabadi SG, Vosoogh S, Saraeva-Lamri R, Raymond L, Trujillo C, Guex N, Antonarakis SE, Ansar M, Darvish H, Liu RJ, Roignant JY, Reymond A. Biallelic variants in NSUN6 cause an autosomal recessive neurodevelopmental disorder. Genet Med. 2023 Sep;25(9):100900. doi: 10.1016/j.gim.2023.100900. Epub 2023 May 21. PMID: 37226891.
Wierczeiko A, Pastore S, Mündnich S, Busch AM, Dietrich V, Helm M, Butto T, Gerber S. NanopoReaTA: a user-friendly tool for nanopore-seq real-time transcriptional analysis. Bioinformatics. 2023 Aug 7:btad492. doi: 10.1093/bioinformatics/btad492. Epub ahead of print. PMID: 37549052.
Yan L, Yin Z, Zhang H, Zhao Z, Wang M, Müller A, Kallenborn F, Wichmann A, Wie Y, Niu B, Schmidt B, Liu W. „RabbitQCPlus 2.0: More Efficient and Versatile Quality Control for Sequencing Data”. Methods 216 (2023), pp. 39-50. https://doi.org/10.1016/j.ymeth.2023.06.007
Pecori R, Chillón I, Lo Giudice C, Arnold A, Wüst S, Binder M, Marcia M, Picardi E, Papavasiliou F N. ADAR RNA editing on antisense RNAs results in apparent U-to-C base changes on overlapping sense transcripts. Front. Cell Dev. Biol., 06 January 2023 Sec. Epigenomics and Epigenetics https://doi.org/10.3389/fcell.2022.1080626
Yan L, Yin Z, Zhang H, Zhao Z, Wang M, Müller A, Kobus R, Wei Y, Beifang N, Schmidt B, Liu W. RabbitQCPlus: More Efficient Quality Control for Sequencing Data, 2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2022, pp. 619-626, doi: 10.1109/BIBM55620.2022.9995332.
Zimmermann RA, Schwickert M, Meidner JL, Nidoieva Z, Helm M, Schirmeister T. An Optimized Microscale Thermophoresis Method for High-Throughput Screening of DNA Methyltransferase 2 Ligands. ACS Pharmacol Transl Sci. 2022 Oct 19;5(11):1079-1085. doi: 10.1021/acsptsci.2c00175. eCollection 2022 Nov 11. PMID: 36407957
Poetz F, Lebedeva S, Schott J, Lindner D, Ohle U, Stoecklin G. Control of immediate early gene expression by CPEB4-repressor complex-mediated mRNA degradation. Genome Biol 23, 193 (2022). https://doi.org/10.1186/s13059-022-02760-5 PMID 36096941
Eiermann N, Stoecklin G, Jovanovic B. Mitochondrial Inhibition by Sodium Azide Induces Assembly of eIF2α Phosphorylation-Independent Stress Granules in Mammalian Cells. Int. J. Mol. Sci. 2022, 23, 5600. https://doi.org/10.3390/ijms23105600 PMID 35628412
García-Vílchez R, Añazco-Guenkova AM, Dietmann S, López J, Morón-Calvente V, D’Ambrosi S, Nombela P, Zamacola K, Mendizabal I, García-Longarte S, Zabala-Letona A, Astobiza I, Fernández S, Paniagua A, Miguel-López B, Marchand V, Alonso-López D, Merkel A, García-Tuñón I, Ugalde-Olano A, Loizaga-Iriarte A, Lacasa-Viscasillas I, Unda M, Azkargorta M, Elortza F, Bárcena L, Gonzalez-Lopez M, Aransay AM, Di Domenico T, Sánchez-Martín MA, De Las Rivas J, Guil S, Motorin Y, Helm M, Pandolfi PP, Carracedo A, Blanco S. METTL1 promotes tumorigenesis through tRNA-derived fragment biogenesis in prostate cancer. Mol Cancer. 2023 Jul 29;22(1):119. doi: 10.1186/s12943-023-01809-8. PMID: 37516825; PMCID: PMC10386714.
Koch J, Neuberger M, Schmidt-Dengler M, Xu J, Carneiro VC, Ellinger J, Kriegmair MC, Nuhn P, Erben P, Michel MS, Helm M, Rodríguez-Paredes M, Nientiedt M, Lyko F. Reinvestigating the clinical relevance of the m6A writer METTL3 in urothelial carcinoma of the bladder. iScience. 2023 Jul 11;26(8):107300. doi: 10.1016/j.isci.2023.107300. PMID: 37554463; PMCID: PMC10405067.
Fradera-Sola A, Nischwitz E, Bayer ME, Luck K, Butter F. RNA-dependent interactome allows network-based assignment of RNA-binding protein function. Nucleic Acids Res. 2023 Jun 9;51(10):5162-5176. doi: 10.1093/nar/gkad245. PMID: 37070168; PMCID: PMC10250244.
Zhang H, Song H, Xu X, Chang Q, Wang M, Wei Y, Yin Z, Schmidt B, Liu W. RabbitFX: Efficient Framework for FASTA/Q File Parsing on Modern Multi-Core Platforms. IEEE/ACM Trans Comput Biol Bioinform. 2023 Jun 5;20(3):2341-2348. doi: 10.1109/TCBB.2022.3219114. Epub 2023 Jun 5. PMID: 36327193.
Rücklé C, Körtel N, Basilicata MF, Busch A, Zhou Y, Hoch-Kraft P, Tretow K, Kielisch F, Bertin M, Pradhan M, Musheev M, Schweiger S, Niehrs C, Rausch O, Zarnack K, Keller Valsecchi CI, König J. RNA stability controlled by m6A methylation contributes to X-to-autosome dosage compensation in mammals. Nat Struct Mol Biol. 2023 May 18. doi: 10.1038/s41594-023-00997-7. PMID: 37202476.
Pecori R, Ren W, Pirmoradian M, Wang X, Liu D, Berglund M, Li W, Tasakis RN, Di Giorgio S, Ye X, Li X, Arnold A, Wüst S, Schneider M, Selvasaravanan KD, Fuell Y, Stafforst T, Amini RM, Sonnevi K, Enblad G, Sander B, Wahlin BE, Wu K, Zhang H, Helm D, Binder M, Papavasiliou FN, Pan-Hammarström Q. ADAR1-mediated RNA editing promotes B cell lymphomagenesis. iScience. 2023 May 12;26(6):106864. doi: 10.1016/j.isci.2023.106864. PMID: 37255666; PMCID: PMC10225930.#
Schwickert M, Zimmermann RA, Habeck T, Hoba SN, Nidoieva Z, Fischer TR, Stark MM, Kersten C, Lermyte F, Helm M, and Schirmeister T. Covalent S-Adenosylhomocysteine-Based DNA Methyltransferase 2 Inhibitors with a New Type of Aryl Warhead. ACS Medicinal Chemistry Letters 2023 May 9; Article ASAP DOI: 10.1021/acsmedchemlett.3c00062
Zimmermann RA, Fischer TR, Schwickert M, Nidoieva Z, Schirmeister T, Kersten C. Chemical Space Virtual Screening against Hard-to-Drug RNA Methyltransferases DNMT2 and NSUN6. Int J Mol Sci. 2023 Mar 24;24(7):6109. doi: 10.3390/ijms24076109. PMID: 37047081 ; PMCID: PMC10094593.
Bessler L, Vogt LM, Lander M, Dal Magro C, Keller P, Kühlborn J, Kampf CJ, Opatz T, Helm M. A New Bacterial Adenosine-Derived Nucleoside as an Example of RNA Modification Damage. Angew Chem Int Ed Engl. 2023 Mar 6;62(11):e202217128. doi: 10.1002/anie.202217128. Epub 2023 Feb 7. PMID: 36629490.
Koshla O, Vogt LM, Rydkin O, Sehin Y, Ostash I, Helm M, Ostash B. Landscape of Post-Transcriptional tRNA Modifications in Streptomyces albidoflavus J1074 as Portrayed by Mass Spectrometry and Genomic Data Mining. J Bacteriol. 2023 Jan 26;205(1):e0029422. doi: 10.1128/jb.00294-22. Epub 2022 Dec 5. PMID: 36468867 ; PMCID: PMC9879100.
Lemsara A, Dieterich C, Naarmann-de Vries IS. Mapping of RNA Modifications by Direct Nanopore Sequencing and JACUSA2. Methods Mol Biol. 2023;2624:241-260. doi: 10.1007/978-1-0716-2962-8_16. PMID: 36723820.
-2022-
Hisaoka M, Schott J, Bortecend T, Lindner D, Krijgsveld J, Stoecklin G. Preferential translation of p53 target genes. RNA Biol 2022;19:437-452.
Poetz F, Corbo J, Levdansky Y, Spiegelhalter A, Lindner D, Magg V, Lebedeva S, Schweiggert J, Schott J, Valkov E, Stoecklin G. RNF219 attenuates global mRNA decay through inhibition of CCR4-NOT complex-mediated deadenylation. Nat Commun 2021;12:7175.
Fischer TR, Meidner L, Schwickert M, Weber M, Zimmermann RA, Kersten C, Schirmeister T, Helm M. Chemical biology and medicinal chemistry of RNA methyltransferases. Nucleic Acids Res. 2022 May 6;50(8):4216-4245. doi: 10.1093/nar/gkac224. PMID: 35412633
Helm M, Motorin Y. Phosphorylation found inside RNA. Nature. 2022 May;605(7909):234-235. doi: 10.1038/d41586-022-01021-6. PMID: 35478019 No abstract available.
Barthels F, Hammerschmidt S, Fischer T, Zimmer C, Kallert E, Helm M, Kersten C, Schirmeister T. A low-cost 3D-printable differential scanning fluorometer for protein and RNA melting experiments. HardwareX, Volume 11, 2022. ISSN 2468-0672, https://doi.org/10.1016/j.ohx.2022.e00256.
Pichot F, Hogg MC, Marchand V, Bourguignon V, Jirström E, Farrell C, Gibriel HA, Prehn JHM, Motorin Y, Helm M. Quantification of substoichiometric modification reveals global tsRNA hypomodification, preferences for angiogenin-mediated tRNA cleavage, and idiosyncratic epitranscriptomes of human neuronal cell-lines. Comput Struct Biotechnol J. 2022 Dec 19;21:401-417. doi: 10.1016/j.csbj.2022.12.020. PMID: 36618980; PMCID: PMC9798144.
Hertler J, Slama K, Schober B, Özrendeci Z, Marchand V, Motorin Y, Helm M. Synthesis of point-modified mRNA. Nucleic Acids Res. 2022 Nov 11;50(20):e115. doi: 10.1093/nar/gkac719. PMID: 36062567; PMCID: PMC9723659.
Henry BA, Marchand V, Schlegel BT, Helm M, Motorin Y, Lee N. Pseudouridylation of Epstein-Barr virus noncoding RNA EBER2 facilitates lytic replication. RNA. 2022 Nov;28(11):1542-1552. doi: 10.1261/rna.079219.122. Epub 2022 Sep 13. PMID: 36100352; PMCID: PMC9745832.
Bessler L, Kaur N, Vogt LM, Flemmich L, Siebenaller C, Winz ML, Tuorto F, Micura R, Ehrenhofer-Murray AE, Helm M. Functional integration of a semi-synthetic azido-queuosine derivative into translation and a tRNA modification circuit. Nucleic Acids Res. 2022 Oct 14;50(18):10785-10800. doi: 10.1093/nar/gkac822. PMID: 36169220; PMCID: PMC9561289.
Kallert E, Fischer TR, Schneider S, Grimm M, Helm M, Kersten C. Protein-Based Virtual Screening Tools Applied for RNA-Ligand Docking Identify New Binders of the preQ1-Riboswitch. J Chem Inf Model. 2022 Sep 12;62(17):4134-4148. doi: 10.1021/acs.jcim.2c00751. Epub 2022 Aug 22. PMID: 35994617.
Ravichandran M, Rafalski D, Davies CI, Ortega-Recalde O, Nan X, Glanfield CR, Kotter A, Misztal K, Wang AH, Wojciechowski M, Rażew M, Mayyas IM, Kardailsky O, Schwartz U, Zembrzycki K, Morison IM, Helm M, Weichenhan D, Jurkowska RZ, Krueger F, Plass C, Zacharias M, Bochtler M, Hore TA, Jurkowski TP. Pronounced sequence specificity of the TET enzyme catalytic domain guides its cellular function. Sci Adv. 2022 Sep 9;8(36):eabm2427. doi: 10.1126/sciadv.abm2427. Epub 2022 Sep 7. PMID: 36070377; PMCID: PMC9451156.
Schwickert M, Fischer TR, Zimmermann RA, Hoba SN, Meidner JL, Weber M, Weber M, Stark MM, Koch J, Jung N, Kersten C, Windbergs M, Lyko F, Helm M, Schirmeister T. Discovery of Inhibitors of DNA Methyltransferase 2, an Epitranscriptomic Modulator and Potential Target for Cancer Treatment. J Med Chem. 2022 Jul 28;65(14):9750-9788. doi: 10.1021/acs.jmedchem.2c00388. Epub 2022 Jul 18. PMID: 35849534.
Pichot F, Marchand V, Helm M, Motorin Y. Machine learning algorithm for precise prediction of 2′-O-methylation (Nm) sites from experimental RiboMethSeq datasets. Methods. 2022 Jul;203:311-321. doi: 10.1016/j.ymeth.2022.03.007. Epub 2022 Mar 18. PMID: 35314341.
Richter F, Plehn JE, Bessler L, Hertler J, Jörg M, Cirzi C, Tuorto F, Friedland K, Helm M. RNA marker modifications reveal the necessity for rigorous preparation protocols to avoid artifacts in epitranscriptomic analysis. Nucleic Acids Res. 2022 May 6;50(8):4201-4215. doi: 10.1093/nar/gkab1150. PMID: 34850949; PMCID: PMC9071408.
Biedenbänder T, de Jesus V, Schmidt-Dengler M, Helm M, Corzilius B, Fürtig B. RNA modifications stabilize the tertiary structure of tRNAfMet by locally increasing conformational dynamics. Nucleic Acids Res. 2022 Feb 28;50(4):2334-2349. doi: 10.1093/nar/gkac040. PMID: 35137185; PMCID: PMC8887418.
Motorin Y, Helm M. RNA nucleotide methylation: 2021 update. Wiley Interdiscip Rev RNA. 2022 Jan;13(1):e1691. doi: 10.1002/wrna.1691. Epub 2021 Dec 15. PMID: 34913259.
-2021-
Poetz F, Corbo J, Levdansky Y, Spiegelhalter A, Lindner D, Magg V, Lebedeva S, Schweiggert J, Schott J, Valkov E, Stoecklin G. RNF219 attenuates global mRNA decay through inhibition of CCR4-NOT complex-mediated deadenylation. Nat Commun. 2021 Dec 9;12(1):7175. doi: 10.1038/s41467-021-27471-6. PMID: 34887419; PMCID: PMC8660800.
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