Newest publications of the TRR319
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.
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.
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.
A continuously updated publication list can be found here.
Chronologically ordered publication list of the TRR319
-2023-
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-
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.
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. 2022 Nov 3;PP. doi: 10.1109/TCBB.2022.3219114. Epub ahead of print. PMID: 36327193.
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.
Garcia-Gonzalez C, Dieterich C, Maroli G, Wiesnet M, Wietelmann A, Li X, Yuan X, Graumann J, Stellos K, Kubin T, Schneider A, Braun T. ADAR1 Prevents Autoinflammatory Processes in the Heart Mediated by IRF7. Circ Res. 2022 Sep 16;131(7):580-597. doi: 10.1161/CIRCRESAHA.122.320839. Epub 2022 Aug 24. PMID: 36000401.
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.
Solé-Boldo L, Raddatz G, Gutekunst J, Gilliam O, Bormann F, Liberio MS, Hasche D, Antonopoulos W, Mallm JP, Lonsdorf AS, Rodríguez-Paredes M, Lyko F. Differentiation-related epigenomic changes define clinically distinct keratinocyte cancer subclasses. Mol Syst Biol. 2022 Sep;18(9):e11073. doi: 10.15252/msb.202211073. PMID: 36121124; PMCID: PMC9484266.
Lüders J, Winkel AR, Reichel M, Bitterer VW, Scheibe M, Widmann C, Butter F, Köster T. Identification of Pri-miRNA Stem-Loop Interacting Proteins in Plants Using a Modified Version of the Csy4 CRISPR Endonuclease. Int J Mol Sci. 2022 Aug 11;23(16):8961. doi: 10.3390/ijms23168961. PMID: 36012225; PMCID: PMC9409100.
Löcherer C, Tosun E, Backes H, Jäschke A. Thiophosphate Analogs of Coenzyme A and Its Precursors-Synthesis, Stability, and Biomimetic Potential. Biomolecules. 2022 Aug 1;12(8):1065. doi: 10.3390/biom12081065. PMID: 36008959; PMCID: PMC9405834.
Delaunay S, Frye M. Localization-dictated function for METTL3. Nat Cell Biol. 2022 Aug;24(8):1188-1189. doi: 10.1038/s41556-022-00972-2. PMID: 35927452.
Ito-Kureha T, Leoni C, Borland K, Cantini G, Bataclan M, Metzger RN, Ammann G, Krug AB, Marsico A, Kaiser S, Canzar S, Feske S, Monticelli S, König J, Heissmeyer V. The function of Wtap in N6-adenosine methylation of mRNAs controls T cell receptor signaling and survival of T cells. Nat Immunol. 2022 Aug;23(8):1208-1221. doi: 10.1038/s41590-022-01268-1. Epub 2022 Jul 25. PMID: 35879451.
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.
Levin M, Butter F. Proteotranscriptomics – A facilitator in omics research. Comput Struct Biotechnol J. 2022 Jul 9;20:3667-3675. doi: 10.1016/j.csbj.2022.07.007. PMID: 35891789; PMCID: PMC9293588.
Delaunay S, Pascual G, Feng B, Klann K, Behm M, Hotz-Wagenblatt A, Richter K, Zaoui K, Herpel E, Münch C, Dietmann S, Hess J, Benitah SA, Frye M. Mitochondrial RNA modifications shape metabolic plasticity in metastasis. Nature. 2022 Jul;607(7919):593-603. doi: 10.1038/s41586-022-04898-5. Epub 2022 Jun 29. PMID: 35768510; PMCID: PMC9300468.
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.
Löcherer C, Bühler N, Lafrenz P, Jäschke A. Staphylococcus aureus Small RNAs Possess Dephospho-CoA 5′-Caps, but No CoAlation Marks. Noncoding RNA. 2022 Jun 28;8(4):46. doi: 10.3390/ncrna8040046. PMID: 35893229; PMCID: PMC9326634.
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.
Schott J, Reitter S, Lindner D, Grosser J, Bruer M, Shenoy A, Geiger T, Mathes A, Dobreva G, Stoecklin G. Nascent Ribo-Seq measures ribosomal loading time and reveals kinetic impact on ribosome density. Nat Methods. 2021 Sep;18(9):1068-1074. doi: 10.1038/s41592-021-01250-z. Epub 2021 Sep 3. Erratum in: Nat Methods. 2023 Feb;20(2):316. PMID: 34480152.
