RNA Modification and Processing

RMaP News

Transregio 319 RMaP extended for a further period

DFG – Deutsche Forschungsgemeinschaft – DFG to Fund Nine New Collaborative Research Centres

Johannes Gutenberg-Universität Mainz mit sieben Anträgen für Sonderforschungsbereiche erfolgreich | Kommunikation und Presse (KOM)

Excellent Franco-German cooperation in the field of RNA Modification research

https://aktuelles.uni-frankfurt.de/english/rna-researchers-from-frankfurt-and-grenoble-receive-franco-german-science-award/

https://www.dfh-ufa.org/pressemitteilungen/deutsch-franzosischer-forcheurs-preis-zeichnet-projekt-im-bereich-krebsforschung-aus

What is RMaP?

Transregio 319 RMaP is a joint venture combining:

Molecular Biology, Biochemistry, Cellular Biology, Chemical Biology, Biophysical Chemistry, Structural Biology, Developmental Biology, Genetics, Bioinformatics.

Members of the Scientific Board

Recent publications from the TRR 319

Kallenborn F, Chacon A, Hundt C, Sirelkhatim H, Didi K, Cha S, Dallago C, Mirdita M, Schmidt B, Steinegger M. GPU-accelerated homology search with MMseqs2. Nat Methods. 2025 Sep 18. https://doi.org/10.1038/s41592-025-02819-8.. Epub ahead of print. PMID: 40968302.

Hoba SN, Schwickert M, Kammerer L, Sabin M, Weldert AC, Nidoieva Z, Meidner JL, Barthels F, Schirmeister T, Kersten C. Parallel synthesis of 5′-amino-5′-deoxy-adenosine derivatives for focused chemical space exploration and their application as methyltransferase inhibitors. RSC Med Chem. 2025 Aug 12. doi: 10.1039/d5md00376h. Epub ahead of print. PMCID: PMC12412055; DOI: 1039/d5md00376h.

Frey AF, Schwan M, Weldert AC, Kadenbach V, Kopp J, Nidoieva Z, Zimmermann RA, Gleue L, Zimmer C, Jörg M, Friedland K, Helm M, Sinning I, Barthels F. DNA-encoded library screening uncovers potent DNMT2 inhibitors targeting a cryptic allosteric binding site. iScience. 2025 Aug 5;28(9):113300. doi: 10.1016/j.isci.2025.113300. PMCID: PMC12396291; DOI: 1016/j.isci.2025.113300

van der Toorn W, Naarmann-de Vries IS, Liu-Wei W, Dieterich C, von Kleist M. WarpDemuX-tRNA: barcode multiplexing for nanopore tRNA sequencing. Nucleic Acids Res. 2025 Sep 5;53(17):gkaf873. doi: 10.1093/nar/gkaf873. PMID: 40930527; DOI: 1093/nar/gkaf873

Naarmann-De Vries IS, Preissendörfer T, König J, Dieterich C. AvaII senses m6A and inosine sites and enables targeted nanopore direct RNA-sequencing. Front Mol Biosci. 2025 Jul 28;12:1593637. DOI: 3389/fmolb.2025.1593637. PMID: 40791658; PMCID: PMC12336230.

Landrock MF, Krutyhołowa R, Böhnert P, Mazur J, Honc M, Hammermeister A, Bessler L, Scherf D, Elms A, Radczuk N, Skupien-Rabian B, Jankowska U, Herberg FW, Helm M, Klassen R, Glatt S, Schaffrath R. Autophosphorylation of conserved yeast and human casein kinase 1 isozymes regulates Elongator-dependent tRNA modifications. Nucleic Acids Res. 2025 Sep 5;53(17):gkaf881. DOI: 1093/nar/gkaf881. PMID: 40930532.

Peschek J, Tuorto F. Interplay Between tRNA Modifications and Processing. J Mol Biol. 2025 Aug 15;437(16):169198. DOI: 1016/j.jmb.2025.169198. Epub 2025 May 22. PMID: 40404521.

Kopietz K, Raorane K, Guo W, Flegler F, Bourguignon V, Thuillier Q, Kilz LM, Weber M, Marchand V, Reuter K, Tuorto F, Helm M, Motorin Y. TGT Damages its Substrate tRNAs by the Formation of Abasic Sites in the Anticodon Loop. J Mol Biol. 2025 Aug 15;437(16):169000. DOI: 10.1016/j.jmb.2025.169000. Epub 2025 Feb 26. PMID: 40011082.

Köhler S, Kopp J, Maiti S, Bujnicki JM, Peschek J. Structure of fungal tRNA ligase Trl1 with RNA reveals conserved substrate-binding principles. Nat Struct Mol Biol. 2025 Jun 25. DOI: 1038/s41594-025-01589-3. Epub ahead of print. PMID: 40563009.

Müller A, Wichmann A, Kallenborn F, Hildebrandt A, Schmidt B. RMapAlign3N: Fast mapping of 3N-Reads, Bioinformatics Advances, 2025; vbaf164. https://doi.org/10.1093/bioadv/vbaf164

Alagna N, Mündnich S, Miedema J, Pastore S, Lehmann L, Wierczeiko A, Friedrich J, Walz L, Jörg M, Butto T, Friedland K, Helm M, Gerber S. ModiDeC: a multi-RNA modification classifier for direct nanopore sequencing. Nucleic Acids Res. 2025 Jul 19;53(14):gkaf673. PMCID: PMC12276011 DOI: 1093/nar/gkaf673.

Hewel C, Wierczeiko A, Miedema J, Hofmann F, Weissbach S, Dietrich V, Friedrich J, Holthoefer L, Haug V, Mündnich S, Schartel L, Jenson K, Diederich S, Sys S, Butto T, Paul N, Koch J, Lyko F, Kraft F, Schweiger S, Lemke EA, Helm M, Linke M, Gerber S: Direct RNA sequencing (RNA004) allows for improved transcriptome assessment and near real-time tracking of methylation for medical applications https://doi.org/10.1101/2024.07.25.605188

Weldert AC, Frey AF, Krone MW, Krähe F, Kuhn H, Kersten C, Barthels F. Structure-guided design of a methyltransferase-like 3 (METTL3) proteolysis targeting chimera (PROTAC) incorporating an indole-nicotinamide chemotype. RSC Med Chem. 2025 Jun 19. doi: 10.1039/d5md00359h. Epub ahead of print. PMID: 40599585; PMCID: PMC12207533 DOI: 1039/d5md00359h

Guo W, Kaczmarczyk I, Kopietz K, Flegler F, Russo S, Cigirgan E, Chramiec-Głąbik A, Koziej Ł, Cirzi C, Peschek J, Reuter K, Helm M, Glatt S, Tuorto F. Queuosine is incorporated into precursor tRNA before splicing. Nat Commun. 2025 Jul 31;16(1):7044. doi: 10.1038/s41467-025-62220-z. PMCID: PMC12313893 DOI: 1038/s41467-025-62220-z

Ćorović M, Hoch-Kraft P, Zhou Y, Hallstein S, König J, Zarnack K. m⁶A in the coding sequence: linking deposition, translation, and decay. Trends Genet. 2025 Jul 7:S0168-9525(25)00132-5. DOI: 10.1016/j.tig.2025.06.002. Epub ahead of print. PMID: 40628588.

Spangenberg J, Mündnich S, Busch A, Pastore S, Wierczeiko A, Goettsch W, Dietrich V, Pryszcz LP, Cruciani S, Novoa EM, Joshi K, Perera R, Di Giorgio S, Arrubarrena P, Tellioglu I, Poon CL, Wan YK, Göke J, Hildebrandt A, Dieterich C, Helm M, Marz M, Gerber S, Alagna N. The RMaP challenge of predicting RNA modifications by nanopore sequencing. Commun Chem. 2025 Apr 12;8(1):115. doi: 10.1038/s42004-025-01507-0. PMID: 40221591;PMCID: PMC11993749.

Teschner D, Gomez-Zepeda D, Łącki MK,Kemmer T, Busch A, Tenzer S, Hildebrandt A. Rustims: An Open-Source Framework for Rapid Development and Processing of timsTOF Data-Dependent Acquisition Data. J Proteome Res. 2025 May 2;24(5):2358-2368. doi: 10.1021/acs.jproteome.4c00966. Epub 2025 Apr 22. PMID: 40260647;PMCID: PMC12053931.

Scherf D, Hammermeister A, Böhnert P, Burkard A, Helm M, Glatt S, Schaffrath R. tRNA binding to Kti12 is crucial for wobble uridine modification by Elongator. Nucleic Acids Res. 2025 Apr 10;53(7):gkaf296. doi: 10.1093/nar/gkaf296. PMID: 40226916; PMCID: PMC11995267.

Kopietz K, Raorane K, Guo W, Flegler F, Bourguignon V, Thuillier Q, Kilz LM, Weber M, Marchand V, Reuter K, Tuorto F, Helm M, Motorin Y. TGT Damages its Substrate tRNAs by the Formation of Abasic Sites in the Anticodon Loop. J Mol Biol. 2025 Feb 25:169000. DOI: 1016/j.jmb.2025.169000. Epub ahead of print. PMID: 40011082.

Gonzalez-Jabalera P, Jäschke A. Flavin adenine dinucleotide (FAD) as a non-canonical RNA cap: Mechanisms, functions, and emerging insights. Arch Biochem Biophys. 2025 Apr;766:110326. DOI: 10.1016/j.abb.2025.110326. Epub 2025 Feb 5. PMID: 39921141.

Nidoieva Z, Sabin MO, Dewald T, Weldert AC, Hoba SN, Helm M, Barthels F. A microscale thermophoresis-based enzymatic RNA methyltransferase assay enables the discovery of DNMT2 inhibitors. Commun Chem. 2025 Feb 3;8(1):32. doi: 10.1038/s42004-025-01439-9. PMCID: PMC11790956  DOI: 1038/s42004-025-01439-9

Morishima T, Fakruddin M, Kanamori Y, Masuda T, Ogawa A, Wang Y, Schoonenberg VAC, Butter F, Arima Y, Akaike T, Moroishi T, Tomizawa K, Suda T, Wei FY, Takizawa H. Mitochondrial translation regulates terminal erythroid differentiation by maintaining iron homeostasis. Sci Adv. 2025 Feb 21;11(8):eadu3011. Epub 2025 Feb 21. PMID: 39983002; PMCID: PMC11844735  DOI: 1126/sciadv.adu3011

He YM, Burkard A, Wu CS, Jin XY, Liu L, Helm M, Cheng L. A Direct Chemical Repair of Etheno-Type RNA Damages. Angew Chem Int Ed Engl. 2025 Jan 15;64(3):e202415417. DOI: 1002/anie.202415417 Epub 2024 Dec 2. PMID: 39589841.

Xu J, Koch J, Schmidt C, Nientiedt M, Neuberger M, Erben P, Michel MS, Rodríguez-Paredes M, Lyko F. Loss of YTHDC1 m⁶A reading function promotes invasiveness in urothelial carcinoma of the bladder. Exp Mol Med. 2025 Feb;57(1):118-130.  DOI: 1038/s12276-024-01377-x. Epub 2025 Jan 1. PMID: 39741187; PMCID: PMC11799412.

Soni K, Horvath A, Dybkov O, Schwan M, Trakansuebkul S, Flemming D, Wild K, Urlaub H, Fischer T, Sinning I. Structures of aberrant spliceosome intermediates on their way to disassembly. Nat Struct Mol Biol. 2025 Jan 20. DOI: 10.1038/s41594-024-01480-7. Epub ahead of print. PMID: 39833470.

A continuously updated publication list can be found here.