RNA Modification and Processing

4th Symposium on Nucleic Acid Modifications

Symposium website

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

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.

Wu CC, Naarmann-de Vries IS, Hartmann J, Nidoieva Z, Kopietz K, Marchand V, Özrendeci Z, Lindner D, Schelchshorn S, Flad S, Frye M, Papavasiliou N, Schirmeister T, Stoecklin G, Schott J, Motorin Y, Tuorto F, Dieterich C, Helm M, Ruggieri A. The two-step purification method ViREn identifies a single NSUN6-mediated 5-methylcytosine modification promoting dengue virus RNA genome turnover. bioRxiv DOI:1101/2025.03.17.643699 preprint.

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.