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Publications (selected)

Altendorfer E, Mundlos S, Mayer A (2025). A transcription coupling model for how enhancers communicate with their target genes. Nature Struct Mol Biol, doi.org/10.1038/s41594-025-01523-7

Ploner, C. Mitteregger, H. Glasner, R. Bereiter, R. Micura, K. Breuker (2025). The intrinsic preference of guanosine bases for cleavage-facilitating interactions with phosphodiester moieties in RNA anions revealed by base modifications and mass spectrometry. Nucleic Acids Res.53, doi.org/10.1093/nar/gkaf494

Hilber S, Marotto A, Mitteregger C, Tollinger M*, Kreutz C* (2025). Methylation of cytidine 1407 increases the lifetimes of the A-site ground and excited states of E. coli 16S ribosomal RNA. J Am Chem Soc, doi.org/10.1021/jacs.5c06523

Trebo M*, Maurer T*, Krendl FJ*, Salcher S*, Martowicz A, Hautz T, Sopper S, Amann A, Cardini B, Poelsler LH, Mair A, Hofmann J, Meszaros AT, Hermann M, Günther M, Ormanns S, Trajanoski Z, Schneeberger S, Wolf D, Oberhuber R, Pircher A (2025). Ex vivo modeling of human colorectal cancer liver metastasis by normotheric machine perfusion. Molecular Cancer, in press. (*contributed equally as first author)

Delazer, I., Bauer, I., Rummel, T., Nykiel, K., Rieder, D., Fickl, M., Tumler, V., Razkova, A., Schaefer, M. R., Scheed, T., Erlacher, M. D., Erhard, F., Micura, R., & Lusser, A. (2025). mRNA turnover dynamics are affected by cell differentiation and loss of the cytosine methyltransferase Nsun2. Nucleic Acids Res, 53(19).doi.org/10.1093/nar/gkaf995

Bereiter R., Flemmich L., Nykiel K., Heel S., Geley S., Hanisch M., Eichler C., Breuker K., Lusser A*., Micura R*. (2025). Engineering covalent small molecule-RNA complexes in living cells. Nat. Chem. Biol. doi.org/10.1038/s41589-024-01801-3.

S.V. Heel, F. Juen, K. Bartosik, R. Micura, C. Kreutz, K. Breuker (2024). Resolving the intricate binding of neomycin B to multiple binding motifs of a neomycin-sensing riboswitch aptamer by native top-down mass spectrometry and NMR spectroscopy. Nucleic Acids Res. 52, 4691-4701 doi.org/ 10.1093/nar/gkae224

*Ulicevic J, *Shao Z, *Jasnovidova O, Bressin A, Gajos M, Ng AHM, Annaldasula S, Meierhofer D, Church GM, Busskamp V, Mayer A (2024). Uncovering the dynamics and consequences of RNA isoform changes during neuronal differentiation. Mol Syst Biol, doi.org/10.1038/s44320-024-00039-4 (*contributed equally as first author)

Salcher S, Heidegger I, Untergasser G, Fotakis G, Scheiber A, Martowicz A, Noureen A, Krogsdam A, Schatz C, Schäfer G, Trajanoski Z, Wolf D, Sopper S, Pircher A (2024). Comparative analysis of 10X Chromium vs. BD Rhapsody whole transcriptome single-cell sequencing technologies in complex human tissues. Heliyon, (doi.org/10.1016/j.heliyon.2024.e28358. 

Kompatscher M, Bartosik K, Erharter K, Plangger R, Juen F, Kreutz C, Micura R, Westhof E, Erlacher MD (2024). Contribution of tRNA sequences and modifications to the decoding preferences of E. coli and M. mycoides tRNAGlyUCC for synonymous glycine codons. Nucleic Acids Res, doi.org/10.1093/nar/gkad1136

Kohl MP, Kompatscher M, Clementi N, Holl L, Erlacher MD (2023). Initiation at AUGUG and GUGUG sequences can lead to translation of overlapping reading frames in E. coli. Nucleic Acids Res, doi.org/10.1093/nar/gkac1175

S.V. Heel, K. Bartosik, F. Juen, C. Kreutz, R. Micura, K. Breuker (2023). Native top-down mass spectrometry uncovers two distinct binding motifs of a functional neomycin-sensing riboswitch aptamer. J. Am. Chem. Soc. 145, 15284-15294,
doi.org/10.1021/jacs.3c02774

*Bressin A, *Jasnovidova O, *Arnold M, Altendorfer E, Trajkovski F, Kratz TA, Handzlik JE, Hnisz D, Mayer A (2023). High-sensitive nascent transcript sequencing reveals BRD4-specific control of widespread enhancer and target gene transcription. Nat Commun, doi.org/10.1038/s41467-023-40633-y  (*contributed equally as first author)

*Nabavizadeh N, *Bressin A, Shboul M, Traspas RM, Chia PH, Bonnard C, Szenker-Ravi E, Sarıbaş B, Beillard E, Altunoglu U, Hojati Z, Drutman S, Freier S, El‑Khateeb M, Fathallah R, Casanova JL, Soror W, Arafat A, Escande-Beillard N, **Mayer A, **Reversade B (2023). A progeroid syndrome caused by a deep intronic variant in TAPT1 is revealed by RNA/SI-NET sequencing. EMBO Mol Med, doi.org/10.15252/emmm.202216478 (*contributed equally as first author, **contributed equally as last authors)

Hautz T, Salcher S*, Fodor M, Sturm G, Ebner S, Mair A, Trebo M, Untergasser G, Sopper S, Cardini B, Martowicz A, Hofmann J, Daum S, Kalb M, Resch T, Krendl F, Weissenbacher A, Otarashvili G, Obrist P, Zelger B, Öfner D, Trajanoski Z, Troppmair J, Oberhuber R, Pircher A, Wolf D, Schneeberger S. (2023). Immune cell dynamics deconvoluted by single-cell RNA sequencing in normothermic machine perfusion of the liver. Nature Communications,  21;14(1):2285. (*contributed equally as first author)
doi.org/10.1038/s41467-023-37674-8.

 R. Bereiter, E. Renard, K. Breuker, C. Kreutz, E. Ennifar, R. Micura, (2023).1-Deazaguanosine modified RNA – The missing piece for functional RNA atomic mutagenesis. J. Am. Chem. Soc., 144, 10344–10352. 
doi.org/10.1021/jacs.2c01877

Salcher S, Sturm G, Horvath L, Untergasser G, Kuempers C, Fotakis G, Panizzolo E, Martowicz A, Trebo M, Pall G, Gamerith G, Sykora M, Augustin F, Schmitz K, Finotello F, Rieder D, Perner S, Sopper S, Wolf D, Pircher A, Trajanoski Z (2022). High-resolution single-cell atlas reveals diversity and plasticity of tissue-resident neutrophils in non-small cell lung cancer. Cancer Cell,12;40(12):1503-1520.e8
doi.org/10.1016/j.ccell.2022.10.008. 

*Arnold M, *Bressin A, Jasnovidova O, Meierhofer D, Mayer A (2021). A BRD4-mediated elongation control point primes transcribing RNA polymerase II for 3’-processing and termination. Mol Cell, doi.org/10.1016/j.molcel.2021.06.026

 L. Flemmich, S. Heel, S. Moreno, K. Breuker, R. Micura (2021). A natural riboswitch scaffold with self-methylation activity. Nat. Commun.,
doi.org/10.1038/s41467-021-24193-7

Hutter K, Lohmüller M, Jukic A, Eichin F, Avci S, Labi V, Szabo TG, Hoser SM, Hüttenhofer A, Villunger A, Herzog S (2020). SAFB2 Enables the Processing of Suboptimal Stem-Loop Structures in Clustered Primary miRNA. Transcripts Mol Cell.,
doi.org/10.1016/j.molcel.2020.05.011

Finotello F, Rieder D, Hackl H, Trajanoski Z. Next-generation computational tools for interrogating cancer immunity. Nat Rev Genet. 2019. 20:724-746
doi.org/10.1038/s41576-019-0166-7.

Plangger R, Juen M, Hoernes T, Nußbaumer F, Kremser J, Strebitzer E, Klingler D, Erharter K, Tollinger M, Erlacher M, Kreutz C (2019). Branch site bulge conformations in domain 6 determine functional sugar puckers in group II intron splicing. Nucleic Acids Res.,
doi.org/10.1093/nar/gkz965.

Hoernes TP, Faserl K, Juen MA, Kremser J, Gasser C, Fuchs E, Shi X, Siewert A, Lindner H, Kreutz C, Micura R, Joseph S, Höbartner C, Westhof E, Hüttenhofer A, Erlacher MD (2018). Translation of non-standard codon nucleotides reveals minimal requirements for codon-anticodon interactions. Nat Commun, doi.org/10.1038/s41467-018-07321-8

C. Riml, T. Amort, D. Rieder, C. Gasser, A. Lusser, R. Micura (2017). Osmium-mediated 4sU-to-C transformation as key to study RNA dynamics by sequencing (TUC-seq). Angew. Chem. Int. Ed. 56, 13479–13483, doi.org/10.1002/anie.201707465