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Chair of Bioinformatics

Publications

Selected Publications

m6A sites in the coding region trigger translation-dependent mRNA decay

Zhou & Ćorović & Hoch-Kraft et al. 2024 - Molecular Cell

Complete Publications by Year

2025[ to top ]
  • Stoffel, N. K., Sankaranarayanan, S., Müntjes, K., Körtel, N., Busch, A., Zarnack, K., König, J., & Feldbrügge, M. (2025). Microbial iCLIP2: enhanced mapping of RNA-protein interaction by promoting protein and RNA stability. RNA (New York, N.Y.), 31(2), 258-272. https://doi.org/10.1261/rna.080193.124
  • Northoff, B. H., Herbst, A., Wenk, C., Weindl, L., Gäbel, G., Brezski, A., Zarnack, K., Küpper, A., Dimmeler, S., Moretti, A., Laugwitz, K.-L., Engelhardt, S., Maegdefessel, L., Boon, R., Doppler, S., Dreßen, M., Lahm, H., Lange, R., Krane, M., … Teupser, D. (2025). CircRNAs increase during vascular cell differentiation and are biomarkers for vascular disease. Cardiovascular Research, cvaf013-. https://doi.org/10.1093/cvr/cvaf013
  • Eudenbach, M., Busam, J., Bouchard, C., Rossbach, O., Zarnack, K., & Bauer, U.-M. (2025). Assessment of PRMT6-dependent alternative splicing in pluripotent and differentiating NT2/D1 cells. Life Science Alliance, 8(4), e202402946-. https://doi.org/10.26508/lsa.202402946
  • Rajagopal, V., Seiler, J., Nasa, I., Cantarella, S., Theiss, J., Herget, F., Kaifer, B., Klostermann, M., Will, R., Schneider, M., Helm, D., König, J., Zarnack, K., Diederichs, S., Kettenbach, A. N., & Caudron-Herger, M. (2025). An atlas of RNA-dependent proteins in cell division reveals the riboregulation of mitotic protein-protein interactions. Nature Communications, 16(1), 2325-2325. https://doi.org/10.1038/s41467-025-57671-3
  • Northoff, B. H., Herbst, A., Wenk, C., Weindl, L., Gäbel, G., Brezski, A., Zarnack, K., Küpper, A., Dimmeler, S., Moretti, A., Laugwitz, K.-L., Engelhardt, S., Maegdefessel, L., Boon, R. A., Doppler, S., Dreßen, M., Lahm, H., Lange, R., Krane, M., … Teupser, D. (2025). Circular RNAs increase during vascular cell differentiation and are biomarkers for vascular disease. Cardiovascular Research, 121(3), 405-423. https://doi.org/10.1093/cvr/cvaf013
2024[ to top ]
  • Niedner-Boblenz, A., Monecke, T., Hennig, J., Klostermann, M., Hofweber, M., Davydova, E., Gerber, A. P., Anosova, I., Mayer, W., Müller, M., Heym, R. G., Janowski, R., Paillart, J.-C., Dormann, D., Zarnack, K., Sattler, M., & Niessing, D. (2024). Intrinsically disordered RNA-binding motifs cooperate to catalyze RNA folding and drive phase separation. Nucleic Acids Research, 52(22), 14205-14228. https://doi.org/10.1093/nar/gkae1107
  • Rosenkranz, R. R. E., Vraggalas, S., Keller, M., Sankaranarayanan, S., McNicoll, F., Löchli, K., Bublak, D., Benhamed, M., Crespi, M., Berberich, T., Bazakos, C., Feldbrügge, M., Schleiff, E., Müller-McNicoll, M., Zarnack, K., & Fragkostefanakis, S. (2024). A plant-specific clade of serine/arginine-rich proteins regulates RNA splicing homeostasis and thermotolerance in tomato. Nucleic Acids Research, 52(19), 11466-11480. https://doi.org/10.1093/nar/gkae730
  • Brezski, A., Murtagh, J., Schulz, M. H., & Zarnack, K. (2024). A systematic analysis of circRNAs in subnuclear compartments. RNA Biology, 21(1), 1-16. https://doi.org/10.1080/15476286.2024.2395718
  • Arnold, B., Riegger, R. J., Okuda, E. K., Slišković, I., Keller, M., Bakisoglu, C., McNicoll, F., Zarnack, K., & Müller-McNicoll, M. (2024). hGRAD: A versatile "one-fits-all" system to acutely deplete RNA binding proteins from condensates. The Journal of Cell Biology, 223(2), e202304030-. https://doi.org/10.1083/jcb.202304030
  • Lewinski, M., Steffen, A., Kachariya, N., Elgner, M., Schmal, C., Messini, N., Köster, T., Reichel, M., Sattler, M., Zarnack, K., & Staiger, D. (2024). Arabidopsis thaliana GLYCINE RICH RNA-BINDING PROTEIN 7 interaction with its iCLIP target LHCB1.1 correlates with changes in RNA stability and circadian oscillation. The Plant Journal : For Cell and Molecular Biology, 118(1), 203-224. https://doi.org/10.1111/tpj.16601
  • Lewinski, M., Brüggemann, M., Köster, T., Reichel, M., Bergelt, T., Meyer, K., König, J., Zarnack, K., & Staiger, D. (2024). Mapping protein-RNA binding in plants with individual-nucleotide-resolution UV cross-linking and immunoprecipitation (plant iCLIP2). Nature Protocols, 19(4), 1183-1234. https://doi.org/10.1038/s41596-023-00935-3
  • von Ehr, J., Oberstrass, L., Yazgan, E., Schnaubelt, L. I., Blümel, N., McNicoll, F., Weigand, J. E., Zarnack, K., Müller-McNicoll, M., Korn, S. M., & Schlundt, A. (2024). Arid5a uses disordered extensions of its core ARID domain for distinct DNA- and RNA-recognition and gene regulation. The Journal of Biological Chemistry, 300(7), 107457-107457. https://doi.org/10.1016/j.jbc.2024.107457
  • Verheyden, N. A., Klostermann, M., Brüggemann, M., Steede, H. M., Scholz, A., Amr, S., Lichtenthaeler, C., Münch, C., Schmid, T., Zarnack, K., & Krueger, A. (2024). A high-resolution map of functional miR-181 response elements in the thymus reveals the role of coding sequence targeting and an alternative seed match. Nucleic Acids Research, 52(14), 8515-8533. https://doi.org/10.1093/nar/gkae416
  • Rajagopal, V., Seiler, J., Nasa, I., Cantarella, S., Theiss, J., Herget, F., Kaifer, B., Schneider, M., Helm, D., König, J., Zarnack, K., Diederichs, S., Kettenbach, A. N., & Caudron-Herger, M. (2024). An atlas of RNA-dependent proteins in cell division reveals the riboregulation of mitotic protein-protein interactions. BioRxiv : The Preprint Server for Biology, 2024.09.25.614981-. https://doi.org/10.1101/2024.09.25.614981
  • Klostermann, M., & Zarnack, K. (2024). racoon_clip-a complete pipeline for single-nucleotide analyses of iCLIP and eCLIP data. Bioinformatics Advances, 4(1), vbae084-vbae084. https://doi.org/10.1093/bioadv/vbae084
  • Zhou, Y., Ćorović, M., Hoch-Kraft, P., Meiser, N., Mesitov, M., Körtel, N., Back, H., Naarmann-de Vries, I. S., Katti, K., Obrdlík, A., Busch, A., Dieterich, C., Vaňáčová, Štěpánka, Hengesbach, M., Zarnack, K., & König, J. (2024). m6A sites in the coding region trigger translation-dependent mRNA decay. Molecular Cell, 84(23), 4576-4593.e12. https://doi.org/10.1016/j.molcel.2024.10.033
  • Stoffel, N. K., Sankaranarayanan, S., Muentjes, K., Kortel, N., Busch, A., Zarnack, K., Konig, J., & Feldbrugge, M. (2024). Microbial iCLIP2: Enhanced mapping of RNA-Protein interaction by promoting protein and RNA stability. RNA (New York, N.Y.), rna.080193.124-. https://doi.org/10.1261/rna.080193.124
  • Prieto-Garcia, C., Matkovic, V., Mosler, T., Li, C., Liang, J., Oo, J. A., Haidle, F., Mačinković, I., Cabrera-Orefice, A., Berkane, R., Giuliani, G., Xu, F., Jacomin, A.-C., Tomaskovic, I., Basoglu, M., Hoffmann, M. E., Rathore, R., Cetin, R., Boutguetait, D., … Dikic, I. (2024). Pathogenic proteotoxicity of cryptic splicing is alleviated by ubiquitination and ER-phagy. Science (New York, N.Y.), 386(6723), 768-776. https://doi.org/10.1126/science.adi5295
  • Pacholewska, A., Lienhard, M., Brüggemann, M., Hänel, H., Bilalli, L., Königs, A., Heß, F., Becker, K., Köhrer, K., Kaiser, J., Gohlke, H., Gattermann, N., Hallek, M., Herling, C. D., König, J., Grimm, C., Herwig, R., Zarnack, K., & Schweiger, M. R. (2024). Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects of SF3B1 mutations. Genome Research, 34(11), 1832-1848. https://doi.org/10.1101/gr.279327.124
2023[ to top ]
  • Acera Mateos, P., Zhou, Y., Zarnack, K., & Eyras, E. (2023). Concepts and methods for transcriptome-wide prediction of chemical messenger RNA modifications with machine learning. Briefings in Bioinformatics, 24(3), bbad163-. https://doi.org/10.1093/bib/bbad163
  • Bauer, R., Meyer, S. P., Raue, R., Palmer, M. A., Guerrero Ruiz, V. M., Cardamone, G., Rösser, S., Heffels, M., Roesmann, F., Wilhelm, A., Lütjohann, D., Zarnack, K., Fuhrmann, D. C., Widera, M., Schmid, T., & Brüne, B. (2023). Hypoxia-altered cholesterol homeostasis enhances the expression of interferon-stimulated genes upon SARS-CoV-2 infections in monocytes. Frontiers in Immunology, 14, 1121864-1121864. https://doi.org/10.3389/fimmu.2023.1121864
  • Fischer, S., Lichtenthaeler, C., Stepanenko, A., Heyl, F., Maticzka, D., Kemmerer, K., Klostermann, M., Backofen, R., Zarnack, K., & Weigand, J. E. (2023). Heterogenous nuclear ribonucleoprotein D-like controls endothelial cell functions. Biological Chemistry, 405(4), 229-239. https://doi.org/10.1515/hsz-2023-0254
  • Molitor, L., Klostermann, M., Bacher, S., Merl-Pham, J., Spranger, N., Burczyk, S., Ketteler, C., Rusha, E., Tews, D., Pertek, A., Proske, M., Busch, A., Reschke, S., Feederle, R., Hauck, S. M., Blum, H., Drukker, M., Fischer-Posovszky, P., König, J., … Niessing, D. (2023). Depletion of the RNA-binding protein PURA triggers changes in posttranscriptional gene regulation and loss of P-bodies. Nucleic Acids Research, 51(3), 1297-1316. https://doi.org/10.1093/nar/gkac1237
  • Rücklé, C., Körtel, N., Basilicata, M. F., 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, C. I., & König, J. (2023). RNA stability controlled by m(6)A methylation contributes to X-to-autosome dosage compensation in mammals. Nature Structural & Molecular Biology, 30(8), 1207-1215. https://doi.org/10.1038/s41594-023-00997-7
  • Sankaranarayanan, S., Haag, C., Petzsch, P., Köhrer, K., Matuszyńska, A., Zarnack, K., & Feldbrügge, M. (2023). The mRNA stability factor Khd4 defines a specific mRNA regulon for membrane trafficking in the pathogen Ustilago maydis. Proceedings of the National Academy of Sciences of the United States of America, 120(34), e2301731120-e2301731120. https://doi.org/10.1073/pnas.2301731120
  • Glaser, S. F., Brezski, A., Baumgarten, N., Klangwart, M., Heumüller, A. W., Maji, R. K., Leisegang, M. S., Guenther, S., Zehendner, C. M., John, D., Schulz, M. H., Zarnack, K., & Dimmeler, S. (2023). Circular RNA circPLOD2 regulates pericyte function by targeting the transcription factor KLF4. Cell Reports, 42(8), 112824-112824. https://doi.org/10.1016/j.celrep.2023.112824
  • Ebersberger, S., Hipp, C., Mulorz, M. M., Buchbender, A., Hubrich, D., Kang, H.-S., Martínez-Lumbreras, S., Kristofori, P., Sutandy, F. X. R., Llacsahuanga Allcca, L., Schönfeld, J., Bakisoglu, C., Busch, A., Hänel, H., Tretow, K., Welzel, M., Di Liddo, A., Möckel, M. M., Zarnack, K., … König, J. (2023). FUBP1 is a general splicing factor facilitating 3’ splice site recognition and splicing of long introns. Molecular Cell, 83(15), 2653-2672.e15. https://doi.org/10.1016/j.molcel.2023.07.002
  • Keil, P., Wulf, A., Kachariya, N., Reuscher, S., Hühn, K., Silbern, I., Altmüller, J., Keller, M., Stehle, R., Zarnack, K., Sattler, M., Urlaub, H., & Sträßer, K. (2023). Npl3 functions in mRNP assembly by recruitment of mRNP components to the transcription site and their transfer onto the mRNA. Nucleic Acids Research, 51(2), 831-851. https://doi.org/10.1093/nar/gkac1206
  • de Oliveira Freitas Machado, C., Schafranek, M., Brüggemann, M., Hernández Cañás, M. C., Keller, M., Di Liddo, A., Brezski, A., Blümel, N., Arnold, B., Bremm, A., Wittig, I., Jaé, N., McNicoll, F., Dimmeler, S., Zarnack, K., & Müller-McNicoll, M. (2023). Poison cassette exon splicing of SRSF6 regulates nuclear speckle dispersal and the response to hypoxia. Nucleic Acids Research, 51(2), 870-890. https://doi.org/10.1093/nar/gkac1225
  • Zarnack, K., & Eyras, E. (2023). ‘Artificial intelligence and machine learning in RNA biology’. Briefings in Bioinformatics, 24(6), Article 6. https://doi.org/10.1093/bib/bbad415
2022[ to top ]
  • Bauer, R., Meyer, S. P., Kloss, K. A., Guerrero Ruiz, V. M., Reuscher, S., Zhou, Y., Fuhrmann, D. C., Zarnack, K., Schmid, T., & Brüne, B. (2022). Functional RNA Dynamics Are Progressively Governed by RNA Destabilization during the Adaptation to Chronic Hypoxia. International Journal of Molecular Sciences, 23(10), 5824-. https://doi.org/10.3390/ijms23105824
  • Elwakeel, E., Brüggemann, M., Wagih, J., Lityagina, O., Elewa, M. A. F., Han, Y., Frömel, T., Popp, R., Nicolas, A. M., Schreiber, Y., Gradhand, E., Thomas, D., Nüsing, R., Steinmetz-Späh, J., Savai, R., Fokas, E., Fleming, I., Greten, F. R., Zarnack, K., … Weigert, A. (2022). Disruption of Prostaglandin E2 Signaling in Cancer-Associated Fibroblasts Limits Mammary Carcinoma Growth but Promotes Metastasis. Cancer Research, 82(7), 1380-1395. https://doi.org/10.1158/0008-5472.CAN-21-2116
  • Jones, A. N., Graß, C., Meininger, I., Geerlof, A., Klostermann, M., Zarnack, K., Krappmann, D., & Sattler, M. (2022). Modulation of pre-mRNA structure by hnRNP proteins regulates alternative splicing of MALT1. Science Advances, 8(31), eabp9153-eabp9153. https://doi.org/10.1126/sciadv.abp9153
  • Cortés-López, M., Schulz, L., Enculescu, M., Paret, C., Spiekermann, B., Quesnel-Vallières, M., Torres-Diz, M., Unic, S., Busch, A., Orekhova, A., Kuban, M., Mesitov, M., Mulorz, M. M., Shraim, R., Kielisch, F., Faber, J., Barash, Y., Thomas-Tikhonenko, A., Zarnack, K., … König, J. (2022). High-throughput mutagenesis identifies mutations and RNA-binding proteins controlling CD19 splicing and CART-19 therapy resistance. Nature Communications, 13(1), 5570-5570. https://doi.org/10.1038/s41467-022-31818-y
2021[ to top ]
  • Schulz, L., Torres-Diz, M., Cortés-López, M., Hayer, K. E., Asnani, M., Tasian, S. K., Barash, Y., Sotillo, E., Zarnack, K., König, J., & Thomas-Tikhonenko, A. (2021). Direct long-read RNA sequencing identifies a subset of questionable exitrons likely arising from reverse transcription artifacts. Genome Biology, 22(1), 190-190. https://doi.org/10.1186/s13059-021-02411-1
  • Schwich, O. D., Blümel, N., Keller, M., Wegener, M., Setty, S. T., Brunstein, M. E., Poser, I., Mozos, I. R. D. L., Suess, B., Münch, C., McNicoll, F., Zarnack, K., & Müller-McNicoll, M. (2021). SRSF3 and SRSF7 modulate 3’UTR length through suppression or activation of proximal polyadenylation sites and regulation of CFIm levels. Genome Biology, 22(1), 82-82. https://doi.org/10.1186/s13059-021-02298-y
  • Körtel, N., Rücklé, C., Zhou, Y., Busch, A., Hoch-Kraft, P., Sutandy, F. X. R., Haase, J., Pradhan, M., Musheev, M., Ostareck, D., Ostareck-Lederer, A., Dieterich, C., Hüttelmaier, S., Niehrs, C., Rausch, O., Dominissini, D., König, J., & Zarnack, K. (2021). Deep and accurate detection of m6A RNA modifications using miCLIP2 and m6Aboost machine learning. Nucleic Acids Research, 49(16), e92-e92. https://doi.org/10.1093/nar/gkab485
  • Koch, I., Andrade-Navarro, M., Schulz, M. H., & Zarnack, K. (2021). Bioinformatics in theory and application - highlights of the 36th German Conference on Bioinformatics. Biological Chemistry, 402(8), 869-870. https://doi.org/10.1515/hsz-2021-0298
2020[ to top ]
  • Fischer, S., Di Liddo, A., Taylor, K., Gerhardus, J. S., Sobczak, K., Zarnack, K., & Weigand, J. E. (2020). Muscleblind-like 2 controls the hypoxia response of cancer cells. RNA (New York, N.Y.), 26(5), 648-663. https://doi.org/10.1261/rna.073353.119
  • Busch, A., Brüggemann, M., Ebersberger, S., & Zarnack, K. (2020). iCLIP data analysis: A complete pipeline from sequencing reads to RBP binding sites. Methods (San Diego, Calif.), 178, 49-62. https://doi.org/10.1016/j.ymeth.2019.11.008
  • König, J., & Zarnack, K. (2020). High-throughput approaches in RNA biology. Methods (San Diego, Calif.), 178, 1-2. https://doi.org/10.1016/j.ymeth.2020.04.002
  • Dold, A., Han, H., Liu, N., Hildebrandt, A., Brüggemann, M., Rücklé, C., Hänel, H., Busch, A., Beli, P., Zarnack, K., König, J., Roignant, J.-Y., & Lasko, P. (2020). Makorin 1 controls embryonic patterning by alleviating Bruno1-mediated repression of oskar translation. PLoS Genetics, 16(1), e1008581-e1008581. https://doi.org/10.1371/journal.pgen.1008581
  • Enculescu, M., Braun, S., Thonta Setty, S., Busch, A., Zarnack, K., König, J., & Legewie, S. (2020). Exon Definition Facilitates Reliable Control of Alternative Splicing in the RON Proto-Oncogene. Biophysical Journal, 118(8), 2027-2041. https://doi.org/10.1016/j.bpj.2020.02.022
  • Alvelos, M. I., Brüggemann, M., Sutandy, F. R., Juan-Mateu, J., Colli, M. L., Busch, A., Lopes, M., Castela, Ângela, Aartsma-Rus, A., König, J., Zarnack, K., & Eizirik, D. L. (2020). The RNA-binding profile of the splicing factor SRSF6 in immortalized human pancreatic β-cells. Life Science Alliance, 4(3), e202000825-. https://doi.org/10.26508/lsa.202000825
  • Zarnack, K., Balasubramanian, S., Gantier, M. P., Kunetsky, V., Kracht, M., Schmitz, M. L., & Sträßer, K. (2020). Dynamic mRNP Remodeling in Response to Internal and External Stimuli. Biomolecules, 10(9), 1310-. https://doi.org/10.3390/biom10091310
  • Monzón-Casanova, E., Matheson, L. S., Tabbada, K., Zarnack, K., Smith, C. W., & Turner, M. (2020). Polypyrimidine tract-binding proteins are essential for B cell development. ELife, 9, e53557-. https://doi.org/10.7554/eLife.53557
  • Kang, H.-S., Sánchez-Rico, C., Ebersberger, S., Sutandy, F. X. R., Busch, A., Welte, T., Stehle, R., Hipp, C., Schulz, L., Buchbender, A., Zarnack, K., König, J., & Sattler, M. (2020). An autoinhibitory intramolecular interaction proof-reads RNA recognition by the essential splicing factor U2AF2. Proceedings of the National Academy of Sciences of the United States of America, 117(13), 7140-7149. https://doi.org/10.1073/pnas.1913483117
2019[ to top ]
  • Elwakeel, E., Brüggemann, M., Fink, A. F., Schulz, M. H., Schmid, T., Savai, R., Brüne, B., Zarnack, K., & Weigert, A. (2019). Phenotypic Plasticity of Fibroblasts during Mammary Carcinoma Development. International Journal of Molecular Sciences, 20(18), Article 18. https://doi.org/10.3390/ijms20184438
  • Olgeiser, L., Haag, C., Boerner, S., Ule, J., Busch, A., Koepke, J., König, J., Feldbrügge, M., & Zarnack, K. (2019). The key protein of endosomal mRNP transport Rrm4 binds translational landmark sites of cargo mRNAs. EMBO Reports, 20(1), e46588-. https://doi.org/10.15252/embr.201846588
  • Biol., T. C. (Ed.). (2019). Membrane-Associated RNA-Binding Proteins Orchestrate Organelle-Coupled Translation.
  • Di Liddo, A., de Oliveira Freitas Machado, C., Fischer, S., Ebersberger, S., Heumüller, A. W., Weigand, J. E., Müller-McNicoll, M., & Zarnack, K. (2019). A combined computational pipeline to detect circular RNAs in human cancer cells under hypoxic stress. Journal of Molecular Cell Biology, 11(10), 829-844. https://doi.org/10.1093/jmcb/mjz094
  • Hildebrandt, A., Brüggemann, M., Rücklé, C., Boerner, S., Heidelberger, J. B., Busch, A., Hänel, H., Voigt, A., Möckel, M. M., Ebersberger, S., Scholz, A., Dold, A., Schmid, T., Ebersberger, I., Roignant, J.-Y., Zarnack, K., König, J., & Beli, P. (2019). The RNA-binding ubiquitin ligase MKRN1 functions in ribosome-associated quality control of poly(A) translation. Genome Biology, 20(1), 216-216. https://doi.org/10.1186/s13059-019-1814-0
  • Scholz, A., Eggenhofer, F., Gelhausen, R., Grüning, B., Zarnack, K., Brüne, B., Backofen, R., & Schmid, T. (2019). uORF-Tools—Workflow for the determination of translation-regulatory upstream open reading frames. PLOS ONE, 14(9), 1-9. https://doi.org/10.1371/journal.pone.0222459
2018[ to top ]
  • Zarnack, K., & Müller-McNicoll, M. (2018). High-Throughput Screens for cis-Acting RNA Sequence Elements That Promote Nuclear Retention. Biochemistry, 57(26), 3542-3543. https://doi.org/10.1021/acs.biochem.8b00479
  • Sutandy, F. X. R., Ebersberger, S., Huang, L., Busch, A., Bach, M., Kang, H.-S., Fallmann, J., Maticzka, D., Backofen, R., Stadler, P. F., Zarnack, K., Sattler, M., Legewie, S., & König, J. (2018). In vitro iCLIP-based modeling uncovers how the splicing factor U2AF2 relies on regulation by cofactors. Genome Research, 28(5), 699-713. https://doi.org/10.1101/gr.229757.117
  • Braun, S., Enculescu, M., Setty, S. T., Cortés-López, M., de Almeida, B. P., Sutandy, F. X. R., Schulz, L., Busch, A., Seiler, M., Ebersberger, S., Barbosa-Morais, N. L., Legewie, S., König, J., & Zarnack, K. (2018). Decoding a cancer-relevant splicing decision in the RON proto-oncogene using high-throughput mutagenesis. Nature Communications, 9(1), 3315-3315. https://doi.org/10.1038/s41467-018-05748-7
2017[ to top ]
  • Haberman, N., Huppertz, I., Attig, J., König, J., Wang, Z., Hauer, C., Hentze, M. W., Kulozik, A. E., Le Hir, H., Curk, T., Sibley, C. R., Zarnack, K., & Ule, J. (2017). Insights into the design and interpretation of iCLIP experiments. Genome Biology, 18(1), 7-7. https://doi.org/10.1186/s13059-016-1130-x
  • Dixit, S., Müller-McNicoll, M., David, V., Zarnack, K., Ule, J., Hashimi, H., & Lukeš, J. (2017). Differential Binding of Mitochondrial Transcripts by MRB8170 and MRB4160 Regulates Distinct Editing Fates of Mitochondrial mRNA in Trypanosomes. MBio, 8(1), e02288-16. https://doi.org/10.1128/mBio.02288-16
  • Hildebrandt, A., Alanis-Lobato, G., Voigt, A., Zarnack, K., Andrade-Navarro, M. A., Beli, P., & König, J. (2017). Interaction profiling of RNA-binding ubiquitin ligases reveals a link between posttranscriptional regulation and the ubiquitin system. Scientific Reports, 7(1), 16582-16582. https://doi.org/10.1038/s41598-017-16695-6
  • Botti, V., McNicoll, F., Steiner, M. C., Richter, F. M., Solovyeva, A., Wegener, M., Schwich, O. D., Poser, I., Zarnack, K., Wittig, I., Neugebauer, K. M., & Müller-McNicoll, M. (2017). Cellular differentiation state modulates the mRNA export activity of SR proteins. The Journal of Cell Biology, 216(7), 1993-2009. https://doi.org/10.1083/jcb.201610051
2016[ to top ]
  • Attig, J., Ruiz de Los Mozos, I., Haberman, N., Wang, Z., Emmett, W., Zarnack, K., König, J., & Ule, J. (2016). Splicing repression allows the gradual emergence of new Alu-exons in primate evolution. ELife, 5, e19545-. https://doi.org/10.7554/eLife.19545
  • Murn, J., Teplova, M., Zarnack, K., Shi, Y., & Patel, D. J. (2016). Recognition of distinct RNA motifs by the clustered CCCH zinc fingers of neuronal protein Unkempt. Nature Structural & Molecular Biology, 23(1), 16-23. https://doi.org/10.1038/nsmb.3140
  • Müller-McNicoll, M., Botti, V., de Jesus Domingues, A. M., Brandl, H., Schwich, O. D., Steiner, M. C., Curk, T., Poser, I., Zarnack, K., & Neugebauer, K. M. (2016). SR proteins are NXF1 adaptors that link alternative RNA processing to mRNA export. Genes & Development, 30(5), 553-566. https://doi.org/10.1101/gad.276477.115
2015[ to top ]
  • Tajnik, M., Vigilante, A., Braun, S., Hänel, H., Luscombe, N. M., Ule, J., Zarnack, K., & König, J. (2015). Intergenic Alu exonisation facilitates the evolution of tissue-specific transcript ends. Nucleic Acids Research, 43(21), 10492-10505. https://doi.org/10.1093/nar/gkv956
  • Diaz-Muñoz, M. D., Bell, S. E., Fairfax, K., Monzon-Casanova, E., Cunningham, A. F., Gonzalez-Porta, M., Andrews, S. R., Bunik, V. I., Zarnack, K., Curk, T., Heggermont, W. A., Heymans, S., Gibson, G. E., Kontoyiannis, D. L., Ule, J., & Turner, M. (2015). The RNA-binding protein HuR is essential for the B cell antibody response. Nature Immunology, 16(4), 415-425. https://doi.org/10.1038/ni.3115
  • Murn, J., Zarnack, K., Yang, Y. J., Durak, O., Murphy, E. A., Cheloufi, S., Gonzalez, D. M., Teplova, M., Curk, T., Zuber, J., Patel, D. J., Ule, J., Luscombe, N. M., Tsai, L.-H., Walsh, C. A., & Shi, Y. (2015). Control of a neuronal morphology program by an RNA-binding zinc finger protein, Unkempt. Genes & Development, 29(5), 501-512. https://doi.org/10.1101/gad.258483.115
2013[ to top ]
  • Zarnack, K., König, J., Tajnik, M., Martincorena, I., Eustermann, S., Stévant, I., Reyes, A., Anders, S., Luscombe, N. M., & Ule, J. (2013). Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements. Cell, 152(3), 453-466. https://doi.org/10.1016/j.cell.2012.12.023
2012[ to top ]
  • König, J., Zarnack, K., Luscombe, N. M., & Ule, J. (2012). Protein-RNA interactions: new genomic technologies and perspectives. Nature Reviews. Genetics, 13(2), 77-83. https://doi.org/10.1038/nrg3141
2011[ to top ]
  • Konig, J., Zarnack, K., Rot, G., Curk, T., Kayikci, M., Zupan, B., Turner, D. J., Luscombe, N. M., & Ule, J. (2011). iCLIP--transcriptome-wide mapping of protein-RNA interactions with individual nucleotide resolution. Journal of Visualized Experiments : JoVE, 50, 2638-. https://doi.org/10.3791/2638
  • Koepke, J., Kaffarnik, F., Haag, C., Zarnack, K., Luscombe, N. M., König, J., Ule, J., Kellner, R., Begerow, D., & Feldbrügge, M. (2011). The RNA-binding protein Rrm4 is essential for efficient secretion of endochitinase Cts1. Molecular & Cellular Proteomics : MCP, 10(12), M111.011213-M111.011213. https://doi.org/10.1074/mcp.M111.011213
  • Tollervey, J. R., Wang, Z., Hortobágyi, T., Witten, J. T., Zarnack, K., Kayikci, M., Clark, T. A., Schweitzer, A. C., Rot, G., Curk, T., Zupan, B., Rogelj, B., Shaw, C. E., & Ule, J. (2011). Analysis of alternative splicing associated with aging and neurodegeneration in the human brain. Genome Research, 21(10), 1572-1582. https://doi.org/10.1101/gr.122226.111
2010[ to top ]
  • Zarnack, K., & Feldbrügge, M. (2010). Microtubule-dependent mRNA transport in fungi. Eukaryotic Cell, 9(7), 982-990. https://doi.org/10.1128/EC.00030-10
  • König, J., Zarnack, K., Rot, G., Curk, T., Kayikci, M., Zupan, B., Turner, D. J., Luscombe, N. M., & Ule, J. (2010). iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nature Structural & Molecular Biology, 17(7), 909-915. https://doi.org/10.1038/nsmb.1838
  • Wang, Z., Kayikci, M., Briese, M., Zarnack, K., Luscombe, N. M., Rot, G., Zupan, B., Curk, T., & Ule, J. (2010). iCLIP predicts the dual splicing effects of TIA-RNA interactions. PLoS Biology, 8(10), e1000530-e1000530. https://doi.org/10.1371/journal.pbio.1000530
2009[ to top ]
  • König, J., Baumann, S., Koepke, J., Pohlmann, T., Zarnack, K., & Feldbrügge, M. (2009). The fungal RNA-binding protein Rrm4 mediates long-distance transport of ubi1 and rho3 mRNAs. The EMBO Journal, 28(13), 1855-1866. https://doi.org/10.1038/emboj.2009.145
  • Vollmeister, E., Haag, C., Zarnack, K., Baumann, S., König, J., Mannhaupt, G., & Feldbrügge, M. (2009). Tandem KH domains of Khd4 recognize AUACCC and are essential for regulation of morphology as well as pathogenicity in Ustilago maydis. RNA (New York, N.Y.), 15(12), 2206-2218. https://doi.org/10.1261/rna.1817609
2008[ to top ]
  • Feldbrügge, M., Zarnack, K., Vollmeister, E., Baumann, S., Koepke, J., König, J., Münsterkötter, M., & Mannhaupt, G. (2008). The posttranscriptional machinery of Ustilago maydis. Fungal Genetics and Biology : FG & B, 45 Suppl 1, S40-S46. https://doi.org/10.1016/j.fgb.2008.03.013
  • Zarnack, K., Eichhorn, H., Kahmann, R., & Feldbrügge, M. (2008). Pheromone-regulated target genes respond differentially to MAPK phosphorylation of transcription factor Prf1. Molecular Microbiology, 69(4), 1041-1053. https://doi.org/10.1111/j.1365-2958.2008.06345.x
2007[ to top ]
  • Zarnack, K., & Feldbrügge, M. (2007). mRNA trafficking in fungi. Molecular Genetics and Genomics : MGG, 278(4), 347-359. https://doi.org/10.1007/s00438-007-0271-8
2006[ to top ]
  • Zarnack, K., Maurer, S., Kaffarnik, F., Ladendorf, O., Brachmann, A., Kämper, J., & Feldbrügge, M. (2006). Tetracycline-regulated gene expression in the pathogen Ustilago maydis. Fungal Genetics and Biology : FG & B, 43(11), 727-738. https://doi.org/10.1016/j.fgb.2006.05.006