Publications

Selected Publications

 (* shared first, # shared correspondence)

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 S., Hengesbach M., Zarnack K.#, König J. # (2024) m6A sites in the coding region trigger translation-dependent mRNA decay. Mol Cell, 84, 4576 - 4593.e12

Ebersberger, S.*, Hipp, C.*, Mulorz, M.M.*, Buchbender, A., Merzhakupova, D., Kang, H.-S., Martínez-Lumbreras, S., Kristofori, P., Sutandy, F.X.R., Llacsahuanga Allcca, L., Schönfeld, J., Bakisoglu, C.,  Busch, A., Hänel, H., Welzel, M., Di Liddo, A., Möckel, M.M., Zarnack, K., Ebersberger, I., Legewie, S., Luck, K.#, Sattler, M.#, and König, J.# (2023) FUBP1 is a general splicing factor facilitating 3' splice site recognition and splicing of long introns. Mol Cell 83, 2653-2672.e15

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., Valsecchi, C.K., and König, J. (2023) RNA stability controlled by m6A methylation mediates X-to-autosome dosage compensation in mammals. Nat Struct Mol Biol 30, 1207-1215

Cortés-López, M.*, Schulz, L.*, Enculescu, M.*, Paret, C, Spiekermann, B., Busch, A., Orekhova, A., Kielisch, F., Quesnel-Vallières, M., Torres-Diz, M., Faber, J., Barash, Y., Thomas-Tikhonenko, A., Zarnack, K.#, Legewie, S.#, König, J.# (2022) High-throughput mutagenesis identifies mutations and RNA-binding proteins controlling CD19 splicing and CART-19 therapy resistance. Nat Commun 13, 5570

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 Biol 22, 190

Körtel, N.*, Rücklé, C.*, Zhou, Y.*, Busch, A., Peter 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 Res 49, e92

Kang, H.S.*, Sanchez-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. PNAS 117, 7140-7149

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 Biol 20, 216

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 Res 28, 699-713

Zarnack, K.*, König, J.*, Tajnik, M., Martincorena, I., Eustermann, S., Stevánt, I., Reyes, A., Anders, S., Luscombe, N.M., and Ule, J. (2013). Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements. Cell 152, 453-466