Buchbender A, Mutter H, Sutandy FXR, Körtel N, Hänel H, Busch A, Ebersberger S and König J (2020) Improved library preparation with the new iCLIP2 protocol. Methods, 178:33–48 Link

Dold A*, Han H*, Liu N*, Hildebrandt A, Brüggemann M, Rücklé C, Hänel H, Busch A, Beli P, Zarnack K, König J, Roignant JY# and Lasko P# (2020) Makorin 1 controls embryonic patterning by alleviating Bruno1-mediated repression of oskar translation. PLOS Genet, 16:e1008581 (*indicates joint contribution, #indicates joint correspondence) Link

Enculescu M#, Braun S, Thonta Setty S, Busch A, Zarnack K, König J# and Legewie S# (2020) Exon Definition Facilitates Reliable Control of Alternative Splicing in the RON Proto-Oncogene. Biophys J, 118:2027–2041 Link

Kang HS*, Sánchez-Rico C*, Ebersberger S, Sutandy FXR, Busch A, Welte T, Stehle R, Hipp C, Schulz L, Buchbender A, Zarnack K, König J# and Sattler M# (2020) An autoinhibitory intramolecular interaction proof-reads RNA recognition by the essential splicing factor U2AF2. Proc Natl Acad Sci, 117:7140–7149 (*indicates joint contribution, #indicates joint correspondence) Link

Soldano A*, Worpenberg L*, Paolantoni C, Longhi S, Mulorz MM, Lence T, Wessels HH, Aiello G, Notarangelo M, Sutandy FXR, Scheibe M, Edupuganti RR, Busch A, Möckel MM, Vermeulen M, Butter F, König J, Ohler U, Dieterich C, Quattrone A# and Roignant JY# (2020) The m6A reader Ythdf restricts axonal growth in Drosophila through target selection modulation of the Fragile X mental retardation protein. bioRxiv, doi: 10.1101/2020.03.04.976886 (*indicates joint contribution, #indicates joint correspondence) Link

Weichmann F, Hett R, Schepers A, Ito-Kureha T, Flatley A, Slama K, Hastert F, Angstmann N, Cardoso CM, König J, Huettelmaier S, Dieterich C, Canzar S, Helm M, Heissmeyer V, Feederle R and Meister G (2020) Validation strategies for antibodies targeting modified ribonucleotides. RNA, 26:1489–1506 Link


Briese M, Haberman N, Sibley CR, Faraway R, Elser AS, Chakrabarti AM, Wang Z, König J, Perera D, Wickramasinghe VO, Venkitaraman AR, Luscombe NM, Saieva L, Pellizzoni L, Smith CWJ, Curk T and Ule J (2019) A systems view of spliceosomal assembly and branchpoints with iCLIP. Nat Struct Mol Biol, 26:930–940 Link

Dold A, Han H, Liu N, Hildebrandt A, Brüggemann M, Rücklé C, Busch A, Beli P, Zarnack K, König J, Roignant JY and Lasko P (2019) Makorin 1 controls embryonic patterning by alleviating Bruno-mediated repression of oskar translation. bioRxiv, doi: 10.1101/501643 Link

Hildebrandt A, Brüggemann M, Rücklé C, Boerner S, Heidelberger JB, Busch A, Hänel H, Voigt A, Möckel MM, Ebersberger S, Scholz A, Dold A, Schmid T, Ebersberger I, Roignant J-Y, Zarnack K#, König J# and Beli P# (2019) The RNA-binding ubiquitin ligase MKRN1 functions in ribosome-associated quality control of poly(A) translation. Genome Biol, 20:216 (#indicates joint correspondence) Link

Olgeiser L, Haag C, Boerner S, Ule J, Busch A, Koepke J, König J, Feldbrügge M and Zarnack K (2019) The key protein of endosomal mRNP transport Rrm4 binds translational landmark sites of cargo mRNAs. EMBO Rep, 20:e46588 Link


Almeida MV, Dietz S, Redl S, Karaulanov E, Hildebrandt A, Renz C, Ulrich HD, König J, Butter F and Ketting RF (2018) GTSF‐1 is required for formation of a functional RNA‐dependent RNA Polymerase complex in Caenorhabditis elegans. EMBO J, 37:e99325 Link

Braun S*, Enculescu M*, Setty ST*, Cortés-López M, de Almeida BP, Sutandy FXR, Schulz L, Busch A, Seiler M, Ebersberger S, Barbosa-Morais NL, Legewie S#, König J# and Zarnack K# (2018) Decoding a cancer-relevant splicing decision in the RON proto-oncogene using high-throughput mutagenesis. Nat Commun, 9:3315 (*indicates joint contribution, #indicates joint correspondence) Link

Sutandy FXR*, Ebersberger S*, Huang L*, Busch A, Bach M, Kang H-S, Fallmann J, Maticzka D, Backofen R, Stadler PF, Zarnack K, Sattler M, Legewie S# and König J# (2018) In vitro iCLIP-based modeling uncovers how the splicing factor U2AF2 relies on regulation by cofactors. Genome Res, 28:699–713 (*indicates joint contribution, #indicates joint correspondence) Link


Haberman N*, Huppertz I*, Attig J, König J, Wang Z, Hauer C, Hentze MW, Kulozik AE, Le Hir H, Curk T, Sibley CR, Zarnack K and Ule J (2017) Insights into the design and interpretation of iCLIP experiments. Genome Biol, 18:7 (*indicates joint contribution) Link

Hildebrandt A, Alanis-Lobato G, Voigt A, Zarnack K, Andrade-Navarro MA, Beli P and König J (2017) Interaction profiling of RNA-binding ubiquitin ligases reveals a link between posttranscriptional regulation and the ubiquitin system. Sci Rep, 7:16582 Link


Attig J, Ruiz de Los Mozos I, Haberman N, Wang Z, Emmett W, Zarnack K, König J# and Ule J# (2016) Splicing repression allows the gradual emergence of new Alu-exons in primate evolution. eLife, 5:e19545 (#indicates joint correspondence) Link

Sutandy FXR*, Hildebrandt A* and König J (2016) Profiling the binding sites of RNA-binding proteins with nucleotide resolution using iCLIP. Pages 175–195 in: Post-transcriptional gene regulation; Methods in Molecular Biology, vol. 1358 (ed. Dassi E), Humana Press, New York (*indicates joint contribution) Link


Coelho MB, Attig J, Bellora N, König J, Hallegger M, Kayikci M, Eyras E, Ule J and Smith CW (2015) Nuclear matrix protein Matrin3 regulates alternative splicing and forms overlapping regulatory networks with PTB. EMBO J, 34:653–668 Link

Tajnik M*, Vigilante A*, Braun S, Hänel H, Luscombe NM, Ule J, Zarnack K# and König J# (2015) Intergenic Alu exonisation facilitates the evolution of tissue-specific transcript ends. Nucleic Acids Res, 43:10492–10505 (*indicates joint contribution, #indicates joint correspondence) Link


Baumann S, König J, Koepke J and Feldbrügge M (2014) Endosomal transport of septin mRNA and protein indicates local translation on endosomes and is required for correct septin filamentation. EMBO Rep, 15:94–102 Link

Huppertz I, Attig J, D’Ambrogio A, Easton LE, Sibley CR, Sugimoto Y, Tajnik M, König J# and Ule J# (2014) iCLIP: Protein-RNA interactions at nucleotide resolution. Methods, 65:274–287 (#indicates joint correspondence) Link

König J, McGlincy NJ and Ule J (2014) Global analysis of protein-RNA interactions with single-nucleotide resolution using iCLIP. Pages 899–918 in: Handbook of RNA Biochemistry (eds. Hartmann RK, Bindereif A, Schön A & Westhof E), Wiley, Weinheim  Link

Rossbach O, Hung L-H, Khrameeva E, Schreiner S, König J, Curk T, Zupan B, Ule J, Gelfand MS and Bindereif A (2014) Crosslinking-immunoprecipitation (iCLIP) analysis reveals global regulatory roles of hnRNP L. RNA Biol, 11:146–155 Link


Anantha RW, Alcivar AL, Ma J, Cai H, Simhadri S, Ule J, König J and Xia B (2013) Requirement of heterogeneous nuclear ribonucleoprotein C for BRCA gene expression and homologous recombination. PLOS One, 8:e61368 Link

Zarnack K*, König J*, Tajnik M, Martincorena I, Eustermann S, Stévant I, Reyes A, Anders S, Luscombe NM and Ule J (2013) Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements. Cell, 152:453–466 (*indicates joint contribution) Link


König J, McGlincy NJ and Ule J (2012) Analysis of protein-RNA interactions with single-nucleotide resolution using iCLIP and next-generation sequencing. Pages 153–169 in: Tag-based next generation sequencing (eds. Habers M & Kahl G), Wiley, Weinheim Link

König J, Zarnack K, Luscombe NM and Ule J (2012) Protein–RNA interactions: New genomic technologies and perspectives. Nat Rev Genet, 13:77–83 Link

Sugimoto Y, König J, Hussain S, Zupan B, Curk T, Frye M and Ule J (2012) Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions. Genome Biol, 13:R67 Link


Koepke J, Kaffarnik F, Haag C, Zarnack K, Luscombe NM, König J, Ule J, Kellner R, Begerow D and Feldbrügge M (2011) The RNA-binding protein Rrm4 is essential for efficient secretion of endochitinase Cts1. Mol Cell Proteomics, 10:M111.011213 Link

Konig J, Zarnack K, Rot G, Curk T, Kayikci M, Zupan B, Turner DJ, Luscombe NM and Ule J (2011) iCLIP - transcriptome-wide mapping of protein-RNA interactions with individual nucleotide resolution. J Vis Exp, e2638 Link

Tollervey JR, Curk T, Rogelj B, Briese M, Cereda M, Kayikci M, König J, Hortobágyi T, Nishimura AL, Župunski V, Patani R, Chandran S, Rot G, Zupan B, Shaw CE and Ule J (2011) Characterizing the RNA targets and position-dependent splicing regulation by TDP-43. Nat Neurosci, 14:452–458 Link


König J*, Zarnack K*, Rot G, Curk T, Kayikci M, Zupan B, Turner DJ, Luscombe NM and Ule J (2010) iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol, 17:909–915 (*indicates joint contribution) Link


König J*, Baumann S*, Koepke J, Pohlmann T, Zarnack K and Feldbrügge M (2009) The fungal RNA-binding protein Rrm4 mediates long-distance transport of ubi1 and rho3 mRNAs. EMBO J, 28:1855–1866 (*indicates joint contribution) Link

Vollmeister E, Haag C, Zarnack K, Baumann S, Konig J, Mannhaupt G and Feldbrugge M (2009) Tandem KH domains of Khd4 recognize AUACCC and are essential for regulation of morphology as well as pathogenicity in Ustilago maydis. RNA, 15:2206–2218 Link


Feldbrügge M, Zarnack K, Vollmeister E, Baumann S, Koepke J, König J, Münsterkötter M and Mannhaupt G (2008) The posttranscriptional machinery of Ustilago maydis. Fungal Genet Biol, 45:S40–S46 Link


Konig J*, Julius C*, Baumann S, Homann M, Goringer HU and Feldbrugge M (2007) Combining SELEX and the yeast three-hybrid system for in vivo selection and classification of RNA aptamers. RNA, 13:614–622 (*indicates joint contribution) Link


Becht P*, Konig J* and Feldbrugge M (2006) The RNA-binding protein Rrm4 is essential for polarity in Ustilago maydis and shuttles along microtubules. J Cell Sci, 119:4964–4973 (*indicates joint contribution) Link


Brachmann A*, König J*, Julius C and Feldbrügge M (2004) A reverse genetic approach for generating gene replacement mutants in Ustilago maydis. Mol Genet Genomics, 272:488 (*indicates joint contribution) Link