König Lab
Research Publications Group Members Biography2024
Lewinski M*, Brüggemann M*, Köster T*, Reichel M, Bergelt T, Meyer K, König J, Zarnack K and Staiger D (2024) Mapping protein-RNA binding in plants with individual-nucleotide-resolution UV cross-linking and immunoprecipitation (plant iCLIP2). Nat Protoc , 19:1183–1234 (*indicates joint contribution) Link
Martínez-Lumbreras S, Träger LK, Mulorz MM, Payr M, Dikaya V, Hipp C, König J and Sattler M (2024) Intramolecular autoinhibition regulates the selectivity of PRPF40A tandem WW domains for proline-rich motifs. Nat Commun , 15:3888 Link
Polo-Generelo S, Rodríguez-Mateo C, Torres B, Pintor-Tortolero J, Guerrero-Martínez JA, König J, Vázquez J, Bonzón-Kulichenco E, Padillo-Ruiz J, de la Portilla F, Reyes JC and Pintor-Toro JA (2024) Serpine1 mRNA confers mesenchymal characteristics to the cell and promotes CD8+ T cells exclusion from colon adenocarcinomas Cell Death Discov , 10:116 Link
Xu M*, Ito-Kureha T*, Kang HS, Chernev A, Raj T, Hoefig KP, Hohn C, Giesert F, Wang Y, Pan W, Ziętara N, Straub T, Feederle R, Daniel C, Adler B, König J, Feske S, Tsokos GC, Wurst W, Urlaub H, Sattler M, Kisielow J, Wulczyn FG, Łyszkiewicz M and Heissmeyer V (2024) The thymocyte-specific RNA-binding protein Arpp21 provides TCR repertoire diversity by binding to the 3'-UTR and promoting Rag1 mRNA expression. Nat Commun , 15:2194 (*indicates joint contribution) Link
Zhou Y*, Ćorović M*, Hoch-Kraft P*, Meiser N, Mesitov M, Körtel N, Back H, Naarmann-de Vries IS, Katti K, Obrdlík A, Busch A, Dieterich C, Vaňáčová Š, Hengesbach M, Zarnack K# and König J# (2024) m6A sites in the coding region trigger translation-dependent mRNA decay. Mol Cell , doi: 10.1016/j.molcel.2024.10.033 (*indicates joint contribution, #indicates joint correspondence) Link
2023
Ebersberger S*, Hipp C*, Mulorz MM*, Buchbender A, Hubrich D, Kang HS, Martínez-Lumbreras S, Kristofori P, Sutandy FXR, Llacsahuanga Allcca L, Schönfeld J, Bakisoglu C, Busch A, Hänel H, Tretow K, Welzel M, Di Liddo A, Möckel MM, 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 (*indicates joint contribution, #indicates joint correspondence) Link
Meindl A, Romberger M, Lehmann G, Eichner N, Kleemann L, Wu J, Danner J, Boesl M, Mesitov M, Meister G, König J, Leidel SA and Medenbach J (2023) A rapid protocol for ribosome profiling of low input samples. Nucleic Acids Res , 51:e68 Link
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 SM, Blum H, Drukker M, Fischer-Posovszky P, König J, Zarnack K# and Niessing D# (2023) Depletion of the RNA-binding protein PURA triggers changes in posttranscriptional gene regulation and loss of P-bodies. Nucleic Acids Res , 51:1297–1316 (*indicates joint contribution, #indicates joint correspondence) Link
Rahmanto AS*, Blum CJ*, Scalera C, Heidelberger JB, Mesitov M, Horn-Ghetko D, Gräf JF, Mikicic I, Hobrecht R, Orekhova A, Ostermaier M, Ebersberger S, Möckel MM, Krapoth N, Da Silva Fernandes N, Mizi A, Zhu Y, Chen JX, Choudhary C, Papantonis A, Ulrich HD, Schulman BA, König J and Beli P (2023) K6-linked ubiquitylation marks formaldehyde-induced RNA-protein crosslinks for resolution. Mol Cell , 83:4272–4289.e10 (*indicates joint contribution) Link
Rücklé C*, Körtel N*, Basilicata MF, 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 CI and König J (2023) RNA stability controlled by m6A methylation contributes to X-to-autosome dosage compensation in mammals. Nat Struct Mol Biol , 30:1207-1215 (*indicates joint contribution) Link
Ziegler N, Cortés-López M, Alt F, Sprang M, Ustjanzew A, Lehmann N, El Malki K, Wingerter A, Russo A, Beck O, Attig S, Roth L, König J, Paret C* and Faber J* (2023) Analysis of RBP expression and binding sites identifies PTBP1 as a regulator of CD19 expression in B-ALL. Oncoimmunology , 12:2184143 (*indicates joint contribution) Link
2022
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 MM, Shraim R, Kielisch F, Faber J, Barash Y, Thomas-Tikhonenko A, Zarnack K#, Legewie S# and König J# (2022) High-throughput mutagenesis identifies mutations and RNA-binding proteins controlling CD19 splicing and CART-19 therapy resistance. Nat Commun , 13:5570 (*indicates joint contribution, #indicates joint correspondence) Link
Ito-Kureha T, Leoni C, Borland K, Cantini G, Bataclan M, Metzger RN, Ammann G, Krug AB, Marsico A, Kaiser S, Canzar S, Feske S, Monticelli S, König J and Heissmeyer V (2022) The function of Wtap in N6-adenosine methylation of mRNAs controls T cell receptor signaling and survival of T cells. Nat Immunol , 23:1208–1221 Link
2021
Alvelos MI, Brüggemann M, Sutandy FXR, Juan-Mateu J, Colli ML, Busch A, Lopes M, Castela Â, Aartsma-Rus A, König J, Zarnack K# and Eizirik DL# (2021) The RNA-binding profile of the splicing factor SRSF6 in immortalized human pancreatic β-cells. Life Sci Alliance , 4:e202000825 (#indicates joint correspondence) Link
Körtel N*, Rücklé C*, Zhou Y*, Busch A, Hoch-Kraft P, Sutandy FXR, Haase J, Pradhan M, Musheev M, Ostareck D, Ostareck-Lederer A, Dieterich C, Hüttelmaier S, Niehrs C, Rausch O, Dominissini D, König J# and Zarnack K# (2021) Deep and accurate detection of m6A RNA modifications using miCLIP2 and m6A boost machine learning. Nucleic Acids Res , 49:e92–e92 (*indicates joint contribution, #indicates joint correspondence) Link
Schulz L*, Torres-Diz M*, Cortés-López M, Hayer KE, Asnani M, Tasian SK, Barash Y, Sotillo E, Zarnack K, König J# and 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 (*indicates joint contribution, #indicates joint correspondence) Link
Worpenberg L, Paolantoni C, Longhi S, Mulorz MM, Lence T, Wessels HH, Dassi E, Aiello G, Sutandy FXR, Scheibe M, Edupuganti RR, Busch A, Möckel MM, Vermeulen M, Butter F, König J, Notarangelo M, Ohler U, Dieterich C, Quattrone A#, Soldano A# and Roignant JY# (2021) Ythdf is a N6‐methyladenosine reader that modulates Fmr1 target mRNA selection and restricts axonal growth in Drosophila. EMBO J , 40:e104975 (#indicates joint correspondence) Link
2020
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 (2020) A systems view of spliceosomal assembly and branchpoints with iCLIP. Nat Struct Mol Biol , 27:768 (*indicates joint contribution) Link
2020
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, 40:e104975 (*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
2019
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
2018
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
2017
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
2016
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
2015
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
2014
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
2013
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
2012
König J, McGlincy NJ and Ule J (2012) Analysis of protein-RNA interactions with single-nucleotide resolution using iCLIP and next-generation sequencing. Wiley, 153–169 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
2011
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
2010
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
2009
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
2008
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
2007
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
2006
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
2004
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