Identification and functional analysis of RNA-binding sites in proteins involved in nuclear mRNP assembly in S. cerevisiae

• Applicants: Professorin Dr. Katja Sträßer; Professor Dr. Henning Urlaub
• Subject Area: General Genetics and Functional Genome Biology ; Biochemistry
• Term: from 2016 to 2023
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 313454814

• Final Report Year: 2024

No abstract available

Publications

• Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins. Nature Methods, 11(10), 1064-1070.
  Kramer, Katharina; Sachsenberg, Timo; Beckmann, Benedikt M; Qamar, Saadia; Boon, Kum-Loong; Hentze, Matthias W; Kohlbacher, Oliver & Urlaub, Henning
  
• Interplay between the catabolite repression control protein Crc, Hfq and RNA in Hfq-dependent translational regulation in Pseudomonas aeruginosa. Nucleic Acids Research, 46(3), 1470-1485.
  Sonnleitner, Elisabeth; Wulf, Alexander; Campagne, Sébastien; Pei, Xue-Yuan; Wolfinger, Michael T; Forlani, Giada; Prindl, Konstantin; Abdou, Laetitia; Resch, Armin; Allain, Frederic H -T; Luisi, Ben F; Urlaub, Henning & Bläsi, Udo
  
• Structural insights into the stimulation of S. pombe Dnmt2 catalytic efficiency by the tRNA nucleoside queuosine. Scientific Reports, 8(1).
  Johannsson, Sven; Neumann, Piotr; Wulf, Alexander; Welp, Luisa M.; Gerber, Hans-Dieter; Krull, Matthias; Diederichsen, Ulf; Urlaub, Henning & Ficner, Ralf
  
• Type IV CRISPR RNA processing and effector complex formation in Aromatoleum aromaticum. Nature Microbiology, 4(1), 89-96.
  Özcan, Ahsen; Pausch, Patrick; Linden, Andreas; Wulf, Alexander; Schühle, Karola; Heider, Johann; Urlaub, Henning; Heimerl, Thomas; Bange, Gert & Randau, Lennart
  
• Insights into the assembly and architecture of a Staufen-mediated mRNA decay (SMD)-competent mRNP. Nature Communications, 10(1).
  Gowravaram, Manjeera; Schwarz, Juliane; Khilji, Sana K.; Urlaub, Henning & Chakrabarti, Sutapa
  
• Analysis of protein-DNA interactions in chromatin by UV induced cross-linking and mass spectrometry. Nature Communications, 11(1).
  Stützer, Alexandra; Welp, Luisa M.; Raabe, Monika; Sachsenberg, Timo; Kappert, Christin; Wulf, Alexander; Lau, Andy M.; David, Stefan-Sebastian; Chernev, Aleksandar; Kramer, Katharina; Politis, Argyris; Kohlbacher, Oliver; Fischle, Wolfgang & Urlaub, Henning
  
• Intrinsically disordered regions of tristetraprolin and DCP2 directly interact to mediate decay of ARE-mRNA. Nucleic Acids Research, 50(18), 10665-10679.
  Maciej, Vincent D; Mateva, Nevena; Schwarz, Juliane; Dittmers, Theresa; Mallick, Megha; Urlaub, Henning & Chakrabarti, Sutapa
  
• 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.
  Keil, Philipp; Wulf, Alexander; Kachariya, Nitin; Reuscher, Samira; Hühn, Kristin; Silbern, Ivan; Altmüller, Janine; Keller, Mario; Stehle, Ralf; Zarnack, Kathi; Sattler, Michael; Urlaub, Henning & Sträßer, Katja
  
• A viral ADP-ribosyltransferase attaches RNA chains to host proteins. Nature, 620(7976), 1054-1062.
  Wolfram-Schauerte, Maik; Pozhydaieva, Nadiia; Grawenhoff, Julia; Welp, Luisa M.; Silbern, Ivan; Wulf, Alexander; Billau, Franziska A.; Glatter, Timo; Urlaub, Henning; Jäschke, Andres & Höfer, Katharina
  
• A type III-Dv CRISPR-Cas system is controlled by the transcription factor RpaB and interacts with the DEAD-box RNA helicase CrhR. Cell Reports, 43(7), 114485.
  Bilger, Raphael; Migur, Angela; Wulf, Alexander; Steglich, Claudia; Urlaub, Henning & Hess, Wolfgang R.
  
• Intensity and retention time prediction improves the rescoring of protein‐nucleic acid cross‐links. PROTEOMICS, 24(8).
  Siraj, Arslan; Bouwmeester, Robbin; Declercq, Arthur; Welp, Luisa; Chernev, Aleksandar; Wulf, Alexander; Urlaub, Henning; Martens, Lennart; Degroeve, Sven; Kohlbacher, Oliver & Sachsenberg, Timo
  
• RNA helicase IGHMBP2 regulates THO complex to ensure cellular mRNA homeostasis. Cell Reports, 43(2), 113802.
  Prusty, Archana Bairavasundaram; Hirmer, Anja; Sierra-Delgado, Julieth Andrea; Huber, Hannes; Guenther, Ulf-Peter; Schlosser, Andreas; Dybkov, Olexandr; Yildirim, Ezgi; Urlaub, Henning; Meyer, Kathrin C.; Jablonka, Sibylle; Erhard, Florian & Fischer, Utz