last update: 2022 May 17
Phea LJ, Ephrussi A. Stably bound adaptor proteins modulate directionality of RNP transport
bioRxiv 13 Apr 2022
Medioni C, Vijayakumar J, Ephrussi A, Besse F. High-Resolution Live Imaging of Axonal RNP Granules in Drosophila Pupal Brain Explants.
Methods in Molecular Biology. 2022;2431:451-462. doi: 10.1007/978-1-0716-1990-2_24.
Bose M, Lampe M, Mahamid J, Ephrussi A. Liquid-to-solid phase transition of oskar ribonucleoprotein granules is essential for their function in Drosophila embryonic development.
Cell. 2022 Apr 14;185(8):1308-1324.e23. doi: 10.1016/j.cell.2022.02.022. Epub 2022 Mar 23.
Bujanic L, Shevchuk O, von Kuegelgen N, Ludwik K, Koppstein D, Zerna N, Sickmann A, and Chekulaeva M (2022). The key features of SARS-CoV-2 leader and NSP1 required for viral escape of NSP1-mediated repression.
RNA 28(5):766-779.
Medioni C, Ephrussi A, Besse F. Live-Imaging of Axonal Cargoes in Drosophila Brain Explants Using Confocal Microscopy.
Methods in Molecular Biology 2022;2417:19-28. doi: 10.1007/978-1-0716-1916-2
Mendonsa S, von Kuegelgen N, Bujanic L and Chekulaeva M (2021). Charcot–Marie–Tooth mutation in glycyl-tRNA synthetase stalls ribosomes in a pre-accommodation state and activates integrated stress response.
Nucleic Acids Research 49(17):10007-10017.
Witte F, Ruiz-Orera J, Ciolli Mattioli C, Blachut S, Adami E, Schulz JF, Schneider-Lunitz V, Hummel O, Patone G, Mücke MB, Silhavy J, Heinig M, Bottolo L, Sanchis D, Vingron M, Chekulaeva M, Pravenec M, Hubner N, van Heesch S. (2021) Trans control of cardiac mRNA translation in a protein length-dependent fashion.
Genome Biology 22:191. https://doi.org/10.1101/2020.06.05.133298
Cassella L, Ephrussi A*. Subcellular spatial transcriptomics identifies three mechanistically different classes of localizing RNAs
bioRxiv 2021.12.05.471303; doi: https://doi.org/10.1101/2021.12.05.471303
Gáspar I*, Phea LJ, McClintock M, Heber S, Bullock S*, Ephrussi A*. An RNA-based feed-forward mechanism ensures motor switching in oskar mRNA transport
bioRxiv. 2021.04.24.441269; doi: https://doi.org/10.1101/2021.04.24.441269
Vaishali, Dimitrova-Paternoga L, Haubrich K, Sun M, Ephrussi A, Hennig J. Validation and classification of RNA binding proteins identified by mRNA interactome capture.
RNA. 2021 Oct;27(10):1173-1185. doi: 10.1261/rna.078700.121. Epub 2021 Jul 2.
Ronchi P, Mizzon G, Machado P, D'Imprima E, Best BT, Cassella L, Schnorrenberg S, Montero MG, Jechlinger M, Ephrussi A, Leptin M, Mahamid J, Schwab Y. High-precision targeting workflow for volume electron microscopy.
Journal of Cell Biology. 2021 Sep 6;220(9):e202104069. doi: 10.1083/jcb.202104069. Epub 2021 Jun 23.
Behrens G, Edelmann SL, Raj T, ... Theurich S, Feske S, Kawakami N, Wurst W, Niessing D, Heissmeyer V. Disrupting Roquin-1 interaction with Regnase-1 induces autoimmunity and enhances antitumor responses.
Nat Immunol. 2021 Dec;22(12):1563-1576. doi: 10.1038/s41590-021-01064-3
Naarmann-de Vries IS, Senatore R, Moritz B, Marx G, Urlaub H, Niessing D, Ostareck DH, Ostareck-Lederer A. Methylated HNRNPK acts on RPS19 to regulate ALOX15 synthesis in erythropoiesis.
Nucleic Acids Res. 2021 Apr 6;49(6):3507-3523. doi: 10.1093/nar/gkab116.
Molitor L, Bacher S, Burczyk S, Niessing D. The Molecular Function of PURA and Its Implications in Neurological Diseases.
Front Genet. 2021 Mar 11;12:638217. doi: 10.3389/fgene.2021.638217.
Janowski R, Niessing D. The large family of PC4-like domains - similar folds and functions throughout all kingdoms of life.
RNA Biol. 2020 Sep;17(9):1228-1238. doi: 10.1080/15476286.2020.1761639.
Dimitrova-Paternoga L, Jagtap PKA, Cyrklaff A, Vaishali, Lapouge K, Sehr P, Perez K, Heber S, Löw C, Hennig J, Ephrussi A. Molecular basis of mRNA transport by a kinesin-1-atypical tropomyosin complex.
Genes & Development. 2021 Jul 1;35(13-14):976-991. doi: 10.1101/gad.348443.121. Epub 2021 Jun 17.
Schulz, L.*, Torres-Diz, M.*, Cortés-López, M.*, Hayer, KE.*, Asnani, M., Tasian, SK., 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 Jun 28;22(1):190. doi: 10.1186/s13059-021-02411-1.
Körtel, N.*, Rücklé, C.*, Zhou, Y.*, Busch, A., Peter 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., Zarnack., K. (2021) Deep and accurate detection of m6A RNA modifications using miCLIP2 and m6Aboost machine learning.
Nucleic Acids Research, gkab485, https://doi.org/10.1093/nar/gkab485.
Müntjes K., Devan S. K., Reichert A. and Feldbrügge M. Linking transport and translation of mRNAs with endosomes and mitochondria.
EMBO Rep 22, e52445 (2021)
Kwon S., Rupp O., Brachmann A., Blum C. F., Kraege A., Goesmann A. and Feldbrügge M. mRNA inventory of extracellular vesicles from Ustilago maydis.
J. Fungi 7: 562 (2021)
Weissinger R., Heinold L., Akram S., Jansen R.P., Hermesh O. RNA Proximity Labeling: A New Detection Tool for RNA-Protein Interactions. Molecules. (2021)
26:2270. doi: 10.3390/molecules26082270.
Kang, HS.*, Sanchez-Rico, C.*, Ebersberger, S., Sutandy FXR., 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.
Busch A., Brüggemann M., Ebersberger S., Zarnack K. iCLIP data analysis: A complete pipeline from sequencing reads to RBP binding sites.
Methods, pii: S1046-2023(18)30494-8 (2020)
Buchbender, A., Mutter, H., FX Sutandy, R., Körtel, N., Hänel, H., Busch, A., Ebersberger, S., and König, J. (2020). Improved library preparation with the new iCLIP2 protocol.
Methods 178, 33-48.
Binas O, Tants JN, Peter SA, Janowski R, Davydova E, Braun J, Niessing D, Schwalbe H, Weigand JE, Schlundt A. Structural basis for the recognition of transiently structured AU-rich elements by Roquin.
Nucleic Acids Res. 2020 Jul 27;48(13):7385-7403. doi: 10.1093/nar/gkaa465.
von Kuegelgen N and Chekulaeva M (2020). Conservation of a core neurite transcriptome across neuronal types and species.
WIREs RNA 14:e1590.
Stein V., Blank-Landeshammer B., Müntjes K., Märker R., Teichert I., Feldbrügge M., Sickmann A., and Kück U. The STRIPAK signaling complex regulates phosphorylation of GUL1, an RNA-binding protein that shuttles on endosomes.
PLoS Genet. 16: e1008819 (2020)
Mukherjee J., Franz-Wachtel M., Maček B., Jansen R.P. RNA Interactome Identification via RNA-BioID in Mouse Embryonic Fibroblasts.
Bio Protoc. (2020) 10:e3476. doi: 10.21769/BioProtoc.3476.
Heber S., Gáspár I., Tants J.-N., Günther J., Fernandez Moya S., Janowski R., Ephrussi A., Sattler M., Niessing D. Staufen2-mediated RNA recognition and localization requires combinatorial action of multiple domains
Nature Communications 10, Article number:1659 (2019)
Hampoelz B, Schwarz A, Ronchi P, Bragulat-Teixidor H, Tischer C, Gaspar I, Ephrussi A, Schwab Y, Beck M. Nuclear Pores Assemble from Nucleoporin Condensates During Oogenesis.
Cell. 2019 Oct 17;179(3):671-686.e17. doi: 10.1016/j.cell.2019.09.022.
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., and Beli, P. (2019). The RNA-binding ubiquitin ligase MKRN1 functions in ribosome-associated quality control of poly(A) translation.
Genome Biol 20, 216.
Schneider T, Hung LH, Aziz M, Wilmen A, Thaum S, Wagner J, Janowski R, Müller S, Schreiner S, Friedhoff P, Hüttelmaier S, Niessing D, Sattler M, Schlundt A, Bindereif A. Combinatorial recognition of clustered RNA elements by the multidomain RNA-binding protein IMP3.
Nat Commun. 2019 May 22;10(1):2266. doi: 10.1038/s41467-019-09769-8.
Olgeiser L., Haag C., Boerner S., Ule J., Busch A., Koepke J., König J., Feldbrügge M., Zarnack K.. The key protein of endosomal mRNP transport Rrm4 binds translational landmark sites of cargo mRNAs.
EMBO Rep 20, e46588 (2019)
Ciolli Mattioli C, Rom A, Franke V, Imami K, Arrey G, Terne M, Woehler A, Akalin A, Ulitsky I, and Chekulaeva M (2019). Alternative 3' UTRs direct localization of functionally diverse protein isoforms in neuronal compartments.
Nucleic Acids Research 47(5): 2560.
Jankowski S, Pohlmann T, Baumann S, Müntjes K, Kumar Devan S, Zander S, Feldbrügge M. The multi PAM2 protein Upa2 functions as novel core component of endosomal mRNA transport.
EMBO Rep 24, e47381 (2019)
Mukherjee J., Hermesh O., Eliscovich C., Nalpas N., Franz-Wachtel M., Maček B., Jansen R.P. β-Actin mRNA interactome mapping by proximity biotinylation.
Proc Natl Acad Sci U S A. (2019) 116:12863-12872. doi: 10.1073/pnas.1820737116.
Heber S., Gáspár I., Tants J.-N., Günther J., Fernandez Moya S., Janowski R., Ephrussi A., Sattler M., Niessing D. Staufen2-mediated RNA recognition and localization requires combinatorial action of multiple domains.
Nature Communications 10, Article number:1659 (2019)
Manchalu S, Mittal N, Spang A, Jansen RP. Local translation of yeast ERG4 mRNA at the endoplasmic reticulum requires the brefeldin A resistance protein Bfr1.
RNA. (2019) 25:1661-1672. doi: 10.1261/rna.072017.119.
Wippich F., Ephrussi A. Transcript specific mRNP capture from Drosophila egg-chambers for proteomic analysis.
Methods. 2019 Sep 5. pii: S1046-2023(18)30489-4. doi:10.1016/j.ymeth.2019.09.001. [epub ahead of print]
Durdevic Z., Ephrussi A. Germ Cell Lineage Homeostasis in Drosophila requires the Vasa RNA Helicase.
Genetics. 2019 Sep 4. pii: genetics.302558.2019. doi: 10.1534/genetics.119.302558. [Epub ahead of print]
Obrdlik A., Lin G., Habermann N., Ule J., Ephrussi A. The Transcriptome-wide Landscape and Modalities of EJC Binding in Adult Drosophila.
Cell Rep. 2019 Jul 30;28(5):1219-1236.e11. doi: 10.1016/j.celrep.2019.06.088.
Olgeiser L., Haag C., Boerner S., Ule J., Busch A., Koepke J., König J., Feldbrügge M.*, Zarnack K.*. The key protein of endosomal mRNP transport Rrm4 binds translational landmark sites of cargo mRNAs.
EMBO Rep. 2018: pii: e46588. *shared corresponding authorship
Béthune J., Jansen R.P., Feldbrügge M.*, Zarnack K*. Membrane-associated RNA-binding proteins orchestrate organelle-coupled translation.
Trends in Cell Biol. 2018: In press *shared corresponding authorship
Chamiolo J., Gaspar I., Ephrussi A., Seitz O. In Vivo Visualization and Function Probing of Transport mRNPs Using Injected FIT Probes.
Methods Mol Biol. 2018: 1649:273-287. doi: 10.1007/978-1-4939-7213-5_18.
Durdevic, Z., Pillai, R.S., Ephrussi, A. Transposon silencing in the Drosophila female germline ensures genome stability in progeny embryos.
Life Science Allicance 2018 doi: 10.26508/lsa.201800179
Gaspar I., Hövelmann F., Chamiolo J., Ephrussi A., Seitz O. Quantitative mRNA Imaging with Dual Channel qFIT Probes to Monitor Distribution and Degree of Hybridization.
ACS Chem Biol. 2018 Feb 7. doi: 10.1021/acschembio.7b01007.
Gáspár, I.*, Wippich, F. and Ephrussi, A.* Terminal Deoxynucleotidyl Transferase Mediated Production of Labeled Probes for Single-molecule FISH or RNA Capture.
Bio-protocol 2018 8(5): e2750. doi: 10.21769/BioProtoc.2750.
Gáspár, I.*, Ephrussi, A.* (2017). RNA localization feeds translation.
Science 2017 357:1235-1236. doi: 10.1126/science.aao5796.
Gáspár, I.*, Ephrussi, A.* (2017). Ex vivo ooplasmic extract from developing oocytes for quantitative TIRF microscopy analysis.
Bio Protoc. 2017 Jul 5;7(13). pii: e2380. doi: 10.21769/BioProtoc.2380.
Syed MI, Moorthy BT, Jenner A, Fetka I, Jansen RP.
Signal sequence-independent targeting of MID2 mRNA to the endoplasmic reticulum by the yeast RNA-binding protein Khd1p.
FEBS Lett. 2018 May 17. doi: 10.1002/1873-3468.13098
Berger SM, Fernández-Lamo I, Schönig K, Fernández Moya SM, Ehses J, Schieweck R, Clementi S, Enkel T, Grothe S, von Bohlen Und Halbach O, Segura I, Delgado-García JM, Gruart A, Kiebler MA, Bartsch D. Forebrain-specific, conditional silencing of Staufen2 alters synaptic plasticity, learning, and memory in rats.
Genome Biol. 2017 Nov 17;18(1):222.
Niessing D, Jansen RP, Pohlmann T, Feldbrügge M. mRNA transport in fungal top models.
Wiley Interdiscip Rev RNA. 2017 Oct 10. doi: 10.1002/wrna.1453
Follwaczny P, Schieweck R, Riedemann T, Demleitner A, Straub T, Klemm AH, Bilban M, Sutor B, Popper B, Kiebler MA. Pumilio2 deficient mice show a predisposition for epilepsy.
Dis Model Mech. 2017 Oct 18. pii: dmm.029678.
Sharangdhar T, Sugimoto Y, Heraud-Farlow J, Fernández-Moya SM, Ehses J, Ruiz de Los Mozos I, Ule J, Kiebler MA. A retained intron in the 3'-UTR of Calm3 mRNA mediates its Staufen2- and activity-dependent localization to neuronal dendrites.
EMBO Rep. 2017 Aug 1. pii: e201744334.
Gaspar I, Wippich F, Ephrussi A. Enzymatic production of single molecule FISH and RNA capture probes.
RNA. 2017 Jul 11. pii: rna.061184.117.
Botti V, McNicoll F, Steiner MC, Richter FM, Solovyeva A, Wegener M, Schwich OD, Poser I, Zarnack K, Wittig I, Neugebauer KM, Müller-McNicoll M.
Cellular differentiation state modulates the mRNA export activity of SR proteins.
J Cell Biol. 2017 Jul 3;216(7):1993-2009.
Bauer KE, Kiebler MA, Segura I. Visualizing RNA granule transport and translation in living neurons.
Methods. 2017 Jun 15. pii: S1046-2023(16)30423-6. (Review)
Jeske M, Müller CW, Ephrussi A. The LOTUS domain is a conserved DEAD-box RNA helicase regulator essential for the recruitment of Vasa to the germ plasm and nuage.
Genes Dev. 2017 May 1;31(9):939-952.
Haag, C., Pohlmann, T., Feldbrügge, M. The ESCRT regulator Did2 maintains the balance between long-distance endosomal transport and endocytic trafficking.
PLoS Genet 2017 13(4): e1006734.
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*, Ule J*. Insights into the design and interpretation of iCLIP experiments.
Genome Biol. 2017 Jan 16;18(1):7.
Edelmann FT, Schlundt A, Heym RG, Jenner A, Niedner-Boblenz A, Syed MI, Paillart JC, Stehle R, Janowski R, Sattler M, Jansen RP, Niessing D. Molecular architecture and dynamics of ASH1 mRNA recognition by its mRNA-transport complex.
Nat Struct Mol Biol. 2017 Feb;24(2):152-161.
Gáspár I, Sysoev V, Komissarov A, Ephrussi A. An RNA-binding atypical tropomyosin recruits kinesin-1 dynamically to oskar mRNPs.
EMBO J. 2017 Feb 1;36(3):319-333.
Lazzaretti D, Veith K, Kramer K, Basquin C, Urlaub H, Irion U, Bono F. The bicoid mRNA localization factor Exuperantia is an RNA-binding pseudonuclease.
Nat Struct Mol Biol. 2016 Aug;23(8):705-13.
Zander S, Baumann S, Weidtkamp-Peters S, Feldbrügge M. Endosomal assembly and transport of heteromeric septin complexes promote septin cytoskeleton formation.
J Cell Sci. 2016 Jul 15;129(14):2778-92.
Jambor H, Mejstrik P, Tomancak P. Rapid Ovary Mass-Isolation (ROMi) to Obtain Large Quantities of Drosophila Egg Chambers for Fluorescent In Situ Hybridization.
Methods Mol Biol. 2016;1478:253-262.
Schieweck R, Popper B, Kiebler MA. Co-Translational Folding: A Novel Modulator of Local Protein Expression in Mammalian Neurons?
Trends Genet. 2016 Dec;32(12):788-800. (Review)
Sysoev VO, Fischer B, Frese CK, Gupta I, Krijgsveld J, Hentze MW, Castello A, Ephrussi A. Global changes of the RNA-bound proteome during the maternal-to-zygotic transition in Drosophila.
Nat Commun. 2016 Jul 5;7:12128.
Ehses J, Kiebler MA, Fernández-Moya SM. RNA Transport: From Head to Toe in Radial Glial Cells.
Curr Biol. 2016 Dec 19;26(24):R1285-R1287. (Review)
Baumann S, Zander S, Weidtkamp-Peters S, Feldbrügge M. Live cell imaging of septin dynamics in Ustilago maydis.
Methods Cell Biol. 2016;136:143-59. (Review)
Zarnack K.*, König J.*, Tajnik M., Martincorena I., Eustermann S., Stévant I., Reyes A., Anders S., Luscombe N.M., Ule J.. Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements.
Cell 152, 453-66 (2013)
König J.*, Zarnack K.*, Rot G., Curk T., Kayikci M., Zupan B., Tuner D.J., Luscombe N.M., Ule J.. iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution.
Nat Struct Mol Biol 17, 909-15 (2010)
Forschergruppe 2333
Prof. Dr. Dierk Niessing (Sprecher)
Ulm University - Institute of Pharmaceutical Biotechnology
James Franck Ring N27
89081 Ulm
Phone: +49 89 3187 2176
EMail: info@for2333.de
