Ute Rothbächer

Associate Professor

Picture of Ute Rothbächer

Department of Zoology
University of Innsbruck
Technikerstr. 25
6020 Innsbruck

Room: 7/09

+43 512 507-51842


Current Research

How the dynamic developmental program is inscribed in the genome and inherited to subsequent generations remains poorly understood. Efficient functional readout, notably at DNA level in vivo is often complicated by the complexity of regulatory interactions and the complexity of genomes, particularly in vertebrates.

To unravel fundamental genetic mechanisms that control cell fate choice in vivo, we study embryonic development in a simple marine invertebrate, the ascidian Ciona intestinalis, belonging to the vertebrate sister group, the tunicates. Larval equivalent stages of ascidians and vertebrates have resembling structures such as a central notochord (embryonic structure forming the vertebral colomn in vertebrates), a dorsal neural tube and flanking muscles. Whats more, ascidian embryos develop with a fixed cellular lineage based on few and large cells allowing cellular resolution of cell fate identity. The fully sequenced genome, since compact and unduplicated, gives acces to regulatory DNA segments, isolated for reporter gene essays in vivo. Such DNA constructs, when electroporated in fertilised eggs, produce transiently transgenic embryos and allow rapid gene functional and gene regulatory analyses, in precisely identifyable tissue precursors, from earliest embryonic stages in vivo.

Our research aims on deciphering embryonic gene network signatures in ascidians are:

1) the mechanisms and dynamics for gene regulatory switches affecting the pluripotent ectoderm in vivo. We focus on novel combinatorial codes for transcription factors as nuclear effectors of major signaling pathways, including Wnt and FGF/MEK signaling.

2) the genetic and molecular basis for ascidian bioadhesion motivated by the search for novel biomimetic reagents.

JOVE Movie: Embryo Microinjection and Electroporation in the Chordate Ciona intestinalis


Pictures of Ascidians, larvae, microinjection of th early embryo and the aquarium system

Curriculum vitae

1988 MSc (Diploma), Zoology and Immunology, TU and LMU Munich, Germany
1994 PhD (Dr. rer.nat.), Inst. for Immunology, LMUniversity Munich, Germany
1994-1998 Postdoc Boehringer Ingelheim Fonds, UC Irvine and Caltech, USA
1999-2012 CNRS, Inst. for Developmental Biology Marseille (IBDM), France
2008 Habilitation in Developmental Biology, Univ. Aix-Marseille, France
2012-2015 Assistant Professor, Institute of Zoology, University Innsbruck, Austria
Since 2015 Associate Professor, Institute of Zoology, University Innsbruck, Austria


Cover photos of different journals


Contributions to Books / Journals

Journal Article (Original Paper)

  • Papadogiannis, V.; Pennati, A.; Parker, H.J.; Rothbächer, U.; Patthey, C.; Bronner, M.E.; Shimeld, S.M. (2022): Hmx gene conservation identifies the origin of vertebrate cranial ganglia. In: Nature 605/7911, pp. 701 - 705.  (Web link)


  • Davey, P.A.; Power, A.M.; Santos, R.; Bertemes, P.; Ladurner, P.; Palmowski, P.; Clarke, J.; Flammang, P.; Lengerer, B.; Hennebert, E.; Rothbächer, U.; Pjeta, R.; Wunderer, J.; Zurovec, M.; Aldred, N. (2021): Omics-based molecular analyses of adhesion by aquatic invertebrates. In: Biological Reviews 96/3, pp. 1051 - 1075.  (Web link)


  • Imai, K.; Kobayashi, K.; Kari, W.; Rothbächer, U.; Ookubo, N.; Oda-Ishii, I.; Satou, Y. (2020): Gata is ubiquitously required for the earliest zygotic gene transcription in the ascidian embryo. In: Developmental Biology 458/2, pp. 215 - 227.  (Web link)


  • Peronato, A.; Drago, L.; Rothbächer, U.; Macor, P.; Ballarin, L.; Nicola Franchi, N. (2020): Complement system and phagocytosis in a colonial protochordate. In: Developmental & Comparative Immunology 103, No. 103530. (Web link)


  • Zeng, F.; Wunderer, J.; Salvenmoser, W.; Ederth, T.; Rothbächer, U. (2019): Identifying adhesive components in a model tunicate.In: Philosophical Transactions of The Royal Society B - Biological Sciences 374/1784, No. 20190197.  (Web link)


  • Zeng, F.; Wunderer, J.; Salvenmoser, W.; Hess, M.W.; Ladurner, P.; Rothbächer, U. (2019): Papillae revisited and the nature of the adhesive secreting collocytes. In: Developmental Biology 448/2, pp. 183 - 198.  (Web link)


  • Kari, W.; Zeng, F.; Zitzelsberger, L.; Will, J.P.; Rothbächer, U. (2016): Embryo Microinjection and Electroporation in the Chordate Ciona intestinalis. In: Jove-Journal of Visualized Experiments 116, Nr. e54313. (Full-text)  (Web link)


  • Oda-Ishii, I.; Kubo, A.; Kari, W.; Suzuki, N.; Rothbächer, U.; Satou, Y. (2016): A Maternal System Initiating the Zygotic Developmental Program through Combinatorial Repression in the Ascidian Embryo. In: PLoS Genetics 12/5, Nr. e1006045. (Web link)


  • Gilchrist, M.J.; Sobral, D.; Khoueiry, P.; Daian, F.; Laporte, B.; Patrushev, I.; Matsumoto, J.; Dewar, K.; Hastings, K.E.M.; Satou, Y.; Lemaire, P.; Rothbächer, U. (2015): A pipeline for the systematic identification of non-redundant full-ORF cDNAs for polymorphic and evolutionary divergent genomes: Application to the ascidian Ciona intestinalis. In: Developmental Biology 404/2, pp. 149 - 163. (Web link)


  • Murgan, S.; Kari, W.; Rothbächer, U.; Iché-Torres, M.; Mélénec, P.; Hobert, O.; Bertrand, V. (2015): Atypical transcriptional activation by TCF via a Zic transcription factor in C. elegans neuronal precursors. In: Developmental Cell 33/6, pp. 737 - 745. (Web link)


  • Pennati, R.; Rothbächer, U. (2015): Bioadhesion in ascidians: a developmental and functional genomics perspective. In: Interface Focus 5/1, No. 20140061. (Web link)


  • Pasini, A.; Manenti, R.; Rothbächer, U.; Lemaire, P. (2012): Antagonizing retinoic acid and FGF/MAPK pathways control posterior body patterning in the invertebrate chordate Ciona intestinalis. In: PLoS One 7/9, p. e46193. (Web link)


Book Chapter (Original Paper)

  • Zeng, F.; Peronato, A.; Ballarin, L.; Rothbächer, U. (2022): Sweet Tunicate Blood Cells: A Glycan Profiling of Haemocytes in Three Ascidian Species. In: Ballarin, L.; Rinkevich, B.; Hobmayer, B.: Advances in Aquatic Invertebrate Stem Cell Research: From Basic Research to Innovative Applications. Basel: MDPI AG., ISBN 978-3-0365-1636-3, pp. 351 - 379. (Web link)
  •  Tassy, O., Dauga, D., Daian, F., Sobral, D., Robin, F., Khoueiry, P., Salgado, D., Fox, V., Caillol, D., Schiappa, R., Laporte, B., Rios, A., Luxardi, G., Kusakabe, T., Joly, J.S., Darras, S., Christiaen, L., Contensin, M., Auger, H., Lamy, C., Hudson, C., Rothbächer, U., Gilchrist, M.J., Makabe, K.W., Hotta, K., Fujiwara, S., Satoh, N., Satou, Y.and Lemaire, P. (2010). The ANISEED database: digital representation, formalization, and elucidation of a chordate developmental program. Genome Res 20, 1459-1468. doi:10.1101/gr.108175.110 (Web link)


  • Khoueiry, P., Rothbächer, U., Ohtsuka, Y., Daian, F., Frangulian, E., Roure, A., Dubchak, I.and Lemaire, P. (2010). A cis-regulatory signature in ascidians and flies, independent of transcription factor binding sites. Curr Biol 20, 792-802. doi:10.1016/j.cub.2010.03.063


  • Roure, A., Rothbächer, U., Robin, F., Kalmar, E., Ferone, G., Lamy, C., Missero, C., Mueller, F.and Lemaire, P. (2007). A multicassette Gateway vector set for high throughput and comparative analyses in ciona and vertebrate embryos. PLoS One 2, e916. doi:10.1371/journal.pone.0000916


  • Rothbächer, U. , Bertrand, V., Lamy, C.and Lemaire, P. (2007). A combinatorial code of maternal GATA, Ets and beta-catenin-TCF transcription factors specifies and patterns the early ascidian ectoderm. Development 134, 4023-4032. doi:10.1242/dev.010850


  • Pasini, A., Amiel, A., Rothbächer, U., Roure, A., Lemaire, P.and Darras, S. (2006). Formation of the ascidian epidermal sensory neurons: insights into the origin of the chordate peripheral nervous system. PLoS Biol 4, e225. doi:10.1371/journal.pbio.0040225


  • Lamy, C., Rothbächer, U., Caillol, D.and Lemaire, P. (2006). Ci-FoxA-a is the earliest zygotic determinant of the ascidian anterior ectoderm and directly activates Ci-sFRP1/5. Development 133, 2835-2844. doi:10.1242/dev.02448


  • Rothbächer, U. and Lemaire, P. (2002). Creme de la Kremen of Wnt signalling inhibition. Nat Cell Biol 4, E172-173. doi:10.1038/ncb0702-e172


  • Wallingford, J.B., Rowning, B.A., Vogeli, K.M., Rothbächer, U., Fraser, S.E.and Harland, R.M. (2000). Dishevelled controls cell polarity during Xenopus gastrulation. Nature 405, 81-85. doi:10.1038/35011077


  • Rothbächer, U. , Laurent, M.N., Deardorff, M.A., Klein, P.S., Cho, K.W.and Fraser, S.E. (2000). Dishevelled phosphorylation, subcellular localization and multimerization regulate its role in early embryogenesis. EMBO J 19, 1010-1022. doi:10.1093/emboj/19.5.1010


  • Louie, A.Y., Huber, M.M., Ahrens, E.T., Rothbächer, U., Moats, R., Jacobs, R.E., Fraser, S.E.and Meade, T.J. (2000). In vivo visualization of gene expression using magnetic resonance imaging. Nat Biotechnol 18, 321-325. doi:10.1038/73780


  • Hobmayer, B., Rentzsch, F., Kuhn, K., Happel, C.M., von Laue, C.C., Snyder, P., Rothbächer, U.and Holstein, T.W. (2000). WNT signalling molecules act in axis formation in the diploblastic metazoan Hydra. Nature 407, 186-189. doi:10.1038/35025063


  • Bauer, A., Chauvet, S., Huber, O., Usseglio, F., Rothbächer, U., Aragnol, D., Kemler, R.and Pradel, J. (2000). Pontin52 and reptin52 function as antagonistic regulators of beta-catenin signalling activity. EMBO J 19, 6121-6130. doi:10.1093/emboj/19.22.6121


  • Ahrens, E.T., Rothbächer, U., Jacobs, R.E.and Fraser, S.E. (1998). A model for MRI contrast enhancement using T1 agents. Proc Natl Acad Sci U S A 95, 8443-8448.


  • Laurent, M.N., Blitz, I.L., Hashimoto, C., Rothbächer, U.and Cho, K.W. (1997). The Xenopus homeobox gene twin mediates Wnt induction of goosecoid in establishment of Spemann's organizer. Development 124, 4905-4916.


  • Johnson, J.P., Rummel, M.M., Rothbächer, U.and Sers, C. (1996). MUC18: A cell adhesion molecule with a potential role in tumor growth and tumor cell dissemination. Curr Top Microbiol Immunol 213 ( Pt 1), 95-105.


  • Watabe, T., Kim, S., Candia, A., Rothbächer, U., Hashimoto, C., Inoue, K.and Cho, K.W. (1995). Molecular mechanisms of Spemann's organizer formation: conserved growth factor synergy between Xenopus and mouse. Genes Dev 9, 3038-3050.


  • Rothbächer, U. , Laurent, M.N., Blitz, I.L., Watabe, T., Marsh, J.L.and Cho, K.W. (1995). Functional conservation of the Wnt signaling pathway revealed by ectopic expression of Drosophila dishevelled in Xenopus. Dev Biol 170, 717-721. doi:10.1006/dbio.1995.1249


  • Sers, C., Kirsch, K., Rothbächer, U., Riethmuller, G.and Johnson, J.P. (1993). Genomic organization of the melanoma-associated glycoprotein MUC18: implications for the evolution of the immunoglobulin domains. Proc Natl Acad Sci U S A 90, 8514-8518.


  • Johnson, J.P., Rothbächer, U.and Sers, C. (1993). The progression associated antigen MUC18: a unique member of the immunoglobulin supergene family. Melanoma Res 3, 337-340.


  • Lehmann, J.M., Holzmann, B., Rothbächer, U., Riethmuller, G.and Johnson, J.P. (1989). [Step-wise expression of melanoma-associated antigens in tumor progression]. Onkologie 12, 273-276.


  • Johnson, J.P., Lehmann, J.M., Stade, B.G., Rothbächer, U., Sers, C.and Riethmuller, G. (1989). Functional aspects of three molecules associated with metastasis development in human malignant melanoma. Invasion Metastasis 9, 338-350.

Citation index

Nach oben scrollen