A17 - Ettwiller

Our understanding of vertebrate brain development is limited by our ability to identify the precise mechanisms that lead a progenitor cell to commit to specific cell fates. The players are complex networks of trans-acting factors that act on cis-regulatory sequences to activate or repress given sets of genes.

Mechanistically, cis-regulatory sequences integrate the proper combination of trans-acting signals via the arrangement of sets of motifs in a precise orientation and spacing for the affinity binding of these factors. Consequently, the information for such integration is hard-coded in the DNA sequence and defines the ‘grammar’ of cis-regulation in a given cell type.

Thus the elucidation of such grammar is key for understanding regulatory networks during development.  We plan to address the underlying logic of cis-regulatory grammars governing precise spacio-temporal transcription during the establishment of neuronal diversity in vertebrates.

The strategy consists of systematically testing sequences that are likely to be involved in gene regulation using the in vivo enhancer assay in fish that we developed and successfully tested. The result of that analysis is the precise description of the outcomes (exemplified by the reporter gene expression in the medaka embryo) of many combinatorial regulatory elements hardcoded in these sequences.

Focusing on a limited number of neuronal cell types, sequences with enhancer activity in these cells will be further analysed using new and established algorithms. Commonalities between these sequences are indicative of the specific regulatory grammar of these cells.

The validation of the predicted grammar can be addressed by site-directed mutagenesis but also by our ability, using this grammar, to de-novo predict regulatory regions with similar function. This validation procedure will provide additional datasets that will be fed back to the computational analysis for refinement of the methodology.

Additionally this analysis will dramatically expand the catalogue of fish enhancer that have been characterised in vivo and the transgenic lines obtained will be valuable material for further characterization of individual neuronal structure.

Unser Verständnis der Gehirnentwicklung von Wirbeltieren wird durch unsere Fähigkeit begrenzt, die präzisen Mechanismen der Spezifikation von Vorläuferzellen zu identifizieren.  An diesem Prozess der Zellspezifikation sind komplexe Netzwerke von trans-agierenden Faktoren beteiligt, die durch ihre Interaktion mit cis-regulatorischen Elementen definierte Gruppen von Genen aktivieren oder reprimieren. Die Information für die Regulation ist also in der Sequenz der DNA kodiert und beschreibt die cis-regulatorische “Grammatik” in einem bestimmten Zelltyp.

Wir planen, die solchen cis-regulatorischen Gammatiken zugrunde liegende Logik zu untersuchen, die die präzise zeitliche und räumliche Transkription zur Erzeugung neuronaler Diversität in Wirbeltieren steuert. Die Strategie basiert auf der systematischen Analyse von wahrscheinlichen cis-regulatorischen Sequenzen mittels in vivo enhancer assays im japanischen Reisfisch Medaka, welche von uns entwickelt und erfolgreich getestet wurden.

Own project-related publications

Blanchette, M., Bataille, A. R., Chen, X., Poitras, C., Laganiere, J., Lefebvre, C., Deblois, G., Giguere, V., Ferretti, V., Bergeron, D., Coulombe, B., and Robert, F. (2006) Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression. Genome Res 16: 656-668

Grabher, C., and Wittbrodt, J. (2007) Meganuclease and transposon mediated transgenesis in medaka. Genome Biol 8 Suppl 1: S10

Kawakami, K. (2007) Tol2: a versatile gene transfer vector in vertebrates. Genome Biol 8 Suppl 1: S7

Kasahara, M., Naruse, K., Sasaki, S., Nakatani, Y., Qu, W., Ahsan, B., Yamada, T., Nagayasu, Y., Doi, K., Kasai, Y., Jindo, T., Kobayashi, D., Shimada, A., Toyoda, A., Kuroki, Y., Fujiyama, A., Sasaki, T., Shimizu, A., Asakawa, S., Shimizu, N., Hashimoto, S., Yang, J., Lee, Y., Matsushima, K., Sugano, S., Sakaizumi, M., Narita, T., Ohishi, K., Haga, S., Ohta, F., Nomoto, H., Nogata, K., Morishita, T., Endo, T., Shin, I. T., Takeda, H., Morishita, S., and Kohara, Y. (2007) The medaka draft genome and insights into vertebrate genome evolution. Nature 447: 714-719

Del Bene F#, Ettwiller L#, Birney E, and Wittbrodt J (2007) In vivo Validation of a Computationally Predicted Conserved Ath5 Target Gene Set. PLoS Genetics. August 1. #equally contributing

Ettwiller L, Paten B, Ramialison M, and Wittbrodt J (2007) Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation. Nature Methods. 4(7):563-565.

Ettwiller L, Paten B, Souren M, Wittbrodt J, and Birney E (2005) The discovery, positioning and verification of a set of transcription-associated motifs in vertebrates. Genome Biology. 6(12):R104.

Ettwiller L, Rung J, and Birney E (2003) Discovering novel cis-regulatory motifs using functional networks. Genome Research. May 13; 5:883-95.

Own project-related publications (submitted / in preparation)

Ettwiller L#, Budd A, Spitz F, and Wittbrodt J (submitted) Dynamics of evolution of transcriptional regulation in animals. Manuscript submitted. #corresponding author

Selected publications from other projects outside the SFB since 2005

Sakkou M, Wiedmer P, Anlag K, Hamm A, Seuntjens E, Ettwiller L, Tschöp M, and Treier M (2007) A role for brain-specific homeobox factor bsx in the control of hyperphagia and locomotory behavior. Cell Metabolism.;5(6):450-463.

Ettwiller L, and Veitia R (2007) Protein coevolution and isoexpression in yeast macromolecular complexes. Comparative and Functional Genomics. 58721.

Potier MC, Rivals I, Mercier G, Ettwiller L, Moldrich RX, Laffaire J, Personnaz, Rossier J, and Dauphinot L (2006) Transcriptional disruptions in Down syndrome: a case study in the Ts1Cje mouse cerebellum during post-natal development. Journal of Neurochemistry.Suppl 1:104-109.

Ettwiller L, and Patten BJ (2004) Guilt by mutliple association. Heredity. Jun; 92(6):481-2.

Ureta-Vidal A, Ettwiller L, and Birney E (2003) Comparative genomics: genome-wide analysis in metazoan eukaryotes. Nature Review Genetics. Apr 4; 4:251-62.

Laurence Ettwiller

Institut für Zoologie
Im Neuenheimer Feld 230
69120 Heidelberg

Phone:  06221-546495
email:    laurence.ettwiller@zoo.uni-heidelberg.de