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The Center for Integrative Genomics Report 2005–2006

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The Center for Integrative Genomics Report 2005–2006 The Center for integrative genomics Report 2005–2006 $FOUSFJOUÏHSBUJG EFHÏOPNJRVF Index PRESENTATION Director’s message 4 Scientific advisory committee 6 Organigram of the CIG 7 RESEARCH The structure and function of genomes and their evolution Alexandre reymond – Genome structure and expression 10 Henrik Kaessmann – Evolutionary genomics 12 Victor Jongeneel – Cancer genomics 14 The regulation of gene expression Nouria hernandez – Mechanisms of transcription regulation 16 Winship herr – Regulation of cell proliferation 18 Christian Fankhauser – Light–regulated development in plants 20 The genomics of complex functions Mehdi tafti – Genetics of sleep and the sleep EEG 22 Paul Franken – Genetics and energetics of sleep homeostasis and circadian rythms 24 Walter Wahli – Peroxisome Proliferator–Activated Receptors (PPARs) as regulators of metabolic and tissue repair processes 26 Béatrice Desvergne – PPARbeta and fine tuning of cell fate decision 30 Liliane Michalik – Roles of PPARs in skin biology and angiogenesis 34 Bernard thorens – Molecular and physiological analysis of energy homeostasis in health and disease 36 CORE fACILITIES Core facilities of the CIG 39 DNA array facility – DAF 40 Protein analysis facility – PAF 42 Core facilities associated with the CIG 44 EdUCATION Lectures and courses 48 Seminars at the CIG 51 CIG retreat 56 The CIG & the public 56 FUNDING (ACKNOwlEDGEMENTS) 58 PEOplE 59 CIG Timeline CIG Timeline Inauguration of the Pro- tein Analysis Facility (PAF – December 2002) Inauguration of the DNA Array Facility (DAF – March 2003) Arrival of Prof. Kaessmann (September 2003) Installation Arrival of of Vital–IT Prof. Thorens in the Génopode (October 2003) Arrival of Inauguration of the Prof. Hernandez The construction of Prof. Hernandez, Cellular Imaging Facility becomes the second the big animal facility Herr and Tafti at the Génopode CIG director is rejected by popular (September 2004) referendum Arrival of Arrival of Arrival Arrival Inauguration First CIG retreat Prof. Reymond Prof. Fankhauser of Dr. Franken of Prof. Desvergne, of the CIG in Saas Fee (October 2004) Wahli and Dr. Michalik 01 02 03 04 05 06 07 08 09 10 11 12 2003 2004 2005 2 CIG 2005/2006 Installation HeLa in the «Journées de «passeports vacances» Lectures Inauguration of the hall of the Génopode la recherche en (July and August) «continuing Center for Investigation (until December 2006) génétique» education» and Research on Sleep (CIRS) UNIL Second CIG Installation of the Mouse open house days retreat in Metabolic Evaluation Saas Fee Facility (MEF) 01 02 03 04 05 06 07 08 09 10 11 12 2007 2006 3 Presentation | Message from the Director Message from the Director WE ARE IN THE MIDST OF A first Faculty of Biology and Medicine in Switzerland. It also resulted in her knowledge of mouse work to help in the design of the CIG ani- REVOLUtiON IN THE BIOLOgicAL the creation of two research axes, one focused on functional genomics mal house. The renovation was officially completed in May 2005, and SciENCES. and the other on human and social sciences. the last group to move in, that of Bernard Thorens, arrived in October 2005, just in time for the inauguration! This revolution, started with the sequen- What form the functional genomics axis of the SVS program would cing of the human genome and then that take was of great interest to W. Wahli (UNIL) and D. Duboule (UNIGE) After several years of relentless work to see the CIG evolve from an of a number of other organisms, conti- who composed, as early as 1999, a first document describing a “Swiss idea, formulated in early 1999, to a reality, Walter Wahli resigned as nues with the spectacular development of Center of Genetics/Genomics”. The missions of this proposed center CIG Director as of September 2005, having decided, I think, that it was technologies that allow the interrogation included cutting–edge research and teaching in genomics, data collec- time for the CIG to “fly with its own wings”, and that it was time for of thousands of molecules in one experiment. We can now not only tion and analysis, the development of core facilities, the development him to go back to teaching and research. We at the CIG are all indeb- compare the genome structures of, for example, a normal cell and a of interactions between fundamental and biomedical research, and the ted to Walter and it is fitting that he be thanked here, in this first bien- cancer cell, but also the expression pattern of an entire genome in dif- facilitation of technology transfer, an ambitious set of goals indeed! nial report of CIG, for having devoted so much effort and energy to the ferent cells, at different times, and under different conditions. Any mo- development of this very unique center! And on my part, I thank him lecule of interest can be analyzed in such a global manner, from mRNAs, In the following year, the project was further studied by two com- for having helped immensely the next CIG director learn the ropes! small RNAs, and proteins to metabolites and other compounds. The mittees, the “groupe de réflexion stratégique lausannois” on the one techniques that allow these types of experiments are powerful, but hand, and a group of three people representing the three SVS pro- The CIG inauguration was closely followed by the success of the popu- they offer a challenge to the individual research laboratory: they rely gram institutions and charged with developing its genomic aspect on lar referendum against the construction of a large animal house, the on costly instruments, unaffordable for the typical research group, and the other hand. These documents already mentioned the Center by its last piece of the CIG project, that was to be built underground on the on highly specialized know–how, and this not only for the generation present name, the Center for Integrative Genomics, and mentioned its south side of the Génopode. This was indeed a depressing moment for of the data but also for their analysis. location in the Pharmacy Building of the UNIL. The CIG was viewed the just inaugurated CIG and was to have profound long–term conse- as a place where genetic models then absent at the UNIL would be quences for the UNIL at large, all of which have yet to be fully grasped. It is in the context of this biological revolution that the Center for Inte- introduced, where bioinformatics would be developed, and where core One consequence was the impossibility for the CIG to develop further grative Genomics was created, a center combining research groups facilities would be established. The second document described the research using the mouse as an animal model, and another was the working on functional genomics with core facilities offering, not only CIG as a new type of structure, perhaps a foundation, co–owned by greatly increased difficulty to regroup basic research on the Dorigny to the Center itself but to the entire surrounding region, the latest tech- the three SVS members. campus. It is with these new elements that the CIG completed its first nologies in genome analyses. The Center was officially inaugurated on year in the Génopode. the 27th of October 2005. The inauguration was followed on the 28th In 2001, a final report was presented to the Rectorate of the UNIL by a by the inaugural CIG Symposium “Genomics, a new road for science group composed of professors from the Faculty of Sciences and from With all its groups now in a single building, the CIG could start taking and society”. These public events that marked the birth of the CIG the Faculty of Medicine. One of the important points of this report was care of recruiting new colleagues. One of the first undertakings was were the culmination of an enormous amount of work that involved the realization that the financing of the CIG, originally imagined as pro- the organization, in large part through the efforts of C. Fankhauser, many scientists in the Lemanic region. vided by the three SVS institutions, would in fact be provided by the A. Reymond, and B. Thorens, of a seminar series in which we invited a UNIL; this led to the eventual incorporation of the CIG into the UNIL as number of young people eligible to apply for a “professeur boursier” The conception of the CIG was intimately linked to the project “Sci- a department of its Faculty of Biology and Medicine. position to present their work and meet CIG faculty. A few months ence, Vie, Société” (SVS), in which, in an unprecedented collaborative after this recruitment effort, a second recruitment was launched to fill effort, the Universities of Lausanne (UNIL) and Geneva (UNIGE), and In 2002, Walter Wahli was appointed the founding director of the CIG, our last CIG faculty position. The recruiting committee included profes- the EPFL (Ecole Polytechnique Fédérale de Lausanne) agreed to redis- and in Autumn 2004, work started in the building now known as the sors S. Antonarakis (UNIGE), M. Swartz (EPFL), J. Beckmann, L. Keller, tribute some of their competences to avoid redundancies and optimize Génopode to prepare it for the move of the first CIG groups. Several P. Moreillon, J. Tschopp, and myself, as well as M. Haenni who re- the use of resources. The SVS project was developed in the years 2000 people gave a lot of their time to the transformation of the Pharma- presented the “corps intermédiaire” and L. Baratali who represented and 2001 and resulted in the transfer of the UNIL sections of Che- cy Building into the Génopode, in particular Liliane Michalik, the de- the students (all UNIL). The committee was presided by I. Stamenko- mistry, Mathematics, and Physics to the EPFL, in the fusion of the UNIL legate of the Rectorate to the renovation of the building, who worked vic (UNIL).
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