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Research Report 2015 Max Planck Institute for Molecular Genetics, Berlin MPIMG Research Report 2015 Max Planck Institute for Molecular Genetics, Berlin Max Planck Institute Underground / U-Bahn Bus routes / Buslinien for Molecular Genetics .U3/Oskar-Helene-Heim .M11, 110 - Ihnestr. 63–73 .U3/Thielplatz Saarge münder Str./ 14195 Berlin Urban rail system / S-Bahn Bitscher Str. Germany .S1 / Sundgauer Str. .X10, 115, 285 - Clayallee/Leichhardtstr. or Schützallee .M48, 101 - Berliner Straße/Holländische Genetics (MPIMG) Molecular Max Planck Institute for Report 2015 Research Mühle 4c_U1-U4_maxplanck_Titel_2015.indd 1 13.10.2015 14:29:25 Imprint | Research Report 2015 Published by the Max Planck Institute for Molecular Genetics (MPIMG), Berlin, Germany, Oktober 2015 Editorial Board: Bernhard G. Herrmann & Martin Vingron Coordination: Patricia Marquardt Photos & Scientifi c Illustrations: MPIMG Production: Thomas Didier, Meta Druck Copies: 500 Contact: Max Planck Institute for Molecular Genetics Ihnestr. 63 – 73 14195 Berlin Germany Phone: +49 (0)30 8413-0 Fax: +49 (0)30 8413-1207 Email: [email protected] For further information about the MPIMG, see http://www.molgen.mpg.de Cover image 3D-rendered light sheet micrograph of the caudal end of an E9.5 mouse embryo illustrating the generation of neuroectoderm (green cells) and mesoderm (red cells) from common progenitor cells (yellow cells, mostly located deep in the tissue) during trunk development. The neuroectoderm gives rise to the spinal cord, the mesoderm to the vertebral column, skeletal muscles and other tissues. Picture taken by Frederic Koch, Manuela Scholze, and Matthias Marks, MPIMG. 44c_U1-U4_maxplanck_Titel_2015.inddc_U1-U4_maxplanck_Titel_2015.indd 2 113.10.20153.10.2015 114:29:264:29:26 MPI for Molecular Genetics Research Report 2015 1 Research Report 2015 Max Planck Institute for Molecular Genetics Berlin, September 2015 The Max Plank Institute for Molecular Genetics 2 Ada Yonath, Nobel laureate in chemistry 2009 and former member of the MPIMG, at the celebratory symposium on the occasion of the institute’s 50th anniversary in December 2014. MPI for Molecular Genetics Research Report 2015 Table of contents The Max Planck Institute for Molecular Genetics 7 Department of Developmental Genetics (B.G. Herrmann) 21 Introduction 22 Scientific achievements and findings 23 General information about the whole department 37 Department of Computational Molecular Biology (M. Vingron) 45 Introduction 45 Transcriptional Regulation Group (M. Vingron) 51 Sequencing & Genomics Group (S. Haas) 59 Bioinformatics Group (R. Herwig) 65 Diploid Genomics Group (M. Hoehe) 71 Mechanisms of Transcriptional Regulation Group (S. Meijsing) 79 Research Group Evolutionary Genomics (P. Arndt) 85 General information about the whole department 94 Research Group Development & Disease (S. Mundlos) 113 Introduction 114 Scientific achievements and findings 116 3 Chromosome Rearrangements & Disease group (V. Kalscheuer) 127 General information about the whole research group 133 Otto Warburg Laboratory Max Planck Research Group Epigenomics (H.-R. Chung) 153 Research Group RNA Bioinformatics (A. Marsico) 163 Sofja Kovalevskaja Research Group Long non-coding RNA (U.A. Ørom) 173 BMBF Research Group Nutrigenomics & Gene Regulation (S. Sauer) 183 Max Planck Research Group Regulatory Networks in Stem Cells (E. Schulz) 195 Max Planck Research Group Molecular Interaction Networks (U. Stelzl) 203 Research Group Gene Regulation and Systems Biology of Cancer (M.-L. Yaspo) 215 BMBF Research Group Cell Signaling Dynamics (Z. Zi) 229 Minerva Group Neurodegenerative disorders (S. Krobitsch) 235 The Max Plank Institute for Molecular Genetics Max Planck Fellow Group Efficient Algorithms for Omics Data (K. Reinert) 245 Emeritus Group Vertebrate Genomics (H. Lehrach) 255 Introduction 256 Scientific methods and achievements 259 Project groups within the department 260 General information about the whole department 264 Emeritus Group Human Molecular Genetics (H.-H. Ropers) 309 20 years of human genetics at the MPIMG 310 Scientific activities and results, 2012-2015 312 Epilogue 316 General information about the whole department 319 Scientific services Animal facility 343 Transgenic unit 345 Sequencing core facility 349 Mass spectrometry facility 365 4 Microscopy & Cryo-Electron Microscopy Group 373 IT Group 385 Library 395 Research Support Administration 397 Technical management & workshops 401 MPI for Molecular Genetics Research Report 2015 Foreword It is our pleasure to present the 2015 Research Report of the Max Planck Institute for Molecular Genetics (MPIMG) in Berlin, covering the period from 2009 to mid-2015. Many changes have marked the last years. First of all, the retirement of Hans Lehrach und Hans-Hilger Ropers in late au- tumn of 2014 made a deep cut in our daily life at the institute. Two major departments were closed and many activities of the MPIMG are geared towards the appointment of new directors or are deferred until their arrival. On the other hand, a very positive development has taken place at the Otto Warburg laboratory with five new groups having started since 2011. In 2013, the construction of the long expected tower 3 has been finished and the bioinformaticians and computer scientists of the institute moved in. Immediately afterwards, the refurbishment of tower 2 commenced, promising new and state-of-the-art labs to all our “wet lab” scientists. All 5 refurbishment work as well as the construction of tower 3 has taken place during full research operations, which led to considerable disturbances, in particular of vibration-sensitive experimental work. Founded in 1964, the MPIMG marked its 50th anniversary in 2014 with a large celebratory symposium, bringing together many former and current scientists of the MPIMG. Today, the institute is established as a centre for research at the interface of genome research and genetics, concentrating on genome analysis of humans and other organisms to elucidate cellular processes and genetic diseases. Due to current developments, prompted by the search for two new directors within the institute as well as by the tech- nological advances of the last years, the focus of research at the MPIMG shifts towards the systematic study of gene regulation from a whole-ge- nome viewpoint, leading to the study of gene regulatory networks and their role in development and disease. With this report, we want to give a broad summary of the scientific work of the MPIMG during the last years and describe the ongoing changes. We hope that it will provide a clear im- pression of the institute and the work we are doing here. September 2015 Bernhard G. Herrmann & Martin Vingron The Max Plank Institute for Molecular Genetics 6 Scientific Advisory Board Board of Trustees Board of Directors Bernhard G. Herrmann, Martin Vingron, N.N., N.N. Scientific Coordination, Public Relations Administration, Research Support Patricia Marquardt Managing Director Christoph Krukenkamp Martin Vingron Technical Management & Administration Workshops Christoph Krukenkamp Ulf Bornemann Research Group Dept. of Max Planck Fellow Dept. of Computational Otto Warburg Scientific Services Development & Developmental New Dept. A New Dept. B Emeritus groups Knut Reinert Molecular Biology Christoph Krukenkamp Disease Genetics N.N. N.N. Laboratory Martin Vingron (Freie Universität Berlin) Stefan Mundlos Bernhard G. Herrmann Epigenomics Development & Disease Transcriptional Regulation Vertebrate Genomics Animal Facility Ho-Ryun Chung Stefan Mundlos Martin Vingron Hans Lehrach Ludger Hartmann (MPRG) Chromosome Rearrange- RNA Bioinformatics Sequencing & Genomics Human Molecular Genetics Transgenic Unit ments & Disease Annalisa Marsico Stefan Haas H.-Hilger Ropers Lars Wittler Vera Kalscheuer (MPIMG + FUB) Long Range Gene Long non-coding RNA Bioinformatics Sequencing Facility Regulation Ulf Ørom Ralf Herwig Bernd Timmermann Dario Lupianez (Humboldt Foundation) Regulatory Networks Diploid Genomics in Stem Cells Mass Spectrometry Institute of Medical Genetics Institute of Medical Genetics, Margret Hoehe Edda Schulz David Meierhofer and Human Genetics, Charité - Charité - Universitätsmedizin (MPRG/Minerva) Universitätsmedizin Berlin Berlin Campus Virchow Campus Benjamin Franklin Molecular Mechanisms of Tran- Microscopy & Cryo Electron Interaction Networks Stefan Mundlos Bernhard G. Herrmann scriptional Regulation Microscopy Ulrich Stelzl Sebastiaan Meijsing Thorsten Mielke (MPRG) Gene Regulation & Systems IT Evolutionary Genomics Biology of Cancer Donald Buczek / Peter Peter Arndt Marie-Laure Yaspo Marquardt IMPRS on Computational Cell Signaling Dynamics Biology & Scientific Library Zhike Zi Computing Sylvia Elliger / Praxedis Leitner (BMBF) Fabian Feutlinske Dept. of Mathematics and Computer Science, Freie Universität Berlin Figure 1: Organization chart of the MPIMG, September 2015 MPI for Molecular Genetics Research Report 2015 The Max Planck Institute for Molecular Genetics Structure and organization of the institute At the time of writing this report, the Max Planck Institute for Molecu- lar Genetics (MPIMG) is undergoing a major transition. In late autumn 2014, Hans Lehrach, head of the Department of Vertebrate Genomics, and Hans-Hilger Ropers, head of the Department of Human Molecular Genet- ics, retired and their departments had been closed. The institute together with the respective committee (the Stammkommission) of the Max Planck Society are actively searching for new directors. However, for the time be- ing, the MPIMG lacks two departments. Although we have tried to coun- teract the loss
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