Contributions to the Yearbook of the Max Planck Society

Contributions to the Yearbook of the Max Planck Society


  • Writing DNA methylation in mammalian genomes

    2019 Galonska, Christina; Charlton, Jocelyn; Mattei, Alexandra; Meissner, Alexander
    During the development of an organism, the sequence of its DNA remains unchanged. Gene activity, however, is epigenetically controlled by reversible modifications of the DNA sequence, such as methylation of cytosines. We are working on the development of a system for targeted methylation of the genome at defined positions. Thus, we hope to gain a comprehensive understanding of the role of DNA methylation for the regulation of gene activity, thereby paving the way for the development of new therapeutic approaches for a range of diseases.


  • Molecular dissection of colorectal cancer in pre-clinical models identifies biomarkers predicting sensitivity to EGFR inhibitors

    2018 Risch, Thomas; Abdavi-Azar, Nilofar; Jandrasits, Christine; Amstislavskiy, Vyacheslav; Worth, Catherine L.; Warnatz, Hans-Jörg; Sultan, Marc; Herwig, Ralf; Lehrach, Hans; Yaspo, Marie-Laure; in Kooperation mit dem OncoTrack Konsortium (
    Colorectal carcinomas (CRC) are clinically challenging tumors. To identify novel predictive biomarkers of the therapeutic response, the OncoTrack consortium recruited 106 CRC patients for establishing a biobank of organoids and xenografts models analysed by sequencing and tested in a pre-clinical platform. This unique resource generated a compendium of data for advancing our understanding of CRC. Linking molecular patterns with drug response profiles identified novel biomarkers, including a signature outperforming RAS/RAF mutations in predicting sensitivity to the EGFR inhibitor cetuximab.


  • From possibilities and necessities in epigenetics

    2017 Kinkley, Sarah; Helmuth, Johannes; Chung, Ho-Ryun
    Chromatin modifications provide information above the DNA sequence. The modifications correlate with transcriptional activity, constitute a memory of past decisions, and are thought to provide a state that enables future decisions. The direct measurement of a at the end conflicting combination of chromatin modifications revealed that this combination is not a reflection of molecular potential, as has been thought, but is required to dampen the mutation rate within important genes. Hence, chromatin modifications are key players keeping the DNA sequence in shape and thereby influence evolution.


  • Our genome in 3D - how DNA-folding regulates our genes

    2016 Mundlos, Stefan

    The folding of chromatin is an inherent property of the genome to incorporate the DNA in the cell nucleus. Recent advances using chromosome conformation capture technologies have shown that the genome is folded in structured domains, so-called TADs.  Structural variations, as they often occur in human genetic disease, can interfere with TAD configuration and thus result in altered gene expression and consecutive disease. By re-engineering human aberrations in mice it was shown that TADs and their boundaries are an essential component when interpreting structural variations.


  • Molecular networks in genome and proteome analysis

    2015 Stelzl, Ulrich
    Molecular networks are data-based descriptions of molecular interactions in a cell. Today, a wealth of physiologically relevant protein information is available, obtained from cells under different conditions, from different systems or disease states, including information on genetic variation, protein levels, and post-translational modification. Molecular networks are useful frameworks to distinguish causal from other molecular alterations that are only consequence or do not substantially contribute to the phenotype. This way, molecular networks are also increasingly important for medicine.


  • Long non-coding RNAs as regulators of transcription in human

    2014 Ørom, Ulf
    The "Long non-coding RNAs" (ncRNAs) research group is focusing on the molecular mechanisms of long non-coding RNAs. In particular, the scientists are studying how these transcripts are involved in transcriptional regulation and long-range gene activating functions. The goal is a better understanding of fundamental processes underlying regulation of gene expression. The detailed understanding of the complex class of ncRNAs is limited, however, their importance for gene regulation and disease progression is obvious, following studies in both basic science as well as clinical research.
  • Are there two classes of promoters?

    2014 Vingron, Martin

    A mathematical analysis of human gene promoter sequences shows that these promoters fall into two distinct classes. A number of features correlate with these two classes, suggesting that this distinction is actually a reflection of different regulatory mechanisms. This article summarizes sequence features and biological properties specific for the promoters of the two classes. We explain how a mathematical analysis of whole-genome data could point towards particular biological mechanisms.


  • A truly selfish gene and its supporters

    2013 Herrmann, Bernhard G.
    At fertilisation, we get one set of chromosomes from each parent and, in general, pass on either the paternal or the maternal allele of each gene with equal frequency to our children. This has been taught by Mendel. According to Richard Dawkins’ hypothesis, however, there are selfish genes which are not content with random selection and thus actively promote their increased transmission to the next generation. Evidence for this assumption comes from a mouse gene that is transmitted at a frequency of up to 99% from males to their offspring.
  • Novel systems biology research for a personalized medicine in cancer

    2013 Nietfeld, Wilfried; Lehrach, Hans
    The solution of many medically important aspects depends on the prediction of the behaviour of complex networks, e.g. biological networks active within a tumor but also in other tissues of a patient under complex conditions, for example a particular therapy. So far, it is not possible to predict the success of a specific therapy for a specific patient. We are sequencing the genome of individual cancer patients as well as the genome and transcriptome of their tumor as a basis of a virtual-patient-model, used to predict effect and side effects of specific therapies on the individual patient.


  • Nutrigenomics: natural modulation of gene expression

    2012 Sauer, Sascha
    The scientific focus of the research group lies on the systematic analysis of the modulation of gene and protein expression. This process can be specifically influenced by the interaction of genes and natural products, which are e.g. derived from food. We analyse if and by which mechanisms natural products interfere with genes or gene products. The interdisciplinary approach comprises basic and applied research. The results can be useful for optimised application of natural products to improve various metabolic processes.
  • Better late than never: Genome research turns to rare diseases

    2012 Ropers, Hans-Hilger
    For more than 15 years, genome research has looked for clinically relevant genetic risk factors for common diseases, with meagre results. Now rare disorders come into focus of genome research worldwide. Scientists at the Department of Human Molecular Genetics have successfully dealt with rare genetic disorders for many years. Since the introduction of novel, affordable sequencing techniques it has become possible, in principle, to elucidate the molecular causes of all single gene disorders, with far-reaching consequences for diagnosis, prevention and therapy.


  • Neurodegenerative disorders – from yeast to neurodegenerative processes

    2011 Krobitsch, Sylvia
    Late onset neurodegenerative disorders are progressive disorders, which usually strike during mid-age of affected individuals and with age result in profound neuronal degeneration. Even though these diseases are quite common worldwide, the mechanisms responsible for their pathogenesis are, in most cases, poorly understood, and effective preventative therapies for these devastating disorders are currently not at hand.


  • Give me five! Or six? Or seven?

    2010 Kuss, Pia
    Give me five, high five, hello and good bye - all shown to others with one hand. Certainly everyone knows that this hand comprises five digits. But not everyone is born with exactly five digits. In humans, occasionally hereditary skeletal limb malformations do occur. One malformation, the so-called synpolydactyly, implies that patients are born with additional digits, and those are fused above all. This phenotype develops due to a mutation within the Hoxd13 gene, leading to a lack of retinoic acid and thereby causing uncontrolled cartilage production at wrong sites in the extremity.
  • Protein networks: How protein interactions define shape and function of cells

    2010 Stelzl, Ulrich
    Systematic protein interaction studies are an important part of functional genomics research. A powerful method to decipher protein-protein interaction networks is the yeast two-hybrid system that allows studying the possible interaction of billions of protein pairs. Resulting interactions are represented in protein networks which provide a framework for a systems understanding of the molecular biology of the cell and contribute to medical practice, facilitating identification of human disease genes and an improved interpretation of patient samples and records.


  • Computational modelling of biological processes

    2009 Wierling, Christoph; Herwig, Ralf
    The development of computational models for biological processes opens the possibility to predict new effects of virtual targeted perturbations that can in turn be validated by experimental observations. Such predictions are highly relevant for many practical applications, for example the development of new drugs. Through the last years, the Bioinformatics group has been developing different tools, methods, and databases that support the computational modeling of biological processes, such as the pathway integration database ConsensusPathDB and the modeling system PyBioS.
  • The interconnection of mutagenic and cellular processes during the evolution of mammals

    2009 Arndt, Peter F.
    The huge amount of DNA sequence data derived from a multitude of species, which is at our disposal today, allows comparative studies of genome evolution. Such studies afford to trace back the evolution of genomic DNA sequences and to single out and study the processes that play an important role in changing and shaping the genomes of mammals. The interaction of these processes with other cellular operations is now being investigated and better understood.


  • Interaction networks in protein structures

    2008 Lappe, Michael
    The central topic of the Bioinformatics / Structural Proteomics group is the analysis and prediction of protein structures via networks. Methods are developed to reconstruct the 3D structure from such networks with the aim to identify the determining contacts in these structure networks. This interdisciplinary work provides potential application in protein and drug design.
  • Regulatory networks of trunk formation in mammals

    2008 Herrmann, Bernhard G.
    Mesoderm formation is an important process of embryonic development. It plays an essential role in trunk formation and organ development in mammals. It is controlled by several interacting signalling pathways, which also play an important role in tumour progression. Novel methods are utilized for deciphering the complex regulatory networks comprising thousands of gene products, which control mesoderm formation in the embryo and in tumours.


  • Mathematical models demonstrate the integration of information through cellular signal transduction pathways

    2007 Klipp, Edda
    Molecular approaches reveal components and mechanisms of cellular stress sensing and adaptation. In addition, mathematical modeling has proven to foster the understanding of some basic principles of signal transduction and signal processing as well as of sensitivity and robustness of information perception and cellular response. Main modeling principles are exemplified here for a model organism, the yeast Saccharomyces cerevisiae.
  • Newly recognized functions of monoaminergic hormones: protein monoaminylation

    2007 Walther, Diego J.
    After the finalization of the human genome project, investigations into the transcriptome, proteome, and metabolome have been largely increased, since their concurrence determines the functionality of genes. In this context, recent mechanistic discoveries have induced a kind of “paradigm shift” regarding the mode of action of hormones and widened our understanding of these compounds in cell and gene regulation, particularly when involved in human diseases.


  • Molecular mechanisms of skeletal development

    2006 Mundlos, Stefan
    The research group Development & Disease focuses on the molecular basis by which form and structure of the skeleton are regulated during vertebrate development. Our approach combines research on human genetic disorders with gene function analysis in vitro and in animal models. The studies are carried out in close collaboration with the Institute of Medical Genetics at the Charité, Berlin. Recent advances in the identification and functional analysis of human gene mutations have provided new insights into the biology and pathology of limb malformations and, in particular, in the mechanisms of joint formation. Genetic screens have identified a large number of novel genes that are currently investigated for their role in normal bone development, in disease, and during the regeneration of bone and cartilage.
  • Ribosomes, the cellular production plants of proteins, loose their secrets

    2006 Fucini, Paola; Nierhaus, Knud H.
    Ribosomes translate the genetic DNA information into the amino-acid sequence of proteins and are one of the most complicated structures of the cell. High resolution methods such as X-ray analysis and cryo-electron microscopy as well as improved functional methods have led to a quantum leap in our understanding of the mechanisms of the ribosome by deducing functionality from structure.


  • Analysis of binding sites for the activation of genes

    2005 Vingron, Martin
    Transcription factors play a central role for the regulation of genes. The Department of Computational Biology at the MPI for Molecular Genetics utilizes a panel of mathematical methods to analyze function and interaction of transcription factors in order to achieve new insights into gene regulation.
  • From genetic information to the treatment of diseases

    2005 Lehrach, Hans
    Thanks to the sequencing of the human genome, we have access to detailed and extensive information about the complexity of biological processes. The comparison of the human genome with the chimpanzee genome leeds to a better understanding of molecular processes. This will set up a basis for the advancement of new medical diagnostics and treatments.


  • Molecular basis of hereditary cognitive disorders

    2004 Ropers, Hans-Hilger
    Mental retardation is the biggest unsolved problem of Medical Genetics and a major burden for Health Care. Most severe forms of mental retardation are due to chromosome aberrations and gene defects, but so far, only a small proportion of these defects is known. For the mapping and identification of the relevant genetic factors we employ four different complementary strategies: i. investigation of patients with balanced chromosome rearrangements; ii. development and application of methods for high-resolution detection of unbalanced changes in the DNA; iii. systematic search for mutations in families with X-linked mental retardation; and iv. mapping of autosomal recessive gene defects by identifying homozygous genome segments in children of consanguineous parents. During recent years we have already identified numerous molecular causes of cognitive disorders. The characterization of these genes promises major progress for the diagnosis and prevention of mental retardation as well as new insights into normal and disturbed brain development and function.
  • Regulatory networks during embryogenesis of vertebrates

    2004 Herrmann, Bernhard G.
    The development of the body anlage with its organs is controlled by a multitude of complex regulatory mechanisms which follow a strict order. On top of these processes is the formation of mesenchyme, an event with similarities to metastasis formation of tumors. Novel methods are utilized to unravel regulatory networks controlling mesenchyme formation and tissue differentiation.
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