SFB 1064:  Chromatin Dynamics

• Subject Area: Biology
• Term: since 2013
• Website: Homepage
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 213249687

The CRC explores the nature of dynamic transitions of chromatin organisation. It aims to understand principles and mechanisms that endow chromatin organisation with diversity, flexibility and plasticity to respond to environmental, metabolic and developmental cues. CRC research strives for an integrated understanding of chromatin structure and function, involving identification and biochemical characterization of enzymes and metabolites, multi-omic analyses and imaging of cells in diverse physiological states and during ontogeny of model organisms. Chromatin-based regulation relies on genome- and locus-specific chromatin organisation. We explore the chromatin landscape along the chromosomes defined by chromatin modification patterns, nucleosome remodelling, histone variants, associated proteome and polymer condensation of the chromatin fibre and how it changes during physiological and experimentally induced cell-fate transitions, nutrient availability and the DNA damage response. We observe how the three fundamental genome functions transcription, replication and maintenance of genome integrity and their unavoidable interference on the chromosome are accompanied by structural adaptation of chromatin. In this third reporting period the CRC two transversal themes provide new viewpoints and opportunities for discovery. One transversal theme can be described as ‘time lines’ in chromatin dynamics, where we consider mechanisms of reversible transitions (‘turnover’), irreversible emergence of stable states (‘trajectory’) and cyclical dynamics (‘cycle’). A second transversal theme considers various aspects of the intersections between local chromatin organisation and cell metabolism. The 23 CRC projects are led by Principal Investigators from four research organisations in Munich: the Ludwig-Maximilians-University, the Helmholtz Zentrum, the Max-Planck-Institute for Biochemistry and the Technical University. The research is supported by central projects on proteomics and bioinformatics. All PhD students are members of an Integrated Research Training Group.

• DFG Programme: Collaborative Research Centres

Current projects

• A01 - Domino nucleosome remodeling complexes and histone H2A.V dynamics in transcription and DNA repair (Project Head Becker, Peter Burkhard )
• A03 - Domino nucleosome remodeling complexes and histone H2A.V dynamics in transcription and DNA repair (Project Head Ladurner, Ph.D., Andreas Gerhard )
• A04 - Genome-wide reconstitution of dynamics in nucleosome positioning, collision, eviction, and histone exchange (Project Head Korber, Philipp )
• A06 - Mechanisms of Regulation and Information Processing by the INO80 Remodeler (Project Head Hopfner, Karl-Peter )
• A11 - Silencing mechanisms of endogenous retroviruses (Project Head Schotta, Gunnar )
• A12 - Histone H4K20 demethylation in cell cycle-controlled differentiation (Project Head Rupp, Ralph A. W. )
• A15 - Structural basis of nucleosome binding and chromatin compaction by PRC1 (Project Head Müller, Jürg )
• A16 - Metabolic coupling of histone modification during chromatin assembly (Project Head Imhof, Axel )
• A17 - Role and Regulation of DNA Modifications (Project Head Leonhardt, Heinrich )
• A20 - Metabolic impact on chromatin dynamics - understanding control of gene expression through metabolic enzymes and their products (Project Head Schneider, Robert )
• A21 - Nutritional reprogramming of chromatin interactions by the glucocorticoid receptor (Project Head Uhlenhaut, Nina Henriette )
• A22 - Coordination and crosstalk of epigenetic pathways via non-catalytic functions of TET proteins (Project Head Bultmann, Sebastian )
• A24 - Identification of the molecular and biophysical determinants controlling heterochromatin formation and silencing in the mouse embryo (Project Head Torres-Padilla, Maria Elena )
• A26 - Establishment and Role of Chromatin Structure around Chromosome Replication Origins (Project Head Kurat, Christoph )
• A27 - Cell Cycle-Dependent Regulation of the ORC-associated Protein LRWD1 by Phosphorylation of an Intrinsically Disordered Domain (Project Head Bartke, Till )
• A28 - Characterization of the chromatin organization response to food deprivation in the intestine of C. elegans (Project Head Cabianca, Ph.D., Daphne Selvaggia )
• A29 - Compositional and structural analysis of DNA replication origins by locus-specific chromatin isolation (Project Head Hamperl, Stephan )
• A30 - Propagation of active chromatin states in embryos via histone modifications (Project Head Hörmanseder, Eva )
• A32 - Protein and phosphorylation nuclear dynamics in time and space and its modulation by metabolism (Project Head Robles Martinez, Ph.D., Maria S. )
• A33 - The role of chromatin in the establishment of inter-chromosomal DNA-DNA interactions (Project Head Siegel, Tim Nicolai )
• A34 - Detection and repair of covalent DNA-histone crosslinks (Project Head Stingele, Julian )
• A35 - Functional analysis and targeted manipulation of chromatin dynamics on mammalian rRNA genes and Nucleolar Organizer Regions (NORs) (Project Head Stricker, Stefan )
• MGK - Integrated Research Training Group (IRTG) (Project Heads Böke, Jörn ;  Korber, Philipp )
• Z01 - Central Tasks (Project Head Becker, Peter Burkhard )
• Z03 - Chromatin Proteomics (Project Head Imhof, Axel )
• Z04 - The Bioinformatics Core (Project Head Straub, Tobias )

Completed projects

• A02 - Chromatin regulation at promoters and enhancers, a molecular-mechanistic analysis (Project Head Gaul, Ulrike )
• A05 - Dynamic chromatin in replication origin determination (Project Head Schepers, Aloys )
• A07 - Nucleosome spacing in a folded chromatin environment (Project Head Müller-Planitz, Felix )
• A08 - RNA Pol II CTD interactions with chromatin - crosstalk between the codes (Project Head Eick, Dirk )
• A09 - Structure of RNA polymerase II transcribing a nucleosome (Project Head Cramer, Patrick )
• A10 - Deposition mechanisms and functions of novel histone H3 and H2A.Z variants (Project Head Hake, Sandra Brigitte )
• A13 - Epstein-Barr virus DNA acquires cellular chromatin early in infection (Project Head Hammerschmidt, Wolfgang )
• A14 - Analysis of signaling-to-chromatin pathways mediating epigenetic adaptations to cellular stress (Project Head Classen, Anne-Kathrin )
• A19 - Maintenance of chromatin organization by Isw1a during gene transcription (Project Head Smolle, Michaela )
• A23 - Chromatin as limiting factor in the regulation of DNA repair pathway choice (Project Head Pfander, Boris )
• A25 - Role of the nuclear membrane protein Lem2 in retrotransposon silencing and RNA surveillance (Project Head Braun, Sigurd )
• Z02 - Production of monoclonal antibodies (Project Head Kremmer, Elisabeth )
• Z05 - Advanced Light Microscopy (Project Head Neumann, Jürgen )

• Applicant Institution: Ludwig-Maximilians-Universität München
• Participating Institution: Helmholtz Zentrum München; Deutsches Forschungszentrum für Gesundheit und Umwelt; Max-Planck-Institut für Biochemie (MPIB)
• Participating University: Technische Universität München (TUM)
• Spokesperson: Professor Dr. Peter Burkhard Becker