Karsten Rippe

Summary

Affiliation: University of Heidelberg
Country: Germany

Publications

  1. ncbi request reprint Dynamic organization of the cell nucleus
    Karsten Rippe
    Deutsches Krebsforschungszentrum and BIOQUANT, Division of Genome Organization and Function, Im Neuenheimer Feld 280, D 69120 Heidelberg, Germany
    Curr Opin Genet Dev 17:373-80. 2007
  2. pmc Human ISWI chromatin-remodeling complexes sample nucleosomes via transient binding reactions and become immobilized at active sites
    Fabian Erdel
    Research Group Genome Organization and Function, Deutsches Krebsforschungszentrum and BIOQUANT, 69120 Heidelberg, Germany
    Proc Natl Acad Sci U S A 107:19873-8. 2010
  3. doi request reprint Taking into account nucleosomes for predicting gene expression
    Vladimir B Teif
    Research Group Genome Organization and Function, Deutsches Krebsforschungszentrum DKFZ and BioQuant, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
    Methods 62:26-38. 2013
  4. doi request reprint Statistical-mechanical lattice models for protein-DNA binding in chromatin
    Vladimir B Teif
    Research Group Genome Organization and Function, Deutsches Krebsforschungszentrum and BIOQUANT, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
    J Phys Condens Matter 22:414105. 2010
  5. doi request reprint Targeting chromatin remodelers: signals and search mechanisms
    Fabian Erdel
    Research Group Genome Organization and Function, Deutsches Krebsforschungszentrum DKFZ and BioQuant, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
    Biochim Biophys Acta 1809:497-508. 2011
  6. pmc Multiscale analysis of dynamics and interactions of heterochromatin protein 1 by fluorescence fluctuation microscopy
    Katharina P Müller
    Deutsches Krebsforschungszentrum and BIOQUANT, Research Group Genome Organization and Function, Heidelberg, Germany
    Biophys J 97:2876-85. 2009
  7. doi request reprint Force spectroscopy of chromatin fibers: extracting energetics and structural information from Monte Carlo simulations
    Nick Kepper
    Deutsches Krebsforschungszentrum and BIOQUANT, Research Group Genome Organization and Function, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
    Biopolymers 95:435-47. 2011
  8. doi request reprint Modeling nucleosome position distributions from experimental nucleosome positioning maps
    Robert Schöpflin
    Institute for Applied Computer Science, University of Applied Sciences Stralsund, Zur Schwedenschanze 15, Stralsund 18435, Germany and Deutsches Krebsforschungszentrum DKFZ and BioQuant, Im Neuenheimer Feld 280, Heidelberg 69120, Germany
    Bioinformatics 29:2380-6. 2013
  9. doi request reprint Analysis of protein mobilities and interactions in living cells by multifocal fluorescence fluctuation microscopy
    Gerrit Heuvelman
    Research Group Genome Organization and Function, Deutsches Krebsforschungszentrum and BIOQUANT, Heidelberg, Germany
    Eur Biophys J 38:813-28. 2009
  10. ncbi request reprint Histone acetylation increases chromatin accessibility
    Sabine M Görisch
    Division of Molecular Genetics, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
    J Cell Sci 118:5825-34. 2005

Collaborators

Detail Information

Publications35

  1. ncbi request reprint Dynamic organization of the cell nucleus
    Karsten Rippe
    Deutsches Krebsforschungszentrum and BIOQUANT, Division of Genome Organization and Function, Im Neuenheimer Feld 280, D 69120 Heidelberg, Germany
    Curr Opin Genet Dev 17:373-80. 2007
    ..These can rearrange into different functional states in response to specific modifications of the constituting components or changes in the nuclear environment...
  2. pmc Human ISWI chromatin-remodeling complexes sample nucleosomes via transient binding reactions and become immobilized at active sites
    Fabian Erdel
    Research Group Genome Organization and Function, Deutsches Krebsforschungszentrum and BIOQUANT, 69120 Heidelberg, Germany
    Proc Natl Acad Sci U S A 107:19873-8. 2010
    ..Due to the relatively high intranuclear remodeler concentrations cellular response times for repositioning a given nucleosome were calculated to be in the range of tens of seconds to minutes...
  3. doi request reprint Taking into account nucleosomes for predicting gene expression
    Vladimir B Teif
    Research Group Genome Organization and Function, Deutsches Krebsforschungszentrum DKFZ and BioQuant, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
    Methods 62:26-38. 2013
    ..We discuss strategies that address these issues to efficiently compute transcription factor binding in chromatin...
  4. doi request reprint Statistical-mechanical lattice models for protein-DNA binding in chromatin
    Vladimir B Teif
    Research Group Genome Organization and Function, Deutsches Krebsforschungszentrum and BIOQUANT, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
    J Phys Condens Matter 22:414105. 2010
    ..The results have a number of applications for quantitative models for the regulation of gene expression...
  5. doi request reprint Targeting chromatin remodelers: signals and search mechanisms
    Fabian Erdel
    Research Group Genome Organization and Function, Deutsches Krebsforschungszentrum DKFZ and BioQuant, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
    Biochim Biophys Acta 1809:497-508. 2011
    ..This article is part of a Special Issue entitled:Snf2/Swi2 ATPase structure and function...
  6. pmc Multiscale analysis of dynamics and interactions of heterochromatin protein 1 by fluorescence fluctuation microscopy
    Katharina P Müller
    Deutsches Krebsforschungszentrum and BIOQUANT, Research Group Genome Organization and Function, Heidelberg, Germany
    Biophys J 97:2876-85. 2009
    ..These findings impose a number of constraints for the mechanism by which HP1 is able to maintain a heterochromatin state...
  7. doi request reprint Force spectroscopy of chromatin fibers: extracting energetics and structural information from Monte Carlo simulations
    Nick Kepper
    Deutsches Krebsforschungszentrum and BIOQUANT, Research Group Genome Organization and Function, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
    Biopolymers 95:435-47. 2011
    ..We demonstrate how the relative contributions of DNA bending and twisting, nucleosome unstacking and unwrapping the nucleosomal DNA from the histone octamer can be dissected for a given fiber geometry...
  8. doi request reprint Modeling nucleosome position distributions from experimental nucleosome positioning maps
    Robert Schöpflin
    Institute for Applied Computer Science, University of Applied Sciences Stralsund, Zur Schwedenschanze 15, Stralsund 18435, Germany and Deutsches Krebsforschungszentrum DKFZ and BioQuant, Im Neuenheimer Feld 280, Heidelberg 69120, Germany
    Bioinformatics 29:2380-6. 2013
    ..To study the organization of nucleosomes along the genome and to understand the mechanisms of nucleosome translocation, it is necessary to retrieve features of specific conformations from the population average...
  9. doi request reprint Analysis of protein mobilities and interactions in living cells by multifocal fluorescence fluctuation microscopy
    Gerrit Heuvelman
    Research Group Genome Organization and Function, Deutsches Krebsforschungszentrum and BIOQUANT, Heidelberg, Germany
    Eur Biophys J 38:813-28. 2009
    ..The results demonstrate the unique capabilities of the STFM for characterizing the position-dependent translocations and interactions of proteins in the cell...
  10. ncbi request reprint Histone acetylation increases chromatin accessibility
    Sabine M Görisch
    Division of Molecular Genetics, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
    J Cell Sci 118:5825-34. 2005
    ..In mitotic chromosomes, the chromatin exclusion limit was 10-20 nm and independent of the histone acetylation state...
  11. pmc Binding kinetics of human ISWI chromatin-remodelers to DNA repair sites elucidate their target location mechanism
    Fabian Erdel
    Research Group Genome Organization and Function, Deutsches Krebsforschungszentrum and BIOQUANT, Heidelberg, Germany
    Nucleus 2:105-12. 2011
    ..In comparison to the mobility of PCNA (proliferating cell nuclear antigen) that also accumulates at DNA repair sites the specifics of substrate location by chromatin remodelers are further characterized...
  12. doi request reprint Dissecting chromatin interactions in living cells from protein mobility maps
    Fabian Erdel
    Deutsches Krebsforschungszentrum and BIOQUANT, Research Group Genome Organization and Function, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
    Chromosome Res 19:99-115. 2011
    ..The application and synergy effects of the different approaches to obtain protein mobility and interaction maps in the nucleus are illustrated for the analysis of heterochromatin protein 1...
  13. doi request reprint Establishing epigenetic domains via chromatin-bound histone modifiers
    Fabian Erdel
    Deutsches Krebsforschungszentrum DKFZ and BioQuant, Research Group Genome Organization and Function, Im Neuenheimer Feld 280, Heidelberg, Germany
    Ann N Y Acad Sci 1305:29-43. 2013
    ..Thus, locus-specific tethering of these enzymes to chromatin could have the potential to establish, maintain, or modulate epigenetic patterns of characteristic domain size. ..
  14. ncbi request reprint On the mechanism of nucleosome assembly by histone chaperone NAP1
    Jacek Mazurkiewicz
    Molecular Biophysics Group, Kirchhoff Institut für Physik, Ruprecht Karls Universitat Heidelberg, Im Neuenheimer Feld 227, D 69120 Heidelberg, Germany
    J Biol Chem 281:16462-72. 2006
    ..7 +/- 3.7) . 10(3) m(-1) s(-1). The activity of the chromatin remodeling complex ACF did not increase the kinetics of the mononucleosome assembly process...
  15. doi request reprint Coding RNAs with a non-coding function: maintenance of open chromatin structure
    Maïwen Caudron-Herger
    Research Group Genome Organization and Function, Deutsches Krebsforschungszentrum DKFZ and BioQuant, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
    Nucleus 2:410-24. 2011
    ..Based on these results we propose that ciRNAs could act as genome organizing architectural factors of actively transcribed chromatin compartments...
  16. ncbi request reprint Mobility of multi-subunit complexes in the nucleus: accessibility and dynamics of chromatin subcompartments
    Sabine M Görisch
    Division of Molecular Genetics, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
    Histochem Cell Biol 123:217-28. 2005
    ..As reviewed here, properties of the chromatin environment can be identified from these experiments that determine the mobility of Cajal and PML bodies and other supramolecular complexes...
  17. doi request reprint Nuclear architecture by RNA
    Maïwen Caudron-Herger
    Research Group Genome Organization and Function, Deutsches Krebsforschungszentrum and BIOQUANT, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
    Curr Opin Genet Dev 22:179-87. 2012
    ..The latter group comprises largely different structures that require RNA for the formation of active or repressive chromatin compartments with respect to gene expression as well as separating boundaries between these...
  18. pmc Predicting nucleosome positions on the DNA: combining intrinsic sequence preferences and remodeler activities
    Vladimir B Teif
    Research Group Genome Organization and Function, Deutsches Krebsforschungszentrum and BIOQUANT, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
    Nucleic Acids Res 37:5641-55. 2009
    ..Cell 132, p. 887] it was concluded that the redistribution of a nucleosome map to a new state is greatly facilitated if the remodeler complex translocates the nucleosome with a preferred directionality...
  19. doi request reprint Nucleosome mediated crosstalk between transcription factors at eukaryotic enhancers
    Vladimir B Teif
    BioQuant and German Cancer Research Center, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
    Phys Biol 8:044001. 2011
    ..In addition, the proposed model offers explanations for other distance-dependent effects at eukaryotic enhancers...
  20. pmc A lattice model for transcription factor access to nucleosomal DNA
    Vladimir B Teif
    BioQuant and German Cancer Research Center, Heidelberg, Germany
    Biophys J 99:2597-607. 2010
    ..These findings indicate that partial unwrapping of DNA from the histone octamer needs to be taken into account in quantitative models of gene regulation in chromatin...
  21. pmc Retrieving the intracellular topology from multi-scale protein mobility mapping in living cells
    Michael Baum
    Deutsches Krebsforschungszentrum DKFZ and BioQuant, Research Group Genome Organization and Function, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
    Nat Commun 5:4494. 2014
    ..Our method links multi-scale mobility measurements with a quantitative description of intracellular structure that can be applied to evaluate how drug-induced perturbations affect protein transport and interactions. ..
  22. doi request reprint Affinity, stoichiometry and cooperativity of heterochromatin protein 1 (HP1) binding to nucleosomal arrays
    Vladimir B Teif
    Deutsches Krebsforschungszentrum and BIOQUANT, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
    J Phys Condens Matter 27:064110. 2015
    ....
  23. doi request reprint De novo assembly of a PML nuclear subcompartment occurs through multiple pathways and induces telomere elongation
    Inn Chung
    German Cancer Research Center and BioQuant, Research Group Genome Organization and Function, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
    J Cell Sci 124:3603-18. 2011
    ..X phosphorylation, and an increase of the telomere repeat length. These activities were absent after recruitment of the APB factors to a pericentric locus and establish APBs as functional intermediates of the ALT pathway...
  24. pmc Nuclear body movement is determined by chromatin accessibility and dynamics
    Sabine M Görisch
    Division of Molecular Genetics, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, D 69120 Heidelberg, Germany
    Proc Natl Acad Sci U S A 101:13221-6. 2004
    ..This finding suggests that the body mobility reflects the dynamics and accessibility of the chromatin environment, which might target bodies to specific nuclear subcompartments where they exert their biological function...
  25. pmc Nucleosome geometry and internucleosomal interactions control the chromatin fiber conformation
    Nick Kepper
    Deutsches Krebsforschungszentrum and BIOQUANT, Research Group Genome Organization and Function, 69120 Heidelberg, Germany
    Biophys J 95:3692-705. 2008
    ..These were found to be in very good agreement with changes induced by linker histone H1 binding as predicted from the high resolution model structures...
  26. doi request reprint The viscoelastic properties of chromatin and the nucleoplasm revealed by scale-dependent protein mobility
    Fabian Erdel
    Deutsches Krebsforschungszentrum DKFZ and BioQuant, Research Group Genome Organization and Function, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
    J Phys Condens Matter 27:064115. 2015
    ..By calculating how long molecules remember their previous position in dependence on their size, we evaluate how the nuclear environment affects search processes of chromatin targets. ..
  27. ncbi request reprint NAP1 modulates binding of linker histone H1 to chromatin and induces an extended chromatin fiber conformation
    J Felix Kepert
    Kirchhoff Institut für Physik, Molecular Biophysics Group, Ruprecht Karls Universitat Heidelberg, Im Neuenheimer Feld 227, D 69120 Heidelberg, Germany
    J Biol Chem 280:34063-72. 2005
    ..4 +/- 0.8 nm. The findings suggest a possible role of NAP1 in chromatin remodeling processes involved in transcription and replication by modulating the local linker histone content...
  28. pmc DNA sequence- and conformation-directed positioning of nucleosomes by chromatin-remodeling complexes
    Karsten Rippe
    Division of Genome Organization and Function, Deutsches Krebsforschungszentrum and BIOQUANT, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
    Proc Natl Acad Sci U S A 104:15635-40. 2007
    ....
  29. pmc Structure of a bacterial pyridoxal 5'-phosphate synthase complex
    Marco Strohmeier
    Heidelberg University Biochemistry Center, Im Neuenheimer Feld 328, D 69120 Heidelberg, Germany
    Proc Natl Acad Sci U S A 103:19284-9. 2006
    ..Mutagenesis permitted identification of the remote glutaminase and synthase catalytic centers and led us to propose a mechanism whereby ammonia shuttles between these active sites through a methionine-rich hydrophobic tunnel...
  30. pmc Dissecting the nascent human transcriptome by analysing the RNA content of transcription factories
    Maïwen Caudron-Herger
    Deutsches Krebsforschungszentrum DKFZ and BioQuant, D 69120 Heidelberg, Germany
    Nucleic Acids Res 43:e95. 2015
    ..Hence, we verify that transcription factories produce most nascent RNA and confer a regulatory role via their association with a set of specifically-retained non-coding transcripts. ..
  31. pmc Hypermutation of the inactive X chromosome is a frequent event in cancer
    Natalie Jäger
    Division of Theoretical Bioinformatics, German Cancer Research Center DKFZ, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
    Cell 155:567-81. 2013
    ..Our data suggest that hypermutation of the inactive X chromosome is an early and frequent feature of tumorigenesis resulting from DNA replication stress in aberrantly proliferating cells...
  32. pmc Structural insights into tail-anchored protein binding and membrane insertion by Get3
    Gunes Bozkurt
    Heidelberg University Biochemistry Center, Im Neuenheimer Feld 328, D 69120 Heidelberg, Germany
    Proc Natl Acad Sci U S A 106:21131-6. 2009
    ..We postulate that ATP hydrolysis is needed to release Get3 from its receptor. Taken together, our results provide mechanistic insights into posttranslational targeting of TA membrane proteins by Get3...
  33. ncbi request reprint Association states of nucleosome assembly protein 1 and its complexes with histones
    Katalin Fejes Toth
    Kirchhoff Institut für Physik, AG Molekulare Biophysik, Ruprecht Karls Universitat Heidelberg, Im Neuenheimer Feld 227, Heidelberg, Germany
    J Biol Chem 280:15690-9. 2005
    ..Based on these results a model for a cell cycle-dependent shift of the NAP1 dimer-octamer equilibrium is proposed that reflects different biological functions of NAP1...
  34. ncbi request reprint Trichostatin A-induced histone acetylation causes decondensation of interphase chromatin
    Katalin Fejes Toth
    Kirchhoff Institut für Physik, AG Molekulare Biophysik, Ruprecht Karls Universitat Heidelberg, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany
    J Cell Sci 117:4277-87. 2004
    ..An analysis by flow cytometry showed that the addition of TSA led to a significant arrest of cells in S phase and induced apoptosis. The concentration dependence of both processes was studied...
  35. ncbi request reprint Capturing chromosome conformation
    Job Dekker
    Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
    Science 295:1306-11. 2002
    ..Furthermore, functionally distinct AT- and GC-rich domains were found to exhibit different conformations, and a population-average 3D model of chromosome III could be determined. Chromosome III emerges as a contorted ring...