Nucleosome geometry and internucleosomal interactions control the chromatin fiber conformation.

Biophysical Journal
Nick KepperKarsten Rippe

Abstract

Based on model structures with atomic resolution, a coarse-grained model for the nucleosome geometry was implemented. The dependence of the chromatin fiber conformation on the spatial orientation of nucleosomes and the path and length of the linker DNA was systematically explored by Monte Carlo simulations. Two fiber types were analyzed in detail that represent nucleosome chains without and with linker histones, respectively: two-start helices with crossed-linker DNA (CL conformation) and interdigitated one-start helices (ID conformation) with different nucleosome tilt angles. The CL conformation was derived from a tetranucleosome crystal structure that was extended into a fiber. At thermal equilibrium, the fiber shape persisted but relaxed into a structure with a somewhat lower linear mass density of 3.1 +/- 0.1 nucleosomes/11 nm fiber. Stable ID fibers required local nucleosome tilt angles between 40 degrees and 60 degrees. For these configurations, much higher mass densities of up to 7.9 +/- 0.2 nucleosomes/11 nm fiber were obtained. A model is proposed, in which the transition between a CL and ID fiber is mediated by relatively small changes of the local nucleosome geometry. These were found to be in very good agreement wit...Continue Reading

References

Jun 20, 1992·Journal of Molecular Biology·P H DravesJ Widom
Feb 1, 1992·Proceedings of the National Academy of Sciences of the United States of America·J Widom
Jan 25, 1992·Nucleic Acids Research·J O ThomasJ T Finch
Aug 1, 1990·Journal of Biomolecular Structure & Dynamics·S I DimitrovI G Pashev
Aug 1, 1990·Journal of Biomolecular Structure & Dynamics·M KubistaB Nordén
Nov 1, 1987·Proceedings of the National Academy of Sciences of the United States of America·S E Gerchman, V Ramakrishnan
Jul 15, 1980·Journal of Molecular Biology·P J Butler, J O Thomas
Aug 1, 1994·Biophysical Journal·J Garcia de la TorreJ J Lopez Cascales
Oct 1, 1993·Proceedings of the National Academy of Sciences of the United States of America·C L WoodcockN Whitaker
Feb 1, 1996·Journal of Molecular Graphics·W HumphreyK Schulten
Oct 1, 1996·Proceedings of the National Academy of Sciences of the United States of America·K van Holde, J Zlatanova
Jan 1, 1997·Critical Reviews in Eukaryotic Gene Expression·V Ramakrishnan
Apr 29, 1998·Biochemistry·J R Daban, A Bermúdez
Jun 13, 1998·The Journal of Biological Chemistry·L HoweJ Ausió
May 20, 1998·Biophysical Journal·J ZlatanovaK van Holde
Nov 25, 1998·Proceedings of the National Academy of Sciences of the United States of America·J BednarC L Woodcock
Dec 10, 1998·Nature Structural Biology·M Vignali, J L Workman
Mar 24, 1999·Trends in Biochemical Sciences·A Travers
Jan 5, 2000·Proceedings of the National Academy of Sciences of the United States of America·Y Cui, C Bustamante
Dec 12, 2001·Trends in Biochemical Sciences·K Rippe
Feb 16, 2002·Science·Job DekkerNancy Kleckner
May 4, 2002·Annual Review of Biophysics and Biomolecular Structure·Jeffrey C Hansen
May 23, 2002·Biophysical Journal·Gero Wedemann, Jörg Langowski
Jul 18, 2002·Biochemistry·Naila M MamoonSusan E Wellman
Aug 2, 2002·EMBO Reports·Frédéric CatezMichael Bustin
Jul 11, 2003·Nucleic Acids Research·M M Srinivas BharathM R S Rao
Aug 25, 2004·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Boris MergellHelmut Schiessel
May 28, 2005·Proceedings of the National Academy of Sciences of the United States of America·Jian SunTamar Schlick
Aug 18, 2005·The Journal of Biological Chemistry·J Felix KepertKarsten Rippe
Sep 15, 2005·Nature Reviews. Genetics·Duncan SproulWendy A Bickmore
Feb 8, 2006·Nature Structural & Molecular Biology·David T BrownTom Misteli
Mar 1, 2006·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·Karolin Luger
Mar 1, 2006·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·Christopher L WoodcockYuhong Fan
Mar 15, 2006·The Journal of Biological Chemistry·Jacek MazurkiewiczKarsten Rippe
Mar 17, 2006·Current Opinion in Structural Biology·Christopher L Woodcock
Apr 18, 2006·Proceedings of the National Academy of Sciences of the United States of America·Philip J J RobinsonDaniela Rhodes
May 23, 2006·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Frank AumannJörg Langowski

❮ Previous
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Citations

Feb 4, 2009·European Biophysics Journal : EBJ·Isaac GállegoJoan-Ramon Daban
Mar 21, 2009·The Journal of Physical Chemistry. a·Gaurav Arya, Tamar Schlick
Jun 23, 2012·Nature Reviews. Molecular Cell Biology·Karolin LugerDavid J Tremethick
Apr 21, 2009·Nature Structural & Molecular Biology·Maarten KruithofJohn van Noort
Aug 5, 2009·Proceedings of the National Academy of Sciences of the United States of America·Sergei A GrigoryevTamar Schlick
Apr 27, 2013·Journal of Biochemistry·Hajime KimuraTakashi Ohyama
Mar 1, 2011·Nucleic Acids Research·Georgi V PachovRebecca C Wade
Dec 21, 2012·Nucleic Acids Research·Jun-ichi Nishikawa, Takashi Ohyama
Nov 8, 2008·PLoS Genetics·Tobias WarneckeLaurence D Hurst
Dec 21, 2010·PLoS Genetics·Christine VoglerRobert Schneider
Feb 7, 2012·Current Opinion in Structural Biology·Nikolay KorolevLars Nordenskiöld
Jun 28, 2011·Micron : the International Research and Review Journal for Microscopy·Joan-Ramon Daban
Jul 20, 2010·Progress in Biophysics and Molecular Biology·Vladimir B Teif, Klemen Bohinc
Mar 20, 2010·Biophysical Chemistry·Anita ScipioniPasquale De Santis
Nov 25, 2014·Biophysical Journal·Oliver MüllerGero Wedemann
Jul 29, 2008·Biophysical Journal·René StehrGero Wedemann
Nov 4, 2010·Biophysical Journal·Philipp M DiesingerDieter W Heermann
Dec 16, 2010·Biophysical Journal·Elena F KosloverAndrew J Spakowitz
Mar 13, 2016·FEBS Letters·Chenyi WuAndrew Travers
Aug 17, 2010·Journal of Molecular Biology·Ognjen PerišićTamar Schlick
May 21, 2015·Biophysical Journal·Davood Norouzi, Victor B Zhurkin
Aug 30, 2008·Biochimica Et Biophysica Acta·Malte WachsmuthKarsten Rippe
Sep 23, 2010·Biophysical Journal·Nikolay KorolevLars Nordenskiöld
Jun 28, 2008·Proceedings of the National Academy of Sciences of the United States of America·Andrew RouthDaniela Rhodes
Jul 31, 2016·BMC Genomics·Guénola DrillonAlain Arneodo
Mar 10, 2011·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Vladimir B Teif, Karsten Rippe
Apr 11, 2019·Nucleic Acids Research·Ognjen PerišićTamar Schlick
Mar 18, 2010·Journal of Biomolecular Structure & Dynamics·Gaurav AryaSergei A Grigoryev
Dec 2, 2014·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Jean-Baptiste BouléChristophe Lavelle
Jun 21, 2019·Nucleic Acids Research·Chenyi Wu, Andrew Travers
Feb 6, 2020·Annual Review of Physical Chemistry·Mehmet Ali ÖztürkRebecca C Wade
Nov 28, 2008·Critical Reviews in Biochemistry and Molecular Biology·Martijn S LuijsterburgRemus Th Dame
May 7, 2010·The Journal of Biological Chemistry·Eric M GeorgeDavid T Brown
Mar 5, 2020·Nucleic Acids Research·Dustin C Woods, Jeff Wereszczynski
Jan 8, 2015·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Vladimir B TeifKarsten Rippe

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