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DNA Dynamics and Nucleosome Positioning Physical aspects of chromatin constituents DNA dynamics and nucleosome positioning Wolfram M¨obius M¨unchen2010 Physical aspects of chromatin constituents DNA dynamics and nucleosome positioning Wolfram M¨obius Dissertation an der Fakult¨atf¨urPhysik der Ludwig{Maximilians{Universit¨at M¨unchen vorgelegt von Wolfram M¨obius aus Eisenach M¨unchen, den 5. M¨arz2010 Erstgutachter: Prof. Dr. Ulrich Gerland Zweitgutachter: Prof. Dr. Jens Michaelis Tag der m¨undlichen Pr¨ufung:6. Mai 2010 Contents Zusammenfassung ix Abstract xi 1. DNA and nucleosomes1 1.1. The structure of DNA...............................2 1.2. DNA and the worm-like chain model.......................4 1.3. DNA as the substrate for nucleosome formation.................6 2. Dynamics of a knotted polymer under strong confinement 13 2.1. Knots........................................ 13 2.2. Polymers under confinement............................ 15 2.3. Knots in strongly confined polymers....................... 16 2.4. Outlook: two overlapping polymers under strong confinement......... 19 2.5. Conclusion..................................... 20 2.6. W. M¨obius,E. Frey, and U. Gerland, Nano Letters, 8, 4518 (2008)...... 21 3. Dynamics of nucleosomal DNA 27 3.1. Introduction to the site exposure mechanism.................. 27 3.1.1. Thermodynamics.............................. 27 3.1.2. Interactions mediated by the nucleosome via site exposure....... 29 3.1.3. Relevance beyond enabling protein binding............... 30 3.2. Dynamics of site exposure............................. 31 3.2.1. Experiments................................ 31 3.2.2. Theoretical description........................... 33 3.3. Outlook: site exposure in nucleosome arrays................... 37 3.4. Optimal flexibility for rotational barrier crossing................ 37 3.5. Conclusion..................................... 39 3.6. W. M¨obius,R. A. Neher, and U. Gerland, Phys. Rev. Lett., 97, 208102 (2006) 41 3.7. R. A. Neher, W. M., E. Frey, U. Gerland, Phys. Rev. Lett., 99, 178101 (2007) 45 4. Nucleosome organization in yeast 49 4.1. Methods to determine nucleosome positions................... 50 4.2. Nucleosome organization close to start sites of genes.............. 51 4.3. Nucleosome positioning determinants....................... 53 4.3.1. Models predicting nucleosome positions based on the DNA sequence. 54 4.3.2. In vitro { in vivo comparisons....................... 56 vi Table of contents 4.4. Statistical positioning............................... 57 4.4.1. Statistical positioning from a biological perspective........... 57 4.4.2. Physics of statistical positioning: the Tonks gas model......... 59 4.4.3. Quantitative test of statistical positioning................ 63 4.5. Outlook: the inverse approach........................... 67 4.6. Conclusion..................................... 69 4.7. W. M¨obiusand U. Gerland, PLoS Comput. Biol., 6, e1000891 (2010)..... 71 A. Simulations and numerical methods 87 A.1. Simulations of polymer dynamics......................... 87 A.2. More general Langevin dynamics......................... 89 A.3. Recursion relations for partition functions.................... 90 Bibliography 93 Danksagung 105 Curriculum Vitae 107 List of Figures 1.1. Structure of double-stranded DNA........................3 1.2. Steps of DNA compaction in a eukaryotic cell..................6 1.3. Microscopic structure of the nucleosome core particle..............7 1.4. Geometries of models proposed to describe the 30-nm fiber.......... 10 2.1. Table of prime knots with at most seven crossings............... 14 2.2. Regimes of confinement for long worm-like chains with self-exclusion..... 15 3.1. Illustration of the site exposure mechanism................... 28 3.2. Equilibrium constants for site exposure, Cooperativity and negative cooperativity mediated by the nucleosome.... 29 3.3. Sketch of dwell times in open and closed nucleosome configurations...... 34 4.1. Typical nucleosome organization close to transcription start sites....... 52 4.2. Particle density for a semi-infinite system of hard rods............. 57 4.3. One realization of a gas or hard rods placed between two fixed particles... 59 4.4. Mapping between binding energy landscape and position dependent density. 69 A.1. Bead-spring model for a polymer......................... 88 A.2. Gas of hard rods on a lattice........................... 90 Zusammenfassung In Eukaryoten findet sich fast die gesamte DNA im Zellkern, jedoch nicht als Polymerkn¨auel, sondern in dicht und kontrolliert gepackter Form. Die DNA bildet einen Komplex mit ver- schiedenen Proteinen, der Chromatin genannt wird. Wichtiger Bestandteil von Chromatin sind Histonproteine, welche eine herausragende Rolle bei der Kompaktifizierung spielen. In regelm¨aßigenAbst¨andensind ungef¨ahr150 Basenpaare fast zweimal um einen Komplex aus acht Histonproteinen gewunden. Die Einheit aus DNA und Histonoktamer bezeichnet man als Nukleosom. Die DNA, welche die einzelnen Nukleosomen verbindet, ist viel k¨urzerals 150 Basenpaare, so dass sich der gr¨oßteTeil der DNA innerhalb von Nukleosomen befindet und damit f¨urdie Bindung von Proteinen und molekularen Maschinen zun¨achst nicht zug¨anglich ist. Alle drei Teile dieser Doktorarbeit besch¨aftigensich mit physikalischen Aspekten von Chromatin beziehungsweise dessen elementaren Bestandteilen: dem Biopolymer DNA, einzel- nen Nukleosomen und schliesslich der Positionierung von vielen Nukleosomen auf der DNA. Als vielleicht bekanntestes Beispiel eines semiflexiblen Polymers ist DNA seit langem Gegen- stand theoretischer und experimenteller Untersuchungen. Seit einigen Jahren ist es m¨oglich, einzelne, m¨oglicherweise verknotete, DNA-Molek¨ulein sehr engen Kan¨alenexperimentell zu beobachten. Motiviert durch solche Experimente untersuchen wir die Dynamik eines lan- gen verknoteten semiflexiblen Polymeres in einem engen Kanal. Wir finden, dass aufgrund thermischer Fluktuationen sowohl die Gr¨oßedes Knotens als auch seine Position entlang der DNA variieren. Die gekoppelte Dynamik von Gr¨oßeund Position f¨uhrt schlussendlich zum Aufl¨osendes Knotens. Unsere Arbeit zeigt, dass die Gr¨oßedes Knotens im Mittel mit der Polymerl¨angevergleichbar ist, kurz bevor der Knoten verschwindet. Eine zus¨atzliche Kraft, angelegt an die Enden des Polymeres, verhindert hingegen ein Wachsen des Knotens, was sich in einem schnelleren Aufl¨osendes Knotens niederschl¨agt. Polymerdynamik steht auch im zweiten Teil dieser Arbeit im Vordergrund, jedoch mo- tiviert von einer g¨anzlich anderen Fragestellung. Wie bereits angedeutet, ist ein großer Teil eukaryotischer DNA in Nukleosomen `verborgen'. Auf den ersten Blick steht somit der gr¨oßte Teil der DNA-Sequenz nicht f¨urdas Binden regulatorischer Proteine zur Verf¨ugung.Jedoch sind Nukleosomen keine statischen Gebilde. Thermische Fluktuationen sorgen daf¨ur,dass sich Teile der DNA von dem Histonkomplex l¨osen k¨onnen. Dieser Prozess wird site expo- sure oder nucleosome breathing genannt und erm¨oglicht das Binden von Proteinen auch an nukleosomale DNA. Mit Hilfe eines vergr¨oberten Modells untersuchen wir die Dynamik der DNA im Nukleosom, insbesondere das Abl¨osenvom und das Binden an den Histonkomplex. Beim Abl¨osenbzw. Binden vollf¨uhrtdie DNA eine Rotationsbewegung, wobei durch ther- mische Fluktuationen induziert eine Energiebarriere ¨uberquert wird. Mit Hilfe eines weiter vereinfachten Modells zeigen wir, dass das Uberqueren¨ der Barriere beschleunigt wird durch die Flexibilit¨atder DNA auf L¨angenskalen deutlich kleiner als die Persistenzl¨ange. Damit k¨onnenwir die Ergebnisse der Simulation unseres Nukleosommodelles verstehen. Zuk¨unftige Experimente werden unsere Vorhersagen best¨atigenoder falsifizieren k¨onnen. In einer Fol- gearbeit ersetzen wir innerhalb unseres vereinfachten Modells das semiflexible Polymer durch eine Scharnierstruktur. Auch hier finden wir, dass bereits kleine Flexibilit¨atengroßen Ein- x 0. Zusammenfassung fluss auf die Rate des Uberquerens¨ der Energiebarriere haben. Zudem wird die Rate bei einer endlichen Flexibilit¨atmaximal. Der dritte und letzte Teil der Arbeit besch¨aftigtsich mit der Positionierung von Nukleo- somen auf der DNA. Die Anordnung von Nukleosomen spielt eine wichtige Rolle bei der Regulation von Genen und wurde in den letzten Jahren intensiv experimentell untersucht, insbesondere f¨urdie Hefe Saccharomyces cerevisiae. Besonderes Augenmerk galt dabei den Regionen um Transkriptionsstartpunkte. Dort findet man (im Mittel) eine nukleosomfreie Region und davon ausgehend zu beiden Seiten Oszillationen der Nukleosomdichte. Wir un- tersuchen die Frage, ob sich die Dichteoszillationen allein mit Hilfe des Tonksgases (d.h., mit einem eindimensionalen System harter St¨abe) beschreiben lassen. Dichteoszillationen treten im Tonksgas in der N¨aheeiner Wand auf, allein aufgrund des Zusammenspiels von Entropie mit der endlichen Breite der St¨abe, ein Effekt, der in der Biologie als \statistische Positionierung" bekannt ist. Unsere systematische quantitative Untersuchung vorhandener experimenteller Daten f¨urHefe [77] zeigt, dass die Dichteoszillationen in der Tat mit dem Tonksgasmodell beschrieben werden k¨onnen.Man muss jedoch unterschiedliche Randbedin- gungen auf beiden Seiten der nukleosomfreien Region in Betracht ziehen. Das Modell des Tonksgases beschreibt die Daten quantitativ, wenn das erste Nukleosom auf der einen Seite der nukleosomfreien Region (downstream) direkt positioniert ist, w¨ahrenddies f¨urdas erste Nukleosom auf der anderen Seite (upstream) nicht gilt. Diese kumulative Doktorarbeit
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