Chromatin

Structure, Dynamics, Regulation

Ralf Blossey

• Publisher: Chapman and Hall/CRC
• Year: 2017
• ISBN:
  9781351646819
• Edition: 1
• Topic: Informatica
• Subtopic: Programmazione di giochi

An invaluable resource for computational biologists and researchers from other fields seeking an introduction to the topic, Chromatin: Structure, Dynamics, Regulation offers comprehensive coverage of this dynamic interdisciplinary field, from the basics to the latest research. Computational methods from statistical physics and bioinformatics are detailed whenever possible without lengthy recourse to specialized techniques.

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Contents

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List of Figures

List of Tables

Preface

CHAPTER 1 ▪ DNA and the nucleosome

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CHAPTER 2 ▪ DNA elasticity and topology

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CHAPTER 3 ▪ Gene regulation without and with chromatin

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CHAPTER 4 ▪ Histones and histone-acting enzymes

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CHAPTER 5 ▪ Regulating chromatin

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CHAPTER 6 ▪ Chromatin beyond transcription: splicing repair and replication

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CHAPTER 7 ▪ Conclusions and Outlook

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Index

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List of Figures

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1.1 The molecular structure of DNA

1.2The X-ray diffraction pattern of DNA

1.3 Schematic views of a nucleosome

1.4 Dinucleotide positioning preferences

1.5 Dinucleotide steps

1.6 Equilibrium constants for nucleosome positioning sequences

1.7 Nucleosomes on a one-dimensonal string

1.8 Statistical positioning of nucleosomes

2.1 Local radius of curvature and torsion

2.2 DNA tethered to a surface and Euler angles

2.3 Tangent vectors to a curve

2.4 An optical trap and measuring tethered DNA

2.5 Supercoiling experiment with magnetic tweezers

2.6 Force-extension curve of λ-phage DNA

2.7 Supercoiling measurements

2.8 Supercoiling due to transcription

2.9 Ribbon representation of a DNA molecule

2.10 Closing the ribbon to a circle

2.11 Closing the ribbon to a circle, but with a twist

2.12 The four possibilities of strand encounters

2.13 Relaxed ribbon, transforming twist into writhe

2.14 Twisted and writhed DNA minicircles

2.15 Single-molecule experiment with topoisomerase II

2.16 Kinetic proofreading scenario of topoisomerase II

2.17 Force-extension curves of a chromatin fiber and a nucleosome

2.18 Schematic of metastable nucleosome conformations upon pulling a chromatin fiber

2.19 Nucleosomes on DNA

2.20 Sketch of the solenoid and zig-zag packing in the 30 nm fiber

2.21 A cellular nucleus

2.22 Chromatin territories: the wool model

2.23 Micro-irradiation experiment on chromatin

2.24 Chromatin structure analysis with polymer models

3.1 A λ-phage infecting E. coli

3.2 Regulatory programming of an operator segment in λ-phage

3.3 Predicted repression curves

3.4 Genome-wide nucleosome occupancy

3.5 Distribution of the apparent chemical potential

3.6 Nucleosome positioning at a housekeeping gene

3.7 The probability distribution P (n) of the self-regulated gene for different parameter values

4.1 Histone structure

4.2 Association of histone modifications with promoters

4.3 Phylogenetic tree of bromodomains

4.4 Bromodomains of GCN5

4.5 Dissociation free energies

4.6 Chromatin remodeler domains

4.7 Cryo-EM reconstruction of the remodeler SWR1

4.8 RSC remodeling assay I: construction

4.9 RSC remodeling assay II: force-time trace

4.10 Speed and processivity of RSC

4.11 FRET assay for ACF remodeling

4.12 Schematic drawing of ACF on a nucleosome

4.13 Three-state model of ACF remodeling

4.14 Extended two-motor model of ACF

4.15 ProbabilitydistributionP(n,t)ofanucleosomeofaDNAstrand

4.16 Motor velocity and effective diffusion constant in the one- motor model

4.17 Motor velocity and effective diffusion constant: ATP dependence of the one-motor model

4.18 Probability density function of remodeling intermediates in the two-motor model

4.19 Motor velocity and effective diffusion constant in the two- motor model

4.20 Effect of sampling between the motors

4.21 Motor velocity in the two-motor model for different ATP concentrations

4.22 Velocity profiles of the continuum Fokker-Planck model and the discrete master equation model for nucleosome remodeling by ACF

4.23 Near steady-state probabilities of the continuum Fokker-Planck model

4.24 Kinetic Monte Carlo of nucleosome positioning with ACF

4.25 Remodeling of a nucleosomal array with ACF

5.1 The regulated nucleosome mobility model

5.2 Kinetic proofreading of chromatin remodeling

5.3 The regulatory region of the IFN-β gene

5.4 Bifurcations in the epigenetic model

5.5 The floral...

Table of contents

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