Modeling the 3D conformation of genomes /
Guido Tiana, Luca Giorgetti.
- 1 online resource.
- Series in computational biophysics ; 4 .
Cover; Half Title; Series Page; Title Page; Copyright Page; Contents; Preface; Editor; Contributors; 1: Job Dekker; 1.1 Introduction; 1.2 Chromosome Conformation Capture; 1.3 3C Variants to Obtain Genome-Scale and High-Resolution Chromatin Interaction Matrices; 1.4 Insights Obtained From Chromosome Interaction Data; 1.5 Dynamics and Cell-to-Cell Variation in Chromatin Interactions; 1.6 Polymer Models for Chromosome Folding; 1.7 Mechanisms of Chromosome Folding and Nuclear Organization; 1.8 Future Perspective; Acknowledgments; Part 1: First-Principles Models; 2: Cédric Vaillant and Daniel Jost 2.1 Introduction2.2 3D Chromatin Organization and Epigenomics; 2.3 Epigenome-Driven Phase Separation of Chromatin; 2.3.1 Block copolymer model; 2.3.2 Simulation methods; 2.3.3 Phase diagram of the model: Towards (micro) phase separation; 2.3.4 Comparison to experiments; 2.3.5 A dynamical, out-of-equilibrium and stochastic organization; 2.3.6 Relation to other approaches; 2.4 Role of 3D Organization in Epigenome Stability; 2.4.1 The "Nano-Reactor" hypothesis; 2.4.2 Epigenomic 1D-3D positive feedback; 2.4.3 The living chromatin model; 2.4.4 Stability of one epigenomic domain 2.4.5 Stability of antagonistic epigenomic domains2.4.6 Towards a quantitative model; 2.5 Discussion and Perspectives; Acknowledgments; References; 3: Simona Bianco, Andrea M. Chiariello, Carlo Annunziatella, Andrea Esposito, Luca Fiorillo, AND Mario Nicodemi; 3.1 Introduction; 3.2. The Basic Features of the Strings AND Binders Switch (SBS) Model; 3.2.1 The strings and binders switch model; 3.2.2 The phase diagram of the SBS homopolymer; 3.2.3 A switch-like control of folding; 3.2.4 Critical exponents of the contact probability; 3.3. A Model of Chromatin Folding 3.3.1 The mixture model of chromatin3.3.2 Pattern formation (TADs) in the SBS block copolymer model; 3.4 The SBS Model of the Sox9 Locus in mESC; 3.4.1 Molecular nature of the binding domains; 3.5. Predicting the effects of mutations on genome 3D architecture; 3.6 Conclusions; Acknowledgments; References; 4: Leonid A. Mirny and Anton Goloborodko; 4.1 Introduction; 4.2 Physics of Loop Extrusion and Chromosome Organization; 4.2.1 Loop extrusion during mitosis; 4.2.2 Loop extrusion during interphase; 4.3 Elements of Polymer Simulations; Acknowledgments; References 5: C. A. Brackley, M. C. Pereira, J. Johnson, D. Michieletto, and D. Marenduzzo5.1 Hi-C Experiments: Compartments, Domains And Loops; 5.2 The Transcription Factor Model: The Bridging-Induced Attraction, Protein Clusters and Nuclear Bodies; 5.3 The Transcription Factor Model: The Bridging-Induced Attraction Drives Chromosome Conformation; 5.4 The Active and Diffusive Loop Extrusion Models; 5.5 Some Consequences of the TF and LE Models; Acknowledgments; 6: Fabrizio Benedetti, Dusan Racko, Julien Dorier, and Andrzej Stasiak; 6.1 Introduction
This book provides a timely summary of physical modeling approaches applied to biological datasets that describe conformational properties of chromosomes in the cell nucleus. Chapters explain how to convert raw experimental data into 3D conformations, and how to use models to better understand biophysical mechanisms that control chromosome conformation. The coverage ranges from introductory chapters to modeling aspects related to polymer physics, and data-driven models for genomic domains, the entire human genome, epigenome folding, chromosome structure and dynamics, and predicting 3D genome structure.