1st Edition

Modeling the 3D Conformation of Genomes

ISBN 9781138500792
Published January 23, 2019 by CRC Press
370 Pages 87 Color Illustrations

USD $190.00

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Book Description

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.

Table of Contents


Preface vii

Contributors xi

1 Chromosome Folding: Contributions of Chromosome

Conformation Capture and Polymer Physics 1

Job Dekker


2 Modeling the Functional Coupling between 3D Chromatin

Organization and Epigenome 21

Cédric Vaillant and Daniel Jost

3 The Strings and Binders Switch Model of Chromatin 57

Simona Bianco, Andrea M. Chiariello, Carlo Annunziatella, Andrea

Esposito, Luca Fiorillo, and Mario Nicodemi

4 Loop Extrusion: A Universal Mechanism of

Chromosome Organization 69

Leonid A. Mirny and Anton Goloborodko

5 Predictive Models for 3D Chromosome Organization: The

Transcription Factor and Diffusive Loop Extrusion Models 97

C. A. Brackley, M. C. Pereira,

J. Johnson, D. Michieletto, and D. Marenduzzo

6 Introducing Supercoiling into Models of Chromosome Structure 115

Fabrizio Benedetti, Dusan Racko, Julien Dorier, and Andrzej Stasiak

7 Structure and Microrheology of Genome Organization: From

Experiments to Physical Modeling 139

Andrea Papale and Angelo Rosa

8 Analysis of Chromatin Dynamics and Search

Processes in the Nucleus 177

Assaf Amitai and David Holcman

9 Chromosome Structure and Dynamics in Bacteria: Theory and

Experiments 207

Marco Gherardi, Vittore Scolari, Remus Thei Dame, and Marco

Cosentino Lagomarsino


10 Restraint-Based Modeling of Genomes and Genomic Domains 233

Marco Di Stefano and Marc A. Marti-Renom

11 Genome Structure Calculation through Comprehensive Data

Integration 253

Guido Polles, Nan Hua, Asli Yildirim, and Frank Alber

12 Modeling the Conformational Ensemble of Mammalian

Chromosomes from 5C/Hi-C Data 285

Guido Tiana and Luca Giorgetti

13 Learning Genomic Energy Landscapes from Experiments 305

Michele Di Pierro, Ryan R. Cheng, Bin Zhang,

José N. Onuchic, and Peter G. Wolynes

14 Physical 3D Modeling of Whole Genomes: Exploring

Chromosomal Organization Properties and Principles 331

Marco Di Stefano, Jonas Paulsen, Eivind Hovig, and

Cristian Micheletti

15 Index 361

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Guido Tiana, PhD, is Associate Professor of Theoretical Biophysics at the University of Milano. He obtained the PhD at the Niels Bohr Institute (Copenhagen) in 2000 and since then has worked on the physics of complex systems of biological interest, such as proteins, DNA, RNA, chromosomes and genetic networks. The methods come from the realm of statistical mechanics, making heavy use of computational tools and some experimental work.

Luca Giorgetti, PhD, is a group leader at the Friedrich Miescher Institute for Biomedical Research in Basel. He obtained his PhD at the European Institute of Oncology (IEO) and University of Milan followed by a postdoctoral training at the Curie Institute in Paris. He is an expert in combining physical modeling and experimental research in chromosome conformation and transcriptional regulation.