From a melt of rings to chromosome territories: The role of topological constraints in genome folding

Abstract

We review pro and contra of the hypothesis that generic polymer properties of topological constraints are behind many aspects of chromatin folding in eukaryotic cells. For that purpose, we review, first, recent theoretical and computational findings in polymer physics related to concentrated, topologically-simple (unknotted and unlinked) chains or a system of chains. Second, we review recent experimental discoveries related to genome folding. Understanding in these fields is far from complete, but we show how looking at them in parallel sheds new light on both.

26 pages, 5 figures Added and updated references, corrected typos. Figures 2 and 4 improved, content remained unchanged. Figure 5 edited to contain only human cell data. Figure captions improved to reflect the changes. Some paragraphs in sections IV B 2, IV B 3, IV D, VI F 2, VII are edited or added for clarity and to be up to date. All results are unchanged

References in corpus (7)

• Molecular Dynamics Simulation Study of Nonconcatenated Ring Polymers in a Melt: I. Statics
• Molecular Dynamics Simulation Study of Nonconcatenated Ring Polymers in a Melt: II. Dynamics
• Annealed lattice animal model and Flory theory for the melt of non-concatenated rings: Towards the physics of crumpling
• Viscoelasticity and primitive path analysis of entangled polymer liquids: From f-actin to polyethylene
• Spatial and topological organization of DNA chains induced by gene co-localization
• Pearlnecklacelike chain conformation of hydrophobic polyelectrolyte: a SANS study of partially sulfonated polystyrene in water
• On the Limits of Analogy Between Self-Avoidance and Topology-Driven Swelling of Polymer Loops

Cited by in corpus (55)

• A Topologically Driven Glass in Ring Polymers
• Chromatin Loops as Allosteric Modulators of Enhancer-Promoter Interactions
• Anomalous diffusion in fractal globules
• Dynamics of a polymer in an active and crowded environment
• Active polymer rings: activity-induced collapse and dynamical arrest
• Slowing down of ring polymer diffusion caused by inter-ring threading
• Effects of topological constraints on globular polymers
• Folding and cytoplasm viscoelasticity contribute jointly to chromosome dynamics
• Mixing and segregation of ring polymers: spatial confinement and molecular crowding effects
• Understanding the dynamics of rings in the melt in terms of annealed tree model
• DNA supercoiling in bacteria: state of play and challenges from a viewpoint of physics based modeling
• Contact statistics highlight distinct organizing principles of proteins and RNA
• Viscoelastic properties of ring-linear DNA blends exhibit non-monotonic dependence on blend composition
• Local loop opening in untangled ring polymer melts: A detailed "Feynman test" of models for the large scale structure
• Dynamics and Rheology of Ring-Linear Blend Semidilute Solutions in Extensional Flow: Single Molecule Experiments
• Topological free volume and quasi-glassy dynamics in melt of ring polymers
• Effect of Chain Stiffness on the Structure of Single-Chain Polymer Nanoparticles
• Ring-o-rings: a new category of supramolecular structures with topologically tunable properties
• Large scale chromosome folding is stable against local changes in chromatin structure
• Entanglement length scale separates threading from branching of unknotted and non-concatenated ring polymers in melts
• Single-Chain Nanoparticles under Homogeneous Shear Flow
• Topological and non-topological mechanisms of loops formation in chromosomes: effects on the contact probability
• Persistence Homology Of Entangled Rings
• Miscibility Phase Diagram of Ring Polymer Blends: A Topological Effect
• Vassiliev measures of complexity for open and closed curves in 3-space
• Rheology and Viscoelasticity of Proteins and Nucleic Acids Condensates
• Segment-Scale, Force-Level Theory of Mesoscopic Dynamic Localization and Entropic Elasticity in Entangled Chain Polymer Liquids
• Many-body contacts in fractal polymer chains and fBm trajectories
• Segregated structure of ring polymer melts near the surface: Molecular dynamics simulation study
• Heterogeneous interactions and polymer entropy decide organization and dynamics of chromatin domains
• Computer simulations of melts of ring polymers with non-conserved topology: A dynamic Monte Carlo lattice model
• Viscoelasticity of model interphase chromosomes
• Monte Carlo Simulations of Lattice Models for Single Polymer Systems
• Unified theory of human genome reveals a constrained spatial chromosomal arrangement in interphase nuclei
• Bacterial chromosome organization II: few special cross-links, cell confinement, and molecular crowders play the pivotal roles
• Brownian motion of flexibly-linked colloidal rings
• On the Validity of Effective Potentials in Crowded Solutions of Linear and Ring Polymers with Reversible Bonds
• Compressing $\Theta$-chain in slit geometry
• Unraveling the glass-like dynamic heterogeneity in ring polymer melts: From semi-flexible to stiff chain
• Bacterial chromosome organization I: crucial role of release of topological constraints and molecular crowders
• Fractal and knot-free chromosomes facilitate nucleoplasmic transport
• Entropic competition in polymeric systems under geometrical confinement
• Role of special cross-links in structure formation of bacterial DNA polymer
• Merging 1D and 3D genomic information: Challenges in modelling and validation
• Amoeba Monte Carlo algorithms for random trees with controlled branching activity: efficient trial move generation and universal dynamics
• Topological Constraints in Directed Polymer Melts
• Nanorheology of active-passive polymer mixtures is topology-sensitive
• Motorized Chromosome Models of Mitosis
• Fractional Brownian motion meets topology: statistical and topological properties of globular macromolecules with volume interactions
• Phase separation in soft repulsive polymer mixtures: foundation and implication for chromatin organization
• Entropy of self-avoiding branching polymers: mean field theory and Monte Carlo simulations
• The configurational entropy of random trees
• Entropic organization of topologically modified ring polymers in spherical confinement
• bioSBM: a random graph model to integrate epigenomic data in chromatin structure prediction
• Entropic alignment of topologically modified ring polymers in cylindrical confinement