D. Michieletto

Single-Molecule Morphology of Topologically Digested Olympic Networks

The paper studies the structure and topology of kinetoplast DNA (kDNA) networks by sequencing and analyzing their morphology after partial digestion with restriction enzymes.

Dynamic ParB-DNA interactions initiate and maintain a partition condensate for bacterial chromosome segregation

This study investigates how ParB-DNA interactions form a dynamic partition condensate for bacterial chromosome segregation using in vitro experiments and simulations.

Loops are Geometric Catalysts for DNA Integration

This study uses Molecular Dynamics simulations to show that DNA loops act as geometric catalysts for DNA integration, influencing site selection and competing with nucleosomes.

Topological Gelation of Reconnecting Polymers

This study investigates topological gelation in semiflexible polymer rings under confinement, showing that stiffness or concentration can trigger a transition from segregated to linked polymer networks.

Single-Molecule Structure and Topology of Kinetoplast DNA Networks

This study presents the first high-resolution single-molecule analysis of kDNA network topology using AFM and simulations, revealing heterogeneous structure and buckling behavior.

ParS-independent recruitment of the bacterial chromosome-partitioning protein ParB

This study shows ParB can recruit itself to DNA independently of parS, enabling long-distance chromosome segregation in bacteria.

Complex small-world regulatory networks emerge from the 3D organisation of the human genome

This study shows that 3D genome organization leads to complex small-world regulatory networks and stochastic transcription, explaining how GWAS results align with overexpression experiments.

Dynamic and Facilitated Binding of Topoisomerase Accelerates Topological Relaxation

This study shows dynamic TopoII binding accelerates topological relaxation of DNA knots, independent of substrate length, by enhancing search efficiency through facilitated diffusion.

Three-Dimensional Loop Extrusion

This paper introduces a 3D 'trans-grabbing' model for loop extrusion that explains Z-loop formation, road-block bypassing, and step sizes larger than SMC size through molecular dynamics simulations.

Topological digestion drives time-varying rheology of entangled DNA fluids

This study investigates DNA-based complex fluids that undergo enzymatic topological changes, showing time-dependent rheological behavior controlled by restriction endonuclease reactions.

Condensin extrudes DNA loops in steps up to hundreds of base pairs that are generated by ATP binding events

This study shows that condensin extrudes DNA loops in steps of up to 500 bp, driven by ATP binding, using magnetic tweezers and simulations.

Non-equilibrium Living Polymers

This paper reviews non-equilibrium living polymers and their potential to inform genome topology regulation in vivo.

Topological Tuning of DNA Mobility in Entangled Solutions of Supercoiled Plasmids

This study combines simulations and experiments to show that supercoiling increases DNA plasmid size and mobility in entangled solutions, challenging existing assumptions about DNA behavior.

Phase separation induced by cohesin SMC protein complexes

Yeast cohesin phase separates with DNA into liquid droplets via ATP-independent DNA bridging.

A nonequilibrium strategy for fast target search on the genome

The paper introduces a nonequilibrium mechanism for efficient DNA target search using chromophoresis, showing it can enhance search efficiency on inaccessible genomic regions.

Magnetic Polymer Models for Epigenetics-Driven Chromosome Folding

This paper uses magnetic polymer models to study how epigenetic modifications affect chromosome folding and gene expression, showing phase transitions and validating results with simulations.

Nonequilibrium Theory of Epigenomic Microphase Separation in the Cell Nucleus

The paper develops a non-equilibrium theory to explain epigenomic microphase separation in the nucleus, showing that non-equilibrium processes stabilize epigenomic domains.

Integrating Transposable Elements in the 3D Genome

This paper introduces a predictive modelling framework using polymer physics to study transposable element integration patterns in the 3D genome.

Synergy of Topoisomerase and Structural-Maintenance-of Chromosomes Proteins Creates a Universal Pathway to Simplify Genome Topology

The paper identifies a synergistic mechanism between Topoisomerase and SMC proteins that simplifies genome topology by localizing entanglements, enabling efficient resolution in various cellular conditions.

Physical Principles of Retroviral Integration in the Human Genome

This study develops a biophysical model to explain retroviral integration site selection in the human genome, showing that physical factors like DNA accessibility and elasticity influence integration preferences.

Lamina and Heterochromatin Direct Chromosome Organisation in Senescence and Progeria

This study uses polymer physics simulations to show that lamina and heterochromatin interactions drive nuclear organization in senescence and progeria through phase transitions.

Shaping Epigenetic Memory via Genomic Bookmarking

This paper introduces a biophysical model of genomic bookmarking to explain how epigenetic domains are maintained and modified through histone marks and protein interactions in Drosophila.

Epigenetic Transitions And Knotted Solitons In Stretched Chromatin

This study investigates how stretching and knotting of chromatin fibers influence epigenetic order through in silico simulations.

Dynamical Scaling And Phase Coexistence In Topologically-Constrained DNA Melting

The paper investigates DNA melting in topologically constrained systems using simulations and theory, finding phase coexistence and topology-dependent scaling laws.

Non-equilibrium chromosome looping via molecular slip-links

This paper introduces a model for chromatin loop formation through diffusive sliding of molecular slip-links, showing it can explain experimental biases without requiring motor activity.