148 citations · 1k across the 43 of their papers we have counts for
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Polymer Modelling Predicts Chromosome Reorganisation in Senescence
Michael Chiang, Davide Michieletto, Chris A. Brackley +4
Lamina-associated domains (LADs) cover a large part of the human genome and are thought to play a major role in shaping the nuclear architectural landscape. Here, we perform polyme…
Simulating topological domains in human chromosomes with a fitting-free model
C. A. Brackley, D. Michieletto, F. Mouvet +4
We discuss a polymer model for the 3D organization of human chromosomes. A chromosome is represented by a string of beads, with each bead being "colored" according to 1D bioinforma…
Extrusion without a motor: a new take on the loop extrusion model of genome organization
C. A. Brackley, J. Johnson, D. Michieletto +4
Chromatin loop extrusion is a popular model for the formation of CTCF loops and topological domains. Recent HiC data have revealed a strong bias in favour of a particular arrangeme…
Competition between local erasure and long-range spreading of a single biochemical mark leads to epigenetic bistability
Marco Ancona, Davide Michieletto, Davide Marenduzzo
The mechanism through which cells determine their fate is intimately related to the spreading of certain biochemical (so-called epigenetic) marks along their genome. The mechanisms…
Integrating Transposable Elements in the 3D Genome
Alexandros Bousios, Hans-Wilhelm Nuetzmann, Dorothy Buck +1
Chromosome organisation is increasingly recognised as an essential component of genome regulation, cell fate and cell health. Within the realm of transposable elements (TEs) howeve…
Transcription-driven DNA Supercoiling: Non-Equilibrium Dynamics and Action-at-a-distance
Y. A. G. Fosado, D. Michieletto, C. A. Brackley +1
We study the effect of transcription on the kinetics of DNA supercoiling in 3D by means of Brownian dynamics simulations of a single nucleotide resolution coarse-grained model for…
Non-equilibrium chromosome looping via molecular slip-links
C. A. Brackley, J. Johnson, D. Michieletto +4
We propose a model for the formation of chromatin loops based on the diffusive sliding of a DNA-bound factor which can dimerise to form a molecular slip-link. Our slip-links mimic…
Ephemeral protein binding to DNA shapes stable nuclear bodies and chromatin domains
C. A. Brackley, B. Liebchen, D. Michieletto +3
Fluorescence microscopy reveals that the contents of many (membrane-free) nuclear "bodies" exchange rapidly with the soluble pool whilst the underlying structure persists; such obs…