Biology subjects

Marenduzzo, D.

Publications and source records attributed to Marenduzzo, D..

10 recordsLinked to original sources

bioRxiv2018

Synergy of SMC and Topoisomerase Creates a Universal Pathway to Simplify Genome Topology

Topological entanglements severely interfere with important biological processes. For this reason, genomes must be kept unknotted and unlinked during most of a cell cycle. Type 2 Topoisomerase (TopoII) enzymes play an important role in this process but the precise mechanisms yielding systematic disentanglement of DNA in vivo are not clear. Here we report computational evidence that Structural Maintenance of Chromosomes (SMC) proteins - such as cohesins and condensins - can cooperate with TopoII to establish a synergistic mechanism to resolve topological entanglements: SMC-driven loop extrusion (or diffusion) induces the spatial localisation of entanglements in turn increasing the topological pressure within knotted or linked regions. As a consequence, knots, links and ensuing entanglements may be readily simplified by Topoisomerase enzymes even in crowded and confined conditions. The mechanism we uncover is universal in that it does not qualitatively depend on the specific substrate, whether DNA or chromatin, or on the processivity of the SMC proteins; we thus argue that this synergy may be at work across organisms and throughout the cell cycle.

biophysics↗

bioRxiv2018

Magnetic Polymer Models for Epigenomic Organisation and Phase Separation

The genetic instructions stored in the genome require an additional layer of information to robustly determine cell fate. This additional regulation is provided by the interplay between chromosome-patterning biochemical (\"epigenetic\") marks and threedimensional genome folding. Yet, the physical principles underlying the dynamical coupling between three-dimensional genomic organisation and one-dimensional epigenetic patterns remain elusive. To shed light on this issue, here we study by mean field theory and Brownian dynamics simulations a magnetic polymer model for chromosomes, where each monomer carries a dynamic epigenetic mark. At the single chromosome level, we show that a first order transition describes the unlimited spreading of epigenetic marks, a phenomenon that is often observed in vivo. At the level of the whole nucleus, experiments suggest chromosomes form micro-phase separated compartments with distinct epigenetic marks. We here discover that for a melt of magnetic polymers such a morphology is thermodynamically unstable, but can be stabilised by a nonequilibrium and ATP-mediated epigenetic switch between different monomer states.

biophysics↗

bioRxiv2018

Polymer Simulations of Heteromorphic Chromatin Predict the 3-D Folding of Complex Genomic Loci

Chromatin folded into 3-D macromolecular structures is often analysed by 3C and FISH techniques, but frequently provide contradictory results. Instead, chromatin can be modelled as a simple polymer comprised of a connected chain of units. By embedding data for epigenetic marks (H3K27ac), genomic disruptions (ATAC-seq) and structural anchors (CTCF) we developed a highly predictive heteromorphic polymer (HiP-HoP) model, where the chromatin fibre varied along its length; combined with diffusing protein bridges and loop extrusion this model predicted the 3-D organisation of genomic loci at a population and single cell level. The model was validated at several gene loci, including the complex Pax6 gene, and was able to determine locus conformations across cell types with varying levels of transcriptional activity and explain different mechanisms of enhancer use. Minimal a priori knowledge of epigenetic marks is sufficient to recapitulate complex genomic loci in 3-D and enable predictions of chromatin folding paths.

molecular biology↗

bioRxiv2018

Complementary chromosome folding by transcription factors and cohesin

The spatial organisation of interphase chromosomes is known to affect genomic function, yet the principles behind such organisation remain elusive. Here, we first compare and then combine two well-known biophysical models, the transcription factor (TF) and loop extrusion (LE) models, and dissect their respective roles in organising the genome. Our results suggest that extrusion and transcription factors play complementary roles in folding the genome: the former are necessary to compact gene deserts or \"inert chromatin\" regions, the latter are sufficient to explain most of the structure found in transcriptionally active or repressed domains. Finally, we find that to reproduce interaction patterns found in HiC experiments we do not need to postulate an explicit motor activity of cohesin (or other extruding factors): a model where co-hesin molecules behave as molecular slip-links sliding diffusively along chromatin works equally well.

biophysics↗

bioRxiv2018

Effect of chromatin flexibility on diffusive loop extrusion via molecular slip-links

We use Brownian dynamics simulations to study the formation of chromatin loops through diffusive sliding of molecular slip links, mimicking the behaviour of cohesin-like molecules. We recently proposed that diffusive sliding is sufficient to explain the extrusion of chromatin loops of hundreds of kilo-base-pairs (kbp), which may then be stabilised by interactions between cohesin and CTCF proteins. Here we show that the elasticity of the chromatin fibre strongly affects this dynamical process, and find that diffusive loop extrusion is more efficient on stiffer chromatin regions. Efficiency is also enhanced if cohesin loading sites are close to regions where CTCF is bound. In light of the heterogeneous physical properties of eukaryotic chromatin, we suggest that our results should be relevant to the looping and organisation of interphase chromosomes in vivo.

biophysics↗

bioRxiv2018

Physical Principles of HIV Integration

Certain retroviruses, including HIV, insert their DNA in a non-random fraction of the host genome via poorly understood selection mechanisms. Here, we develop a biophysical model for retroviral integrations as stochastic and quasi-equilibrium topological reconnections between polymers. We discover that physical effects, such as DNA accessibility and elasticity, play important and universal roles in this process. Our simulations predict that integration is favoured within nucleosomal and flexible DNA, in line with experiments, and that these biases arise due to competing energy barriers associated with DNA deformations. By considering a long chromosomal region in human T-cells during interphase, we discover that at these larger scales integration sites are predominantly determined by chromatin accessibility. Finally, we propose and solve a reaction-diffusion problem that recapitulates the distribution of HIV hot-spots within T-cells. With few generic assumptions, our model can rationalise experimental observations and identifies previously unappreciated physical contributions to retroviral integration site selection.

biophysics↗

bioRxiv2017

Shaping Epigenetic Memory via Genomic Bookmarking

Reconciling the stability of epigenetic patterns with the rapid turnover of histone modifications and their adaptability to external stimuli is an outstanding challenge. Here, we propose a new biophysical mechanism that can establish and maintain robust yet plastic epigenetic domains via genomic bookmarking (GBM). We model chromatin as a recolourable polymer whose segments bear non-permanent histone marks (or colours) which can be modified by \"writer\" proteins. The three-dimensional chromatin organisation is mediated by protein bridges, or \"readers\", such as Polycomb Repressive Complexes and Transcription Factors. The coupling between readers and writers drives spreading of biochemical marks and sustains the memory of local chromatin states across replication and mitosis. In contrast, GBM-targeted perturbations destabilise the epigenetic patterns. Strikingly, we demonstrate that GBM alone can explain the full distribution of Polycomb marks in a whole Drosophila chromosome. We finally suggest that our model provides a starting point for an understanding of the biophysics of cellular differentiation and reprogramming.

biophysics↗

bioRxiv2017

Epigenetic Transitions And Knotted Solitons In Stretched Chromatin

The spreading and regulation of epigenetic marks on chromosomes is crucial to establish and maintain cellular identity. Nonetheless, the dynamical mechanism leading to the establishment and maintenance of a given, cell-line specific, epigenetic pattern is still poorly understood. In this work we propose, and investigate in silico, a possible experimental strategy to illuminate the interplay between 3D chromatin structure and epigenetic dynamics. We consider a set-up where a reconstituted chromatin fibre is stretched at its two ends (e.g., by laser tweezers), while epigenetic enzymes (writers) and chromatin-binding proteins (readers) are flooded into the system. We show that, by tuning the stretching force and the binding affinity of the readers for chromatin, the fibre undergoes a sharp transition between a stretched, epigenetically disordered, state and a crumpled, epigenetically coherent, one. We further investigate the case in which a knot is tied along the chromatin fibre, and find that the knotted segment enhances local epigenetic order, giving rise to \"epigenetic solitons\" which travel and diffuse along chromatin. Our results point to an intriguing coupling between 3D chromatin topology and epigenetic dynamics, which may be investigated via single molecule experiments.

biophysics↗

bioRxiv2017

Dynamical Scaling And Phase Coexistence In Topologically-Constrained DNA Melting

There is a long-standing experimental observation that the melting of topologically constrained DNA, such as circular-closed plasmids, is less abrupt than that of linear molecules. This finding points to an important role of topology in the physics of DNA denaturation, which is however poorly understood. Here, we shed light on this issue by combining large-scale Brownian Dynamics simulations with an analytically solvable phenomenological Landau mean field theory. We find that the competition between melting and supercoiling leads to phase coexistence of denatured and intact phases at the single molecule level. This coexistence occurs in a wide temperature range, thereby accounting for the broadening of the transition. Finally, our simulations show an intriguing topology-dependent scaling law governing the growth of denaturation bubbles in supercoiled plasmids, which can be understood within the proposed mean field theory.

biophysics↗

bioRxiv2016

Non-equilibrium chromosome looping via molecular slip-links

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 the behaviour of cohesin-like molecules, which, along with the CTCF protein, stabilize loops which organize the genome. By combining 3D Brownian dynamics simulations and 1D exactly solvable non-equilibrium models, we show that diffusive sliding is sufficient to account for the strong bias in favour of convergent CTCF-mediated chromosome loops observed experimentally. Importantly, our model does not require any underlying, and energetically costly, motor activity of cohesin. We also find that the diffusive motion of multiple slip-links along chromatin may be rectified by an intriguing ratchet effect that arises if slip-links bind to the chromatin at a preferred \"loading site\". This emergent collective behaviour is driven by a 1D osmotic pressure which is set up near the loading point, and favours the extrusion of loops which are much larger than the ones formed by single slip-links.

biophysics↗