Biology subjects

Bonato, A.

Publications and source records attributed to Bonato, A..

5 recordsLinked to original sources

bioRxiv2026

CpG islands act as topological sinks for transcription-induced DNA supercoiling

Strong evolutionary selection has maintained CpG-dense islands (CGIs) at the promoters of constitutively expressed genes throughout the vertebrate genome, suggesting an important role in regulating DNA topology. Here, using Twist-seq, a psoralen-based approach for quantitative genome-wide profiling of DNA supercoiling, we reveal distinct topological states across human gene promoters. We show that CGI promoters accumulate elevated levels of negative supercoiling relative to non-CGI promoters and define localised topological domains at highly transcribed genes. Integrating genome-wide analyses with reaction-diffusion modelling and coarse-grained molecular dynamics simulations, we find that this behaviour is encoded by the intrinsic physical properties of CGI DNA. The GC-rich sequence context promotes nucleosome depletion and focuses torsional stress onto embedded AT-rich pockets, driving localised DNA melting and plectoneme-tip bubble formation within promoter-proximal nucleosome-free regions. This provides an energetically favourable pathway for redistributing transcription-induced torsional stress through transient strand separation and writhe, consistent with increased ssDNA formation at CGI promoters observed by ssDNA-seq. We propose that CGIs function as sequence-encoded topological sinks that buffer supercoiling while maintaining a promoter architecture permissive for transcription initiation, thereby preserving promoter integrity and genome stability.

molecular biology↗

bioRxiv2022

Topological Gelation of Reconnecting Polymers

DNA recombination is a ubiquitous process that ensures genetic diversity. Contrary to textbook pictures, DNA recombination, as well as generic DNA translocations, occur in a confined and highly entangled environment. Inspired by this observation, here we investigate a solution of semiflexible polymer rings undergoing generic cutting and reconnection operations under spherical confinement. Our setup may be realised using engineered DNA in presence of recombinase proteins or by considering micelle-like components able to form living (or reversibly breakable) polymer rings. We find that in such systems there is a topological gelation transition, which can be triggered by increasing either the stiffness or concentration of the rings. Flexible or dilute polymers break into an ensemble of short, unlinked and segregated rings, whereas sufficiently stiff or dense polymers self-assemble into a network of long, linked and mixed loops, many of which are knotted. We predict the two phases should behave qualitatively differently in elution experiments monitoring the escape dynamics from a permeabilised container. Besides shedding some light on the biophysics and topology of genomes undergoing DNA reconnection in vivo, our findings could be leveraged in vitro to design polymeric complex fluids, e.g., DNA-based complex fluids or living polymer networks, with desired topologies.

biophysics↗

bioRxiv2021

An Inter-strand Loop Extrusion Model

Loop extrusion convincingly describes how certain Structural Maintenance of Chromosome (SMC) proteins mediate the formation of large DNA loops. Yet, most of the existing computational models cannot reconcile recent in vitro observations showing that condensins can traverse each other, bypass large roadblocks and perform steps longer than its own size. To fill this gap, we propose a three-dimensional (3D) "trans-grabbing" model for loop extrusion which not only reproduces the experimental features of loop extrusion by one SMC complex, but also predicts the formation of so-called "Z-loops" via the interaction of two or more SMCs extruding along the same DNA substrate. By performing Molecular Dynamics simulations of this model we discover that the experimentally observed asymmetry in the different types of Z-loops is a natural consequence of the DNA tethering in vitro. Intriguingly, our model predicts this bias to disappear in absence of tethering and a third type of Z-loop, which has not yet been identified in experiments, to appear. Our model naturally explains road-block bypassing and the appearance of steps larger than the SMC size as a consequence of non-contiguous DNA grabbing. Finally, it is the first to our knowledge to address how Z-loops and bypassing might occur in a way that is broadly consistent with existing cis-only 1D loop extrusion models.

biophysics↗

bioRxiv2020

Phase separation induced by cohesin SMC protein complexes

Cohesin is a key protein complex that organizes the spatial structure of chromosomes during interphase. Here, we show that yeast cohesin shows pronounced clustering on DNA in an ATP-independent manner, exhibiting all the hallmarks of phase separation. In vitro visualization of cohesin on DNA shows DNA-cohesin clusters that exhibit liquid-like behavior. This includes mutual fusion and reversible dissociation upon depleting the cohesin concentration, increasing the ionic strength, or adding 1,6-hexanediol, conditions that disrupt weak interactions. We discuss how bridging-induced phase separation can explain the DNA-cohesin clustering through DNA-cohesin-DNA bridges. We confirm that, in vivo, a fraction of cohesin associates with chromatin in yeast cells in a manner consistent with phase separation. Our findings establish that SMC proteins can exhibit phase separation, which has potential to clarify previously unexplained aspects of in vivo SMC behavior and constitute an additional principle by which SMC complexes impact genome organization. One sentence summaryYeast cohesin complex is observed to phase separate with DNA into liquid droplets, which it accomplishes by ATP-independent DNA bridging.

biophysics↗

bioRxiv2019

3D bioprinting of architected hydrogels from entangled microstrands

Hydrogels are an excellent biomimetic of the extracellular matrix and have found great use in tissue engineering. Nanoporous monolithic hydrogels have limited mass transport, restricting diffusion of key biomolecules. Structured microbead-hydrogels overcome some of these limitations, but suffer from lack of controlled anisotropy. Here we introduce a novel method for producing architected hydrogels based on entanglement of microstrands. The microstrands are mouldable and form a porous structure which is stable in water. Entangled microstrands are useable as bioinks for 3D bioprinting, where they align during the extrusion process. Cells co-printed with the microstrands show excellent viability and augmented matrix deposition resulting in a modulus increase from 2.7 kPa to 780.2 kPa after 6 weeks of culture. Entangled microstands are a new class of bioinks with unprecedented advantages in terms of scalability, material versatility, mass transport, showing foremost outstanding properties as a bioink for 3D printed tissue grafts.

bioengineering↗