Giada Forte
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View article: Bridging-Induced Phase Separation and Loop Extrusion Drive Noise in Chromatin Transcription
Bridging-Induced Phase Separation and Loop Extrusion Drive Noise in Chromatin Transcription Open
Cell-to-cell heterogeneity in transcription, or transcriptional noise, is important in cellular development and in disease. The molecular mechanisms driving it are, however, elusive and ill-understood. Here, we use computer simulations to …
View article: Bridging-mediated compaction of mitotic chromosomes
Bridging-mediated compaction of mitotic chromosomes Open
Within living cells, chromosome shapes undergo a striking morphological transition, from loose and uncondensed fibers during interphase to compacted and cylindrical structures during mitosis. ATP driven loop extrusion performed by a specia…
View article: Cluster size determines morphology of transcription factories in human cells
Cluster size determines morphology of transcription factories in human cells Open
Transcription is a fundamental cellular process, and the first step of gene expression. In human cells, it depends on the binding to chromatin of various proteins, including RNA polymerases and numerous transcription factors (TFs). Observa…
View article: Cluster size determines morphology of transcription factories in human cells
Cluster size determines morphology of transcription factories in human cells Open
Transcription is a fundamental cellular process, and the first step of gene expression. In human cells, it depends on the binding to chromatin of various proteins, including RNA polymerases and numerous transcription factors (TFs). Observa…
View article: Modelling transcriptional silencing and its coupling to 3D genome organisation
Modelling transcriptional silencing and its coupling to 3D genome organisation Open
Using 3D simulations, this study uncovers how distinct gene silencing mechanisms reshape chromatin, modulate gene expression noise, and drive unique transcription factor cluster patterns—revealing hidden dynamics of genome regulation.
View article: Modeling the 3D Spatiotemporal Organization of Chromatin Replication
Modeling the 3D Spatiotemporal Organization of Chromatin Replication Open
We propose a polymer model to investigate the dynamics of chromatin replication in three dimensions (PolyRep). Our results indicate that replication complexes, the replisomes, may self-assemble during the process and replicate chromatin by…
View article: Bridging-Induced Phase Separation and Loop Extrusion Drive Noise in Chromatin Transcription
Bridging-Induced Phase Separation and Loop Extrusion Drive Noise in Chromatin Transcription Open
Transcriptional noise, or heterogeneity, is important in cellular development and in disease. The molecular mechanisms driving it are, however, elusive and ill-understood. Here, we use computer simulations to explore the role of 3D chromat…
View article: Modelling the 3D spatiotemporal organisation of chromatin replication
Modelling the 3D spatiotemporal organisation of chromatin replication Open
We propose a polymer model for the dynamics of chromatin replication in three dimensional space. Our simulations indicate that both immobile and tracking replisomes may self-assemble during the process, reconciling previous apparently disc…
View article: Bridging condensins mediate compaction of mitotic chromosomes
Bridging condensins mediate compaction of mitotic chromosomes Open
Eukaryotic chromosomes compact during mitosis into elongated cylinders—and not the spherical globules expected of self-attracting long flexible polymers. This process is mainly driven by condensin-like proteins. Here, we present Brownian-d…
View article: Cluster size determines internal structure of transcription factories in human cells
Cluster size determines internal structure of transcription factories in human cells Open
Transcription is a fundamental cellular process, and the first step of gene expression. In human cells, it depends on the binding to chromatin of various proteins, including RNA polymerases and numerous transcription factors (TFs). Observa…
View article: Bridging-mediated compaction of mitotic chromosomes
Bridging-mediated compaction of mitotic chromosomes Open
SUMMARY Eukaryotic chromosomes compact during mitosis and meiosis into elongated cylinders – and not the spherical globules expected of self-attracting long flexible polymers. This process is mainly driven by condensin-like proteins. Here,…
View article: Transcription modulates chromatin dynamics and locus configuration sampling
Transcription modulates chromatin dynamics and locus configuration sampling Open
In living cells the 3D structure of gene loci is dynamic, but this is not revealed by 3C and FISH experiments in fixed samples, leaving a significant gap in our understanding. To overcome these limitations we applied the “highly predictive…
View article: RNA polymerase II is required for spatial chromatin reorganization following exit from mitosis
RNA polymerase II is required for spatial chromatin reorganization following exit from mitosis Open
Following exit from mitosis, RNA Pol II is required for reestablishing 3D genome folding by loading cohesin complexes onto DNA.
View article: Investigating site-selection mechanisms of retroviral integration in supercoiled DNA braids
Investigating site-selection mechanisms of retroviral integration in supercoiled DNA braids Open
We theoretically study the integration of short viral DNA in a DNA braid made up by two entwined double-stranded DNA molecules. We show that the statistics of single integration events substantially differ in the straight and buckled, or p…
View article: RNA polymerase II is required for spatial chromatin reorganization following exit from mitosis
RNA polymerase II is required for spatial chromatin reorganization following exit from mitosis Open
SUMMARY Mammalian chromosomes are three-dimensional entities shaped by converging and opposing forces. Mitotic cell division induces drastic chromosome condensation, but following reentry into the G1 cell cycle phase, condensed chromosomes…
View article: Plectoneme dynamics and statistics in braided polymers
Plectoneme dynamics and statistics in braided polymers Open
Braids composed of two interwoven polymer chains exhibit a "buckling" transition whose origin has been explained through the onset of plectonemic structures. Here we study, by a combination of simulation and analytics, the dynamics of plec…
View article: Statistical Mechanics of Braiding
Statistical Mechanics of Braiding Open
In this thesis we developed a coarse-grained model based on Brownian Dynamics which allowed us to simulate the formation of two-strands braids.
\nThe statics of the buckling transition was deeply investigated confirming previous results ob…
View article: Safety-Critical Manuals for Agricultural Tractor Drivers: A Method to Improve Their Usability
Safety-Critical Manuals for Agricultural Tractor Drivers: A Method to Improve Their Usability Open
This work sets out the planning phases adopted for the first time to put together a manual on injury and accident prevention in the use of farm tractors. The goal is to convey information more effectively than at present, while taking the …