Biology subjects

Tortora, M. M.

Publications and source records attributed to Tortora, M. M..

3 recordsLinked to original sources

bioRxiv2024

DNA replication and polymer chain duplication reshape the genome in space and time

In eukaryotes, DNA replication constitutes a complex process whereby multiple origins are stochastically fired, and from which the replication machinery proceeds along chromosomes to achieve the faithful synthesis of two identical copies of the genome during the S-phase of the cell cycle. Experimental evidence show a functional correlation between the dynamics of replication and the spatial organization of the genome inside cell nuclei, suggesting that the process of replicating DNA may impact chromosome folding. However, the theoretical and mechanistic bases of such an hypothesis remain elusive. To address that question, we propose a quantitative, minimal framework that integrates the dynamics of replication along a polymer chain by accounting explicitly for the progression of the replication machinery and the resulting formation of sister chromatids. By systematically characterizing the 3D structural consequences of replication, and of possible interactions between active replication machineries, we show that the formation of transient loops may potentially impact chromosome organization across multiple temporal and spatial scales, from the level of individual origins to that of the global polymer chain. Comparison with available microscopy and chromosome conformation capture data in yeast suggests that a replication-dependent loop extrusion process may be acting in vivo, and may shape chromosomes as loose polymer bottle-brushes during the S-phase. Lastly, we explore the post-replication relative organization of sister chromatids and demonstrate the emergence of catenations and intertwined structures, which are regulated by the density of fired origins.

biophysics↗

bioRxiv2023

Topological constraints and finite-size effects in quantitative polymer models of chromatin organization

Polymer physics simulations have provided a versatile framework to quantitatively explore the complex mechanisms driving chromosome organization. However, simulating whole chromosomes over biologically-relevant timescales at high resolution often constitutes a computationally-intensive task -- while genes or other regions of biological interest may typically only span a small fraction of the full chromosome length. Conversely, only simulating the sub-chromosomal region of interest might provide an over-simplistic or even wrong description of the mechanism controlling the 3D organization. In this work, we characterize what should be the minimal length of chromosome to be simulated in order to correctly capture the properties of a given restricted region. In particular, since the physics of long, topologically-constrained polymers may significantly deviate from those of shorter chains, we theoretically investigate how chromosomes being a long polymer quantitatively affects the structure and dynamics of its sub-segments. We show that increasing the total polymer length impacts on the topological constraints acting on the system and thus affects the compaction and mobility of sub-chains. Depending on the entanglement properties of the system, we derive a phenomenological relation defining the minimal total length to account for to maintain a correct topological regime. We finally detail the implications of these conclusions in the case of several specific biological systems. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=85 SRC="FIGDIR/small/545312v2_ufig1.gif" ALT="Figure 1"> View larger version (15K): org.highwire.dtl.DTLVardef@2c8a4eorg.highwire.dtl.DTLVardef@2c1241org.highwire.dtl.DTLVardef@1628d64org.highwire.dtl.DTLVardef@130dd77_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2022

Liquid-liquid phase separation recapitulates the thermodynamics and kinetics of heterochromatin formation

The spatial segregation of pericentromeric heterochromatin (PCH) into distinct, membrane-less nuclear compartments involves the binding of Heterochromatin Protein 1 (HP1) to H3K9me2/3-rich genomic regions. While HP1 exhibits liquid-liquid phase separation properties in vitro, its mechanistic impact on the structure and dynamics of PCH condensate formation in vivo remains largely unresolved. Here, using biophysical modeling, we systematically investigate the mutual coupling between self-interacting HP1-like molecules and the chromatin polymer. We reveal that the specific affinity of HP1 for H3K9me2/3 loci facilitates coacervation in nucleo, and promotes the formation of stable PCH condensates at HP1 levels far below the concentration required to observe phase separation in purified protein assays in vitro. These heterotypic HP1-chromatin interactions give rise to a strong dependence of the nucleoplasmic HP1 density on HP1-H3K9me2/3 stoichiometry, consistent with the thermodynamics of multicomponent phase separation. The dynamical crosstalk between HP1 and the viscoelastic chromatin scaffold also leads to anomalously-slow equilibration kinetics, which strongly depend on the genomic distribution of H3K9me2/3 domains, and result in the coexistence of multiple long-lived, microphase-separated PCH compartments. The morphology of these complex coacervates is further found to be governed by the dynamic establishment of the underlying H3K9me2/3 landscape, which may drive their increasingly abnormal, aspherical shapes during cell development. These findings compare favorably to 4D microscopy measurements of HP1 condensates that we perform in live Drosophila embryos, and suggest a general quantitative model of PCH formation based on the interplay between HP1-based phase separation and chromatin polymer mechanics. SIGNIFICANCE STATEMENTThe compartmentalization of pericentromeric heterochromatin (PCH), the highly-repetitive part of the genome, into membrane-less organelles enriched in HP1 proteins, is critical to both genetic stability and cell fate determination. While HP1 can self-organize into liquid-like condensates in vitro, the roles of HP1 and the polymer chromatin in forming 3D PCH domains in vivo are still unclear. Using molecular simulations, we show that key kinetic and thermodynamic features of PCH condensates are consistent with a phase-separation mode of organization driven by the genomic distribution of methylated domains and HP1 self-attraction and affinity for heterochromatin. Our predictions are corroborated by live-microscopy performed during early fly embryogenesis, suggesting that a strong crosstalk between HP1-based phase separation and chromosome mechanics drive PCH condensate formation.

biophysics↗