Biology subjects

Carlon, E.

Publications and source records attributed to Carlon, E..

8 recordsLinked to original sources

bioRxiv2026

Obstacle bypassing and intrinsically asymmetric loop extrusion in the segment-capture model of Structural Maintenance of Chromosomes complexes

Structural Maintenance of Chromosomes (SMC) complexes are large protein assemblies that play a central role in chromosomal organization across all domains of life by acting as molecular motors that extrude DNA loops. Although the molecular architecture of SMCs has been characterized in considerable detail, their mechanistic mode of action remains actively debated. One proposed mechanism is the segment-capture model, in which SMC complexes undergo an asymmetric conformational change upon ATP binding and hydrolysis, effectively "pumping" short DNA segments through the SMC ring and thereby enlarging loops. While this model accounts for several experimentally observed features of loop extrusion, it has been questioned in light of experiments showing that SMC complexes can traverse large nanoparticle-sized obstacles on DNA. Moreover, recent experimental advances have provided new insights that extend beyond the original formulation of the model. Here we show that, contrary to previous criticisms, the segment-capture model can naturally account for key features of recent experiments, including the bypass of large obstacles when the SMC hinge acts as a bypass gate. Furthermore, we outline a set of targeted experiments designed to critically test the models predictions, providing a clear path toward resolving outstanding questions about the mechanistic basis of loop extrusion.

biophysics↗

bioRxiv2025

Inferring DNA kinkability from biased MD simulations

In several biological processes, such as looping, supercoiling and DNA-protein interactions, DNA is subject to very strong deformations. While coarse-grained models often approximate DNA as a smoothly bendable polymer, experimental and theoretical studies demonstrated that mechanical stress can induce localized kinks. Here, we employ the Rigid Base Biasing of Nucleic Acids (RBB-NA) algorithm to systematically probe the properties of highly deformed DNA in all-atom simulations of a few dodecamers. A simultaneous bias in bending (roll) and twist is applied locally, to two consecutive base-pairs in the center of the dodecamers. Using umbrella sampling we construct free energy landscapes that reveal sequence-dependent effects for kink formation and quantify the energetic cost of kinking. We identify distinct features of the free energies highlighting anharmonic effects, such as asymmetries in the positive vs. negative roll. Our analysis suggests two distinct kinks characterized either by positive roll and undertwisting (twist-bend kinks) or by negative roll without excess twist (pure bend kinks). The former are frequently observed in DNA-protein structures and expected to be favored in-vivo in negatively supercoiled chromosomes. The latter have been observed in DNA simulations of minicircles and are favored in torsionally constrained DNA.

biophysics↗

bioRxiv2023

Chromatin structure from high resolution microscopy: scaling laws and microphase separation

Recent advances in experimental fluorescence microscopy allow high accuracy determination (resolution of 50 nm) of the 3D physical location of multiple (up to [~] 102) tagged regions of the chromosome. We investigate publicly available microscopy data for two loci of the human Chr.21 obtained from multiplexed FISH methods for different cell lines and treatments. Inspired by polymer physics models, our analysis centers around distance distributions between different tags, aiming to unravel the chromatin conformational arrangements. We show that for any specific genomic site, there are (at least) two different conformational arrangements of chromatin, implying coexisting distinct topologies which we refer to as phase and phase {beta}. These two phases show different scaling behaviors: the former is consistent with a crumpled globule while the latter indicates a confined, but more extended conformation, as a looped domain. The identification of these distinct phases sheds light on the coexistence of multiple chromatin topologies and provides insights into the effects of cellular context and/or treatments on chromatin structure.

biophysics↗

bioRxiv2023

Environmental constraints can explain clutch size differences between urban and forest blue tits (Cyanistes caeruleus): insights from an egg removal experiment

Urban environments present novel ecological challenges to wild species. Understanding whether species responses to urban living are adaptive or maladaptive is critical to predicting the impacts of urbanisation on biodiversity. In birds, urban populations generally exhibit reduced reproductive investment (clutch size) compared to forest populations. However, whether smaller clutches are adaptive, or a result of environmental constraints is unclear. Here, to investigate these two hypotheses, we quantified the ability of urban and forest blue tits (Cyanistes caeruleus) to lay new eggs upon egg removal. Consistent with the constraint hypothesis, our results suggest that urban females do not lay new eggs, at least to the same extent as forest birds. Meanwhile, forest birds laid approximately two additional eggs. As urban blue tits did not lay replacement eggs, our experiment resulted in a brood reduction and nestlings from urban experimental nests had higher survival than those from urban control nests, suggesting that females may be misjudging urban habitat quality and produce a clutch too large to be sustained. Taken together, our results suggest that urban females may experience constraints that limit egg formation and/or exacerbate the trade-off between female survival and egg production. This has important implications for urban green space management.

ecology↗

bioRxiv2021

DNA fluctuations reveal the size and dynamics of topological domains

DNA supercoiling is a key regulatory mechanism that orchestrates DNA readout, recombination, and genome maintenance. DNA-binding proteins often mediate these processes by bringing two distant DNA sites together, thereby inducing (transient) topological domains. In order to understand the dynamics and molecular architecture of protein induced topological domains in DNA, quantitative and time-resolved approaches are required. Here we present a methodology to determine the size and dynamics of topological domains in supercoiled DNA in real-time and at the single molecule level. Our approach is based on quantifying the extension fluctuations - in addition to the mean extension - of supercoiled DNA in magnetic tweezers. Using a combination of high-speed magnetic tweezers experiments, Monte Carlo simulations, and analytical theory, we map out the dependence of DNA extension fluctuations as a function of supercoiling density and external force. We find that in the plectonemic regime the extension variance increases linearly with increasing supercoiling density and show how this enables us to determine the formation and size of topological domains. In addition, we demonstrate how transient (partial) dissociation of DNA bridging proteins results in dynamic sampling of different topological states, which allows us to deduce the torsional stiffness of the plectonemic state and the kinetics of protein-plectoneme interactions. We expect our approach to enable quantification of the dynamics and reaction pathways of DNA processing enzymes and motor proteins, in the context of physiologically relevant forces and supercoiling densities. SignificanceIn the cell, long DNA molecules carry the genetic information and must be stored and maintained, yet remain accessible for read out and processing. DNA supercoiling facilitates compaction of DNA, modulates its accessibility, and spatially juxtaposes DNA sites distant in linear DNA sequence. By binding to two sites in supercoiled DNA, DNA bridging proteins can pinch off topological domains and alter DNA plectoneme dynamics. Here we show how DNA bridging and topological domain dynamics can be detected from changes in the extension fluctuations of supercoiled DNA molecules tethered in magnetic tweezers. Our work highlights how considering DNA extension fluctuations, in addition to the mean extension, provides additional information and enables the investigation of protein-DNA interactions that are otherwise invisible.

biophysics↗

bioRxiv2021

DNA tension-modulated translocation and loop extrusion by SMC complexes revealed by molecular dynamics simulations

Structural Maintenance of Chromosomes (SMC) complexes play essential roles in genome organization across all domains of life. To determine how the activities of these large ( 50 nm) complexes are controlled by ATP binding and hydrolysis, we developed a molecular dynamics model that accounts for conformational motions of the SMC and DNA. The model combines DNA loop capture with an ATP-induced "power stroke" to translocate the SMC complex along DNA. This process is sensitive to DNA tension: at low tension (0.1 pN), the model makes loop-capture steps of average 60 nm and up to 200 nm along DNA (larger than the complex itself), while at higher tension, a distinct inchworm-like translocation mode appears. By tethering DNA to an experimentally-observed additional binding site ("safety belt"), the model SMC complex can perform loop extrusion (LE). The dependence of LE on DNA tension is distinct for fixed DNA tension vs. when fixed DNA end points: LE reversal occurs above 0.5 pN for fixed tension, while LE stalling without reversal occurs at about 2 pN for fixed end points. Our model matches recent experimental results for condensin and cohesin, and makes testable predictions for how specific structural variations affect SMC function.

biophysics↗

bioRxiv2018

Twist-bend coupling and the statistical mechanics of DNA: perturbation theory and beyond

The simplest model of DNA mechanics describes the double helix as a continuous rod with twist and bend elasticity. Recent work has discussed the relevance of a little-studied coupling G between twisting and bending, known to arise from the groove asymmetry of the DNA double helix. Here, the effect of G on the statistical mechanics of long DNA molecules subject to applied forces and torques is investigated. We present a perturbative calculation of the effective torsional stiffness Ceff for small twist-bend coupling. We find that the \"bare\" G is \"screened\" by thermal fluctuations, in the sense that the low-force, long-molecule effective free energy is that of a model with G = 0, but with long-wavelength bending and twisting rigidities that are shifted by G-dependent amounts. Using results for torsional and bending rigidities for freely-fluctuating DNA, we show how our perturbative results can be extended to a nonperturbative regime. These results are in excellent agreement with numerical calculations for Monte Carlo \"triad\" and molecular dynamics \"oxDNA\" models, characterized by different degrees of coarse-graining, validating the perturbative and non-perturbative analyses. While our theory is in generally-good quantitative agreement with experiment, the predicted torsional stiffness does systematically deviate from experimental data, suggesting that there are as-yet-uncharacterized aspects of DNA twisting-stretching mechanics relevant to low-force, long-molecule mechanical response, which are not captured by widely-used coarse-grained models.

biophysics↗

bioRxiv2018

Bend-Induced Twist Waves and the Structure of Nucleosomal DNA

Recent work indicates that twist-bend coupling plays an important role in DNA micromechanics. Here we show that this coupling induces standing twist waves in bent DNA, and we provide an analytical solution of the minimum-energy shape of a bent double-helical molecule. This solution is in excellent agreement with both coarse-grained simulations of DNA minicircles and experimental structural data for nucleosomal DNA, which is bent and wrapped around histone proteins in a superhelical conformation. Our analysis shows that the observed twist oscillation in nucleosomal DNA, so far attributed to the interaction with the histone proteins, is an intrinsic feature of free bent DNA, and should be observable in other protein-DNA complexes.

biophysics↗