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Faithful chromosome segregation during bacterial replication requires global reorganization of the nucleoid, where Structural Maintenance of Chromosomes (SMC) complexes play a crucial role. Here, we develop an energy landscape framework that integrates data-driven pairwise interactions with coarse-grained polymer physics to infer the 3D architectural ensembles ofEscherichia coliandBacillus subtilischromosomes throughout replication. We show that SMC-mediated long-range lengthwise compaction reshapes the nucleoid to induce a robust mid-replication transition in which the terminus relocates toward the nucleoid center and duplicated origins segregate toward opposite cell halves. SMC-deficient mutants lack this transition and instead exhibit emergent nematic-like alignment of sister chromosomes that impedes segregation. A distinctive intersister Hi-C signature accompanies the emergence of the nematic alignment. By systematically tuning nonspecific intersister adhesion, we reveal that SMC activity expands the physical regime permitting faithful segregation. This buffering protects segregation against adhesive forces intrinsic to the crowded bacterial nucleoid. Our framework provides mechanistic insight into SMC-dependent coreplication segregation across bacterial species, yielding experimentally testable predictions for imaging and sister-chromosome-resolved Hi-C. 

Compacting chromatin within the cellular nucleus presents a significant challenge for biology. Chromosomes must be both condensed and spatially organized to enable essential processes such as transcription and replication. Chromosome conformation capture experiments (e.g., Hi-C) provide valuable information about the spatial organization and, therefore, the connectivity between different genomic regions. These experiments inspired polymer models that describe the physical mechanism of the chromosomal energy landscape. The Full-Inversion Chromatin model (FI-Chrom), a data-driven approach for modeling genome organization, uses Hi-C contact maps to infer pairwise interaction potentials between all chromosomal loci. It combines Graphics Processing Unit (GPU)-accelerated simulations with efficient training of tens of millions of parameters derived from the maximum-entropy principle to determine 3D structures of chromosomes that accurately reproduce Hi-C-like data. FI-Chrom does not make any a priori assumptions regarding chromosome architecture, making it applicable to any chromosome conformation capture experiment. Its derived structural ensembles capture all essential features from the short- and long-range interactions of typical chromosome organization, such as segregated compartments, chromosome territories, and fully or partially formed loops. Although Hi-C contains only structural information, FI-Chrom extends these data by revealing an emergent dynamical mechanism encoded in the inferred energy landscape. For example, simulations show that chromatin loops are not static architectural features but rather transient structural elements. Statistical analyses further indicate that loops confined within a single compartment occur more frequently than those spanning multiple compartments, highlighting the dynamic and compartment-dependent nature of chromatin organization. 

RNA polymerase (RNAP) is a processive motor that modulates DNA supercoiling and reshapes DNA structures. The feedback loop between the DNA topology and transcription remains elusive. Here, we investigate the impact of potential G-quadruplex forming sequences (PQS) on transcription in response to DNA supercoiling. We find that supercoiled DNA increases transcription frequency 10-fold higher than relaxed DNA, which lead to an abrupt formation of G-quadruplex (G4) and R-loop structures. Moreover, the stable R-loop relieves topological strain, facilitated by G4 formation. The cooperative formation of G4/R-loop effectively alters the DNA topology around the promoter and suppresses transcriptional activity by impeding RNAP loading. These findings highlight negative supercoiling as a built-in spring that triggers a transcriptional burst followed by a rapid suppression upon G4/R-loop formation. This study sheds light on the intricate interplay between DNA topology and structural change in transcriptional regulation, with implications for understanding gene expression dynamics. 

During mitosis, there are significant structural changes in chromosomes. We used a maximum entropy approach to invert experimental Hi-C data to generate effective energy landscapes for chromosomal structures at different stages during the cell cycle. Modeled mitotic structures show a hierarchical organization of helices of helices. High-periodicity loops span hundreds of kilobases or less, while the other low-periodicity ones are larger in genomic separation, spanning several megabases. The structural ensembles reveal a progressive decrease in compartmentalization from interphase to mitosis, accompanied by the appearance of a second diagonal in prometaphase, indicating an organized array of loops. While there is a local tendency to form chiral helices, overall, no preferential left-handed or right-handed chirality appears to develop on the time scale of the cell cycle. Chromatin thus appears to be a liquid crystal containing numerous defects that anneal rather slowly. 

Transcription has a mechanical component, as the translocation of the transcription machinery or RNA polymerase (RNAP) on DNA or chromatin is dynamically coupled to the chromatin torsion. This posits chromatin mechanics as a possible regulator of eukaryotic transcription, however, the modes and mechanisms of this regulation are elusive. Here, we first take a statistical mechanics approach to model the torsional response of topology-constrained chromatin. Our model recapitulates the experimentally observed weaker torsional stiffness of chromatin compared to bare DNA and proposes structural transitions of nucleosomes into chirally distinct states as the driver of the contrasting torsional mechanics. Coupling chromatin mechanics with RNAP translocation in stochastic simulations, we reveal a complex interplay of DNA supercoiling and nucleosome dynamics in governing RNAP velocity. Nucleosomes play a dual role in controlling the transcription dynamics. The steric barrier aspect of nucleosomes in the gene body counteracts transcription via hindering RNAP motion, whereas the chiral transitions facilitate RNAP motion via driving a low restoring torque upon twisting the DNA. While nucleosomes with low dissociation rates are typically transcriptionally repressive, highly dynamic nucleosomes offer less of a steric barrier and enhance the transcription elongation dynamics of weakly transcribed genes via buffering DNA twist. We use the model to predict transcription-dependent levels of DNA supercoiling in segments of the budding yeast genome that are in accord with available experimental data. The model unveils a paradigm of DNA supercoiling-mediated interaction between genes and makes testable predictions that will guide experimental design. 

Understanding the mechanisms governing the structure and dynamics of flexible polymers like chromosomes, especially the signatures of motor-driven active processes, is of great interest in genome biology. We study chromosomes as a coarse-grained polymer model where microscopic motor activity is captured via an additive temporally persistent noise. The active steady state is characterized by two parameters: active force, controlling the persistent-noise amplitude, and correlation time, the decay time of active noise. We find that activity drives correlated motion over long distances and a regime of dynamic compaction into a globally collapsed entangled globule. Diminished topological constraints destabilize the entangled globule, and the active segments trapped in the globule move toward the periphery, resulting in an enriched active monomer density near the periphery. We also show that heterogeneous activity leads to the segregation of the highly dynamic species from the less dynamic one, suggesting a role of activity in chromosome compartmental segregation. Adding activity to experimental-data-derived structures, we find active loci may mechanically perturb and switch compartments established via epigenetics-driven passive self-association. The key distinguishing signatures of activity are enhanced apparent diffusivity, exploration of all the dynamic regimes (subdiffusion, effective diffusion, and superdiffusion) at various lag times, and a broadened distribution of observables like the dynamic exponents. Published by the American Physical Society2024 

Bacterial chromosome segregation, ensuring equal distribution of replicated DNA, is crucial for cell division. During fast growth, replication and segregation co-occur. Overlapping cycles of DNA replication and segregation require efficient segregation of the origin of replication (Ori), which is known to be orchestrated by the protein families SMC and ParAB. We used data-driven physical modeling to study the roles of these proteins in Ori segregation. Developing a polymer model of the Bacillus subtilis genome based on Hi-C data, we analyzed chromosome structures in wild-type cells and mutants lacking SMC or ParAB. Wild-type chromosomes showed clear Ori segregation, while the mutants lacked faithful segregation. The model suggests that the dual role of ParB proteins, loading SMCs near the Ori and interacting with ParA, is crucial for Ori segregation. ParB-loaded SMCs compact individual Ori and introduce an effective inter-sister repulsion that regulates the ParAB-activity to avoid the detrimental scenario of pulling both Ori to the same pole. The model makes testable predictions for sister-chromosome-resolved Hi-C experiments and proposes that replicated sister chromosomes segregate via mechanistic cooperation of SMC and ParAB activity. 

Abstract The link between genomic structure and biological function is yet to be consolidated, it is, however, clear that physical manipulation of the genome, driven by the activity of a variety of proteins, is a crucial step. To understand the consequences of the physical forces underlying genome organization, we build a coarse-grained polymer model of the genome, featuring three fundamentally distinct classes of interactions: lengthwise compaction, i.e., compaction of chromosomes along its contour, self-adhesion among epigenetically similar genomic segments, and adhesion of chromosome segments to the nuclear envelope or lamina. We postulate that these three types of interactions sufficiently represent the concerted action of the different proteins organizing the genome architecture and show that an interplay among these interactions can recapitulate the architectural variants observed across the tree of life. The model elucidates how an interplay of forces arising from the three classes of genomic interactions can drive drastic, yet predictable, changes in the global genome architecture, and makes testable predictions. We posit that precise control over these interactions in vivo is key to the regulation of genome architecture.