Biology subjects

Bhattarcharjee, A.

Publications and source records attributed to Bhattarcharjee, A..

4 recordsLinked to original sources

bioRxiv2026

Nucleosome-resolution inference of chromatin interaction landscapes from Micro-C data using maximum entropy modeling

Chromatin contact maps report population-averaged frequencies that obscure the physical principles of genome folding. Here we show that a sparse, signed interaction landscape - a matrix of Lagrange multipliers,{lambda} , inferred by maximum entropy from Micro-C contact probabilities at nucleosome resolution, encodes regulatory and structural information beyond contact statistics. Sign decomposition reveals context-dependent associations with chromatin state. Attractive interactions ({lambda}-) are enriched at active regulatory elements, whereas repulsive interactions ({lambda}+) identify genomic positions whose contacts are depleted relative to the polymer reference, including Polycomb-associated domains. Top-ranked{lambda} bins show substantially greater enrichment for regulatory chromatin marks than O/E-normalised bins across active, architectural, and repressive classes, demonstrating that{lambda} preferentially identifies regulatory regions over contact-based rankings. Structural information is hierarchically encoded: the strongest 2% of interactions recover domain boundaries, the top 10% reproduces average contact statistics, yet reconstructing the conformational free-energy landscape, including dominant structural sub-populations and occupancies requires the full interaction spectrum. Nucleosome perturbation experiments show that{lambda} detects positional information contact maps largely miss, and targeted removal of CTCF/RAD21-associated{lambda} interactions selectively disrupts loop architecture without altering global polymer statistics. Together, these results establish{lambda} as a physically interpretable intermediate layer linking chromatin contact maps to three-dimensional structural ensembles.

biophysics↗

bioRxiv2025

Uncovering High-Resolution Organization of Genomic Loci using Experimentally Informed Polymer Model

The functionality of an organism depends on gene expression patterns, which are governed by the hierarchical organization of the genome. Numerous efforts, leveraging both polymer physics-based models and experimental imaging technologies, have sought to elucidate the structure-function relationship of chromatin fibers. However, a major challenge remains: the intrinsically multi-scale nature of chromatin organization, which has yet to be fully explored. Here, we present an experimentally informed, polymer physics-based model capable of reconstructing chromatin structural ensembles by integrating low-resolution contact data with MNase-derived nucleosome positioning information. We applied this model to multiple human genomic loci. Our analysis uncovered distinct structural features associated with active and inactive chromatin states, providing key insights into the relationship between genomic organization and transcriptional activity. These findings offer a promising framework for understanding genome structure-function relationships and their implications in developmental disorders and gene misregulation-related diseases.

biophysics↗

bioRxiv2020

Mechanism of Dynamic Binding of Replication Protein A to ssDNA

Replication protein A (RPA) serves as hub protein inside eukaryotic cells, where it coordinates crucial DNA metabolic processes and activates the DNA-damage response system. A characteristic feature of its action is to associate with ssDNA intermediates before handing over them to downstream proteins. The length of ssDNA intermediates differs for different pathways. This means RPA must have mechanisms for selective processing of ssDNA intermediates based on their length, the knowledge of which is fundamental to elucidate when and how DNA repair and replication processes are symphonized. By employing extensive molecular simulations, we investigated the mechanism of binding of RPA to ssDNA of different lengths. We show that the binding involves dynamic equilibrium with a stable intermediate, the population of which increases with the length of ssDNA. The vital underlying factors are decoded through collective variable principal component analysis. It suggests a differently orchestrated set of interactions that define the action of RPA based on the sizes of ssDNA intermediates. We further estimated the association kinetics and probed the diffusion mechanism of RPA to ssDNA. RPA diffuses on short ssDNA through progressive bulge formation. With long ssDNA, we observed a conformational change in ssDNA coupled with its binding to RPA in a cooperative fashion. Our analysis explains how the short-lived, long ssDNA intermediates are processed quickly in vivo. The study thus reveals the molecular basis of several recent experimental observations related to RPA binding to ssDNA and provides novel insights into the RPA functioning in DNA repair and replication. Significance StatementDespite ssDNA be the common intermediate to all pathways involving RPA, how does the latter function differently in the DNA processing events such as DNA repair, replication, and recombination just based on the length of ssDNA intermediates remains unknown. The major hindrance is the difficulty in capturing the transient interactions between the molecules. Even attempts to crystallize RPA complexes with 32nt and 62nt ssDNA have yielded a resolved structure of only 25nt ssDNA wrapped with RPA. Here, we used a state-of-the-art coarse-grained protein-ssDNA model to unravel the detailed mechanism of binding of RPA to ssDNA. Our study illustrates the molecular origin of variations in RPA action during various DNA processing events depending on the length of ssDNA intermediates.

biophysics↗

bioRxiv2019

Structural Basis of Enhanced Facilitated Diffusion of DNA Binding Protein in Crowded Cellular Milieu

DNA binding proteins (DBPs) rapidly recognize and specifically associate with their target DNA sites inside cell nucleus that contains up to 400 g/L macromolecules, most of which are proteins. While the fast association between DBPs and DNA is explained by a facilitated diffusion mechanism, where DBPs adopt a weighted combination of 3D diffusion and 1D sliding and hopping modes of transportation, the role of cellular environment that contains many nonspecifically interacting proteins and other biomolecules is mostly overlooked. By performing large scale computational simulations with an appropriately tuned model of protein and DNA in the presence of nonspecifically interacting bulk and DNA bound crowders (genomic crowders), we demonstrate the structural basis of the enhanced facilitated diffusion of DBPs inside a crowded cellular milieu through novel 1D scanning mechanisms. In the presence of bulk crowders, we identify the protein to float along the DNA under the influence of protein-crowder nonspecific interactions. The search mode is distinctly different compared to usual 1D sliding and hopping dynamics where protein diffusion is regulated by the DNA electrostatics. In contrast, the presence of genomic crowders expedite the target search process by transporting the protein over DNA segments through the formation of a transient protein-crowder bridged complex. By analyzing the ruggedness of the associated potential energy landscape, we underpin the molecular origin of the kinetic advantages of these search modes and show that they successfully explain the experimentally observed acceleration of facilitated diffusion of DBPs by molecular crowding agents and crowder concentration dependent enzymatic activity of transcription factors. Our findings provide crucial insights into gene regulation kinetics inside the crowded cellular milieu.\n\nSIGNIFICANCE10-40% of the intracellular volume is occupied by proteins, and other biomolecules, collectively known as macromolecular crowders. Their presence has been found to promote faster translocation of DNA binding proteins (DBPs) during the search of their target DNA sites for crucial cellular processes. Using molecular simulations, we probe the underlying structural basis and underscore the existence of novel DNA scanning mechanisms actuated by protein-crowder nonspecific interactions. We show that the observed search modes are kinetically beneficial and can successfully explain the acceleration of facilitated diffusion of DBPs by molecular crowding agents and crowderconcentration dependent enzymatic activity of transcription factors.Our study sheds new light on the long-standing facilitated diffusion problem of DBPs in the crowded cellular environment for regulating gene expression.

biophysics↗