ArticleBiophysical journal2020
Computing 3D Chromatin Configurations from Contact Probability Maps by Inverse Brownian Dynamics.
Article in Biophysical journal, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed, 26 citations in OpenAlex.
- Connecting multiway enhancer-promoter interactions to changes in gene expression in cancer.bioRxiv : the preprint server for biology · 2026Article
- An experimentally-informed polymer model reveals high resolution organization of genomic loci.Nature communications · 2026Article
- Compaction of chromatin domains regulates target search times of proteins.PLoS computational biology · 2026Article
- Machine learning unravels inherent structural patterns in Escherichia coli Hi-C matrices and predicts chromosome dynamics.Nucleic acids research · 2024Article
- Diffusion controls local versus dispersed inheritance of histones during replication and shapes epigenomic architecture.PLoS computational biology · 2023Article
- Efficient Hi-C inversion facilitates chromatin folding mechanism discovery and structure prediction.Biophysical journal · 2023Article
- Efficient Hi-C inversion facilitates chromatin folding mechanism discovery and structure prediction.bioRxiv : the preprint server for biology · 2023Article
- Predicting scale-dependent chromatin polymer properties from systematic coarse-graining.Nature communications · 2023Article
- Theory of chromatin organization maintained by active loop extrusion.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Interphase chromosomes of the Aedes aegypti mosquito are liquid crystalline and can sense mechanical cues.Nature communications · 2023Article
- Heterogeneous interactions and polymer entropy decide organization and dynamics of chromatin domains.Biophysical journal · 2022Article
- Navigating the crowd: visualizing coordination between genome dynamics, structure, and transcription.Genome biology · 2020Review
- Multiscale Genome Organization: Dazzling Subject and Inventive Methods.Biophysical journal · 2020Article
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Authors and funding
4 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The three-dimensional (3D) organization of chromatin, on the length scale of a few genes, is crucial in determining the functional state-accessibility and amount of gene expression-of the chromatin. Recent advances in chromosome conformation capture experiments provide partial information on the chromatin organization in a cell population, namely the contact count between any segment pairs, but not on the interaction strength that leads to these contact counts. However, given the contact matrix, determining the complete 3D organization of the whole chromatin polymer is an inverse problem. In this work, a novel inverse Brownian dynamics method based on a coarse-grained bead-spring chain model has been proposed to compute the optimal interaction strengths between different segments of chromatin such that the experimentally measured contact count probability constraints are satisfied. Applying this method to the α-globin gene locus in two different cell types, we predict the 3D organizations corresponding to active and repressed states of chromatin at the locus. We show that the average distance between any two segments of the region has a broad distribution and cannot be computed as a simple inverse relation based on the contact probability alone. The results presented for multiple normalization methods suggest that all measurable quantities may crucially depend on the nature of normalization. We argue that by experimentally measuring predicted quantities, one may infer the appropriate form of normalization.
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