ArticleBiophysical journal2019
Learning the Formation Mechanism of Domain-Level Chromatin States with Epigenomics Data.
Article in Biophysical journal, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT07192159 (Evaluation of a Quantitative Ultrasound Model), which is not on this map. Cited by 24 papers.
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Evaluation of a Quantitative Ultrasound Model(DeepUSFF) for Liver Fat Quantification in Patients With Metabolic Dysfunction-Associated Steatotic Liver Disease: A Multicenter Prospective Study Using MRI-PDFF as the Reference Standard
Who cites it
24 citing papers in PubMed.
- Euchromatin forms condensed domains with short active regions on the surface.Nature genetics · 2026Article
- Formation of topologically associated chromatin domains using quantum annealing.Scientific reports · 2026Article
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- From Nucleosomes to Compartments: Physicochemical Interactions Underlying Chromatin Organization.Annual review of biophysics · 2024Review
- OpenNucleome for high resolution nuclear structural and dynamical modeling.bioRxiv : the preprint server for biology · 2024Article
- Article
- Explicit Ion Modeling Predicts Physicochemical Interactions for Chromatin Organization.bioRxiv : the preprint server for 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
- Compartmentalization with nuclear landmarks yields random, yet precise, genome organization.Biophysical journal · 2023Article
- Phase Separation and Correlated Motions in Motorized Genome.The journal of physical chemistry. B · 2022Article
- Deep-learning-based 3D cellular force reconstruction directly from volumetric images.Biophysical journal · 2022Article
- Generation of dynamic three-dimensional genome structure through phase separation of chromatin.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Enhancing computational enzyme design by a maximum entropy strategy.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Unifying coarse-grained force fields for folded and disordered proteins.Current opinion in structural biology · 2022Review
- Multiscale modeling of genome organization with maximum entropy optimization.The Journal of chemical physics · 2021Article
- Cooperative DNA looping by PRC2 complexes.Nucleic acids research · 2021Article
- Consistent Force Field Captures Homologue-Resolved HP1 Phase Separation.Journal of chemical theory and computation · 2021Article
- Single-molecule and in silico dissection of the interaction between Polycomb repressive complex 2 and chromatin.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Characterizing chromatin folding coordinate and landscape with deep learning.PLoS computational biology · 2020Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Epigenetic modifications can extend over long genomic regions to form domain-level chromatin states that play critical roles in gene regulation. The molecular mechanism for the establishment and maintenance of these states is not fully understood and remains challenging to study with existing experimental techniques. Here, we took a data-driven approach and parameterized an information-theoretic model to infer the formation mechanism of domain-level chromatin states from genome-wide epigenetic modification profiles. This model reproduces statistical correlations among histone modifications and identifies well-known states. Importantly, it predicts drastically different mechanisms and kinetic pathways for the formation of euchromatin and heterochromatin. In particular, long, strong enhancer and promoter states grow gradually from short but stable regulatory elements via a multistep process. On the other hand, the formation of heterochromatin states is highly cooperative, and no intermediate states are found along the transition path. This cooperativity can arise from a chromatin looping-mediated spreading of histone methylation mark and supports collapsed, globular three-dimensional conformations rather than regular fibril structures for heterochromatin. We further validated these predictions using changes of epigenetic profiles along cell differentiation. Our study demonstrates that information-theoretic models can go beyond statistical analysis to derive insightful kinetic information that is otherwise difficult to access.
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