ArticleNucleic acids research2021
Polymer modelling unveils the roles of heterochromatin and nucleolar organizing regions in shaping 3D genome organization in Arabidopsis thaliana.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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28 citing papers in PubMed.
- A scaffolding element rewires local 3D chromatin architecture during differentiation.Nature communications · 2026Article
- Ribosome Heterogeneity in Plants: The Causes of This Phenomenon and Its Implications on Gene Expression.Plants (Basel, Switzerland) · 2026Review
- Cohesin activity accelerates the homology search.bioRxiv : the preprint server for biology · 2026Article
- Investigating Phase Separation in Genome Folding via Multiscale Computational Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Transient histone deacetylase inhibition induces cellular memory of gene expression and 3D genome folding.Nature genetics · 2026Article
- 3D genome folding in epigenetic regulation and cellular memory.Trends in cell biology · 2026Review
- Polymer-derived distance penalties improve chromatin interaction predictions from single-cell data across crop genomes.bioRxiv : the preprint server for biology · 2025Article
- Peripheral heterochromatin tethering is required for chromatin-based nuclear mechanical response.Nucleic acids research · 2025Article
- Understanding and Simulating the Dynamics of a Polymer-Like Chromatin.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Chromatin phase separation and nuclear shape fluctuations are correlated in a polymer model of the nucleus.Nucleus (Austin, Tex.) · 2024Article
- Genetic-epigenetic interplay in the determination of plant 3D genome organization.Nucleic acids research · 2024Article
- An atlas of the tomato epigenome reveals that KRYPTONITE shapes TAD-like boundaries through the control of H3K9ac distribution.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Heterogeneous flexibility can contribute to chromatin segregation in the cell nucleus.Physical review. E · 2024Article
- Physical model of the nuclear membrane permeability mechanism.Biophysical reviews · 2023Review
- Strong interactions between highly dynamic lamina-associated domains and the nuclear envelope stabilize the 3D architecture of Drosophila interphase chromatin.Epigenetics & chromatin · 2023Article
- The Role of Chromatin Modifications in the Evolution of Giant Plant Genomes.Plants (Basel, Switzerland) · 2023Article
- Hypothesis-driven probabilistic modelling enables a principled perspective of genomic compartments.Nucleic acids research · 2023Article
- Consistencies and contradictions in different polymer models of chromatin architecture.Computational and structural biotechnology journal · 2023Review
- Integrative genome modeling platform reveals essentiality of rare contact events in 3D genome organizations.Nature methods · 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
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4 authors.
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Abstract
The 3D genome is characterized by a complex organization made of genomic and epigenomic layers with profound implications on gene regulation and cell function. However, the understanding of the fundamental mechanisms driving the crosstalk between nuclear architecture and (epi)genomic information is still lacking. The plant Arabidopsis thaliana is a powerful model organism to address these questions owing to its compact genome for which we have a rich collection of microscopy, chromosome conformation capture (Hi-C) and ChIP-seq experiments. Using polymer modelling, we investigate the roles of nucleolus formation and epigenomics-driven interactions in shaping the 3D genome of A. thaliana. By validation of several predictions with published data, we demonstrate that self-attracting nucleolar organizing regions and repulsive constitutive heterochromatin are major mechanisms to regulate the organization of chromosomes. Simulations also suggest that interphase chromosomes maintain a partial structural memory of the V-shapes, typical of (sub)metacentric chromosomes in anaphase. Additionally, self-attraction between facultative heterochromatin regions facilitates the formation of Polycomb bodies hosting H3K27me3-enriched gene-clusters. Since nucleolus and heterochromatin are highly-conserved in eukaryotic cells, our findings pave the way for a comprehensive characterization of the generic principles that are likely to shape and regulate the 3D genome in many species.
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