ArticleNature structural & molecular biology2023
Evaluating the role of the nuclear microenvironment in gene function by population-based modeling.
Article in Nature structural & molecular biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed, 28 citations in OpenAlex.
- Effects of chromatin-lamina attachment on extra-long-range chromatin interactions.Biophysical journal · 2026Article
- Mega-enhancers compartmentalize transcriptionally active long genes in the brain.Nature cell biology · 2026Article
- map3C: a computational tool for processing multiomic single-cell Hi-C data.Bioinformatics (Oxford, England) · 2026Article
- GPSeq maps the radial organization of eukaryotic genomes along the nuclear periphery-center axis.Nature protocols · 2026Review
- Article
- Genome-wide modeling of DNA replication in space and time confirms the emergence of replication specific patterns in vivo in eukaryotes.Genome biology · 2025Article
- Generating three-dimensional genome structures with a variational quantum algorithm.Briefings in bioinformatics · 2025Article
- map3C: a computational tool for processing multiomic single-cell Hi-C data.bioRxiv : the preprint server for biology · 2025Article
- 3D genome organization shapes DNA damage susceptibility to platinum-based drugs.Nucleic acids research · 2025Article
- MaxComp: Predicting single-cell chromatin compartments from 3D chromosome structures.PLoS computational biology · 2025Article
- Unveiling the role of chromosome structure morphology on gene function through chromosome conformation analysis.Genome biology · 2025Article
- A Joint Analysis of RNA-DNA and DNA-DNA Interactomes Reveals Their Strong Association.International journal of molecular sciences · 2025Article
- Nuclear speckle biology: At the cross-roads of discovery and functional analysis.Current opinion in cell biology · 2024Review
- Article
- OpenNucleome for high resolution nuclear structural and dynamical modeling.bioRxiv : the preprint server for biology · 2024Article
- Uncovering the Principles of Genome Folding by 3D Chromatin Modeling.Cold Spring Harbor perspectives in biology · 2022Review
- Integrative approaches in genome structure analysis.Structure (London, England : 1993) · 2022Review
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Authors and funding
10 authors at 2 institutions in 1 country.
Funding
Abstract
The nuclear folding of chromosomes relative to nuclear bodies is an integral part of gene function. Here, we demonstrate that population-based modeling-from ensemble Hi-C data-provides a detailed description of the nuclear microenvironment of genes and its role in gene function. We define the microenvironment by the subnuclear positions of genomic regions with respect to nuclear bodies, local chromatin compaction, and preferences in chromatin compartmentalization. These structural descriptors are determined in single-cell models, thereby revealing the structural variability between cells. We demonstrate that the microenvironment of a genomic region is linked to its functional potential in gene transcription, replication, and chromatin compartmentalization. Some chromatin regions feature a strong preference for a single microenvironment, due to association with specific nuclear bodies in most cells. Other chromatin shows high structural variability, which is a strong indicator of functional heterogeneity. Moreover, we identify specialized nuclear microenvironments, which distinguish chromatin in different functional states and reveal a key role of nuclear speckles in chromosome organization. We demonstrate that our method produces highly predictive three-dimensional genome structures, which accurately reproduce data from a variety of orthogonal experiments, thus considerably expanding the range of Hi-C data analysis.
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