ArticlePloS one2010
Diffusion-driven looping provides a consistent framework for chromatin organization.
Article in PloS one, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 74 papers.
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Who cites it
74 citing papers in PubMed, 173 citations in OpenAlex.
- Polymer models of chromatin organization in virally infected cells.Biochemical Society transactions · 2025Review
- Polymer Physics Models Reveal Structural Folding Features of Single-Molecule Gene Chromatin Conformations.International journal of molecular sciences · 2024Article
- Polymer physics models reveal structural folding features of single-molecule gene chromatin conformations.bioRxiv : the preprint server for biology · 2024Article
- Diffusion controls local versus dispersed inheritance of histones during replication and shapes epigenomic architecture.PLoS computational biology · 2023Article
- Partition complex structure can arise from sliding and bridging of ParB dimers.Nature communications · 2023Article
- Mesoscale, long-time mixing of chromosomes and its connection to polymer dynamics.PLoS computational biology · 2023Article
- Compartmentalization with nuclear landmarks yields random, yet precise, genome organization.Biophysical journal · 2023Article
- Unveiling the Machinery behind Chromosome Folding by Polymer Physics Modeling.International journal of molecular sciences · 2023Review
- Consistencies and contradictions in different polymer models of chromatin architecture.Computational and structural biotechnology journal · 2023Review
- The dynamics of three-dimensional chromatin organization and phase separation in cell fate transitions and diseases.Cell regeneration (London, England) · 2022Review
- Loop-extrusion and polymer phase-separation can co-exist at the single-molecule level to shape chromatin folding.Nature communications · 2022Article
- Chrom-Lasso: a lasso regression-based model to detect functional interactions using Hi-C data.Briefings in bioinformatics · 2021Article
- Detecting chromosomal interactions in Capture Hi-C data with CHiCAGO and companion tools.Nature protocols · 2021Article
- Multiscale modeling of genome organization with maximum entropy optimization.The Journal of chemical physics · 2021Article
- Comparison of the Hi-C, GAM and SPRITE methods using polymer models of chromatin.Nature methods · 2021Article
- A DNA Sequence Based Polymer Model for Chromatin Folding.International journal of molecular sciences · 2021Article
- Data-Driven Polymer Model for Mechanistic Exploration of Diploid Genome Organization.Biophysical journal · 2020Article
- Polymer physics indicates chromatin folding variability across single-cells results from state degeneracy in phase separation.Nature communications · 2020Article
- A Lamin-Associated Chromatin Model for Chromosome Organization.Biophysical journal · 2020Article
- Article
14 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Chromatin folding inside the interphase nucleus of eukaryotic cells is done on multiple scales of length and time. Despite recent progress in understanding the folding motifs of chromatin, the higher-order structure still remains elusive. Various experimental studies reveal a tight connection between genome folding and function. Chromosomes fold into a confined subspace of the nucleus and form distinct territories. Chromatin looping seems to play a dominant role both in transcriptional regulation as well as in chromatin organization and has been assumed to be mediated by long-range interactions in many polymer models. However, it remains a crucial question which mechanisms are necessary to make two chromatin regions become co-located, i.e. have them in spatial proximity. We demonstrate that the formation of loops can be accomplished solely on the basis of diffusional motion. The probabilistic nature of temporary contacts mimics the effects of proteins, e.g. transcription factors, in the solvent. We establish testable quantitative predictions by deriving scale-independent measures for comparison to experimental data. In this Dynamic Loop (DL) model, the co-localization probability of distant elements is strongly increased compared to linear non-looping chains. The model correctly describes folding into a confined space as well as the experimentally observed cell-to-cell variation. Most importantly, at biological densities, model chromosomes occupy distinct territories showing less inter-chromosomal contacts than linear chains. Thus, dynamic diffusion-based looping, i.e. gene co-localization, provides a consistent framework for chromatin organization in eukaryotic interphase nuclei.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.