ArticlePloS one2012
Expression-dependent folding of interphase chromatin.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- A guide to studying 3D genome structure and dynamics in the kidney.Nature reviews. Nephrology · 2025Review
- Consistencies and contradictions in different polymer models of chromatin architecture.Computational and structural biotechnology journal · 2023Review
- Mechanisms of Chromosome Folding and Nuclear Organization: Their Interplay and Open Questions.Cold Spring Harbor perspectives in biology · 2022Review
- Computational 3D genome modeling using Chrom3D.Nature protocols · 2018Article
- Transient chromatin properties revealed by polymer models and stochastic simulations constructed from Chromosomal Capture data.PLoS computational biology · 2017Article
- Perspectives: using polymer modeling to understand the formation and function of nuclear compartments.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2017Review
- Article
- Quantified effects of chromosome-nuclear envelope attachments on 3D organization of chromosomes.Nucleus (Austin, Tex.) · 2015Article
- Depletion of the chromatin looping proteins CTCF and cohesin causes chromatin compaction: insight into chromatin folding by polymer modelling.PLoS computational biology · 2014Article
- Modeling epigenome folding: formation and dynamics of topologically associated chromatin domains.Nucleic acids research · 2014Article
- Profiling of the Chromatin-associated Proteome Identifies HP1BP3 as a Novel Regulator of Cell Cycle Progression.Molecular & cellular proteomics : MCP · 2014Article
- DNA double-strand breaks: linking gene expression to chromosome morphology and mobility.Chromosoma · 2014Article
- Investigation of the chromosome regions with significant affinity for the nuclear envelope in fruit fly--a model based approach.PloS one · 2014Article
- Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data.Nature reviews. Genetics · 2013Review
- Modeling and experimental methods to probe the link between global transcription and spatial organization of chromosomes.PloS one · 2012Article
Corrections and comments
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Authors and funding
2 authors.
Funding
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Abstract
Multiple studies suggest that chromatin looping might play a crucial role in organizing eukaryotic genomes. To investigate the interplay between the conformation of interphase chromatin and its transcriptional activity, we include information from gene expression profiles into a polymer model for chromatin that incorporates genomic loops. By relating loop formation to transcriptional activity, we are able to generate chromosome conformations whose structural and topological properties are consistent with experimental data. The model particularly allows to reproduce the conformational variations that are known to occur between highly and lowly expressed chromatin regions. As previously observed in experiments, lowly expressed regions of the simulated polymers are much more compact. Due to the changes in loop formation, the distributions of chromatin loops are also expression-dependent and exhibit a steeper decay in highly active regions. As a results of entropic interaction between differently looped parts of the chromosome, we observe topological alterations leading to a preferential positioning of highly transcribed loci closer to the surface of the chromosome territory. Considering the diffusional behavior of the chromatin fibre, the simulations furthermore show that the higher the expression level of specific parts of the chromatin fibre is, the more dynamic they are. The results exhibit that variations of loop formation along the chromatin fibre, and the entropic changes that come along with it, do not only influence the structural parameters on the local scale, but also effect the global chromosome conformation and topology.
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