ArticleCell2014
Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription.
Article in Cell, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 239 papers.
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Who cites it
239 citing papers in PubMed, 487 citations in OpenAlex.
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- TAD boundaries and gene activity are uncoupled.eLife · 2026Article
- TAD boundaries and gene activity are uncoupled.bioRxiv : the preprint server for biology · 2026Article
- Multiscale chromatin modeling of chromosome X structural changes upon inactivation highlights the differential regulatory mechanism ofbioRxiv : the preprint server for biology · 2026Article
- Jpx RNA controls Xist induction through spatial reorganization of the mouse X-inactivation center.Developmental cell · 2025Article
- RETRACTED: Kinetic organization of the genome revealed by ultraresolution multiscale live imaging.Science (New York, N.Y.) · 2025Article
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- Coarse-grained chromatin dynamics by tracking multiple similarly labeled gene loci.Biophysical journal · 2025Article
- Predicting gene expression changes from chromatin structure modification.NPJ systems biology and applications · 2025Article
- Unveiling the role of chromosome structure morphology on gene function through chromosome conformation analysis.Genome biology · 2025Article
- Structural basis of differential gene expression at eQTLs loci from high-resolution ensemble models of 3D single-cell chromatin conformations.Bioinformatics (Oxford, England) · 2025Article
- Integrative Modeling of 3D Genome Organization by Bayesian Molecular Dynamics Simulations with Hi-C Metainference.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Advancements and future directions in single-cell Hi-C based 3D chromatin modeling.Computational and structural biotechnology journal · 2024Review
- Disorganized chromatin hierarchy and stem cell aging in a male patient of atypical laminopathy-based progeria mandibuloacral dysplasia type A.Nature communications · 2024Article
- Cohesin distribution alone predicts chromatin organization in yeast via conserved-current loop extrusion.Genome biology · 2024Article
- Fdo1, Fkh1, Fkh2, and the Swi6-Mbp1 MBF complex regulate Mcd1 levels to impact eco1 rad61 cell growth in Saccharomyces cerevisiae.Genetics · 2024Article
- Multifaceted role of CTCF in X-chromosome inactivation.Chromosoma · 2024Review
179 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors at 4 institutions in 3 countries.
Funding
Abstract
A new level of chromosome organization, topologically associating domains (TADs), was recently uncovered by chromosome conformation capture (3C) techniques. To explore TAD structure and function, we developed a polymer model that can extract the full repertoire of chromatin conformations within TADs from population-based 3C data. This model predicts actual physical distances and to what extent chromosomal contacts vary between cells. It also identifies interactions within single TADs that stabilize boundaries between TADs and allows us to identify and genetically validate key structural elements within TADs. Combining the model's predictions with high-resolution DNA FISH and quantitative RNA FISH for TADs within the X-inactivation center (Xic), we dissect the relationship between transcription and spatial proximity to cis-regulatory elements. We demonstrate that contacts between potential regulatory elements occur in the context of fluctuating structures rather than stable loops and propose that such fluctuations may contribute to asymmetric expression in the Xic during X inactivation.
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Registered trials
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.