ArticleNature communications2020
Transcriptional activation during cell reprogramming correlates with the formation of 3D open chromatin hubs.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
33 citing papers in PubMed, 63 citations in OpenAlex.
- HiCInterpolate: 4D Spatiotemporal Interpolation of Hi-C Data for Genome Architecture Analysis.bioRxiv : the preprint server for biology · 2026Article
- An experimentally-informed polymer model reveals high resolution organization of genomic loci.Nature communications · 2026Article
- 3D Genome Architecture in Stem Cell Lineage Commitment: from Structural Organization to Precision Regulation.Advanced genetics (Hoboken, N.J.) · 2025Review
- Regulatory roles of three-dimensional structures of chromatin domains.Genome biology · 2025Article
- HiCForecast: dynamic network optical flow estimation algorithm for spatiotemporal Hi-C data forecasting.Bioinformatics (Oxford, England) · 2025Article
- SEE: A Method for Predicting the Dynamics of Chromatin Conformation Based on Single-Cell Gene Expression.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Integrated promoter-capture Hi-C and Hi-C analysis reveals fine-tuned regulation of the 3D chromatin architecture in colorectal cancer.Frontiers in genetics · 2025Article
- Polymer Physics Models Reveal Structural Folding Features of Single-Molecule Gene Chromatin Conformations.International journal of molecular sciences · 2024Article
- Transcription regulates the spatio-temporal dynamics of genes through micro-compartmentalization.Nature communications · 2024Article
- Gene regulation during meiosis.Trends in genetics : TIG · 2024Review
- Enhancer-driven 3D chromatin domain folding modulates transcription in human mammary tumor cells.Life science alliance · 2024Article
- Large-scale data-driven and physics-based models offer insights into the relationships among the structures, dynamics, and functions of chromosomes.Journal of molecular cell biology · 2023Review
- Quantifying the large-scale chromosome structural dynamics during the mitosis-to-G1 phase transition of cell cycle.Open biology · 2023Article
- Techniques for and challenges in reconstructing 3D genome structures from 2D chromosome conformation capture data.Current opinion in cell biology · 2023Review
- Polymer simulations guide the detection and quantification of chromatin loop extrusion by imaging.Nucleic acids research · 2023Article
- Multiscale 3D genome reorganization during skeletal muscle stem cell lineage progression and aging.Science advances · 2023Article
- The dynamics of three-dimensional chromatin organization and phase separation in cell fate transitions and diseases.Cell regeneration (London, England) · 2022Review
- Insights into the cell fate decision-making processes from chromosome structural reorganizations.Biophysics reviews · 2022Article
- The Impact of Space and Time on the Functional Output of the Genome.Cold Spring Harbor perspectives in biology · 2022Review
- Review
Corrections and comments
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Authors and funding
7 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Chromosome structure is a crucial regulatory factor for a wide range of nuclear processes. Chromosome conformation capture (3C)-based experiments combined with computational modelling are pivotal for unveiling 3D chromosome structure. Here, we introduce TADdyn, a tool that integrates time-course 3C data, restraint-based modelling, and molecular dynamics to simulate the structural rearrangements of genomic loci in a completely data-driven way. We apply TADdyn on in situ Hi-C time-course experiments studying the reprogramming of murine B cells to pluripotent cells, and characterize the structural rearrangements that take place upon changes in the transcriptional state of 21 genomic loci of diverse expression dynamics. By measuring various structural and dynamical properties, we find that during gene activation, the transcription starting site contacts with open and active regions in 3D chromatin domains. We propose that these 3D hubs of open and active chromatin may constitute a general feature to trigger and maintain gene transcription.
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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.