ArticlePloS one2012
Modeling and experimental methods to probe the link between global transcription and spatial organization of chromosomes.
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, 31 citations in OpenAlex.
- Material-Induced Nuclear Deformation Controls Chromatin Architecture in Adipose Stem Cells.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Astrocyte Enrichment of 3D Cortical Constructs Enhances Brain Repair.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Implanting mechanically reprogrammed fibroblasts for aged tissue regeneration and wound healing.Aging cell · 2024Article
- Mesoscale, long-time mixing of chromosomes and its connection to polymer dynamics.PLoS computational biology · 2023Article
- Network analysis identifies chromosome intermingling regions as regulatory hotspots for transcription.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Regulation of genome organization and gene expression by nuclear mechanotransduction.Nature reviews. Molecular cell biology · 2017Review
- Orientation and repositioning of chromosomes correlate with cell geometry-dependent gene expression.Molecular biology of the cell · 2017Article
- Superresolution imaging of nanoscale chromosome contacts.Scientific reports · 2017Article
- Optical High Content Nanoscopy of Epigenetic Marks Decodes Phenotypic Divergence in Stem Cells.Scientific reports · 2017Article
- Geometric control and modeling of genome reprogramming.Bioarchitecture · 2016Article
- Chromosome intermingling-the physical basis of chromosome organization in differentiated cells.Nucleic acids research · 2016Article
- The nuclear lamina is mechano-responsive to ECM elasticity in mature tissue.Journal of cell science · 2014Review
- Chromosome positioning from activity-based segregation.Nucleic acids research · 2014Article
- Chromosome territories reposition during DNA damage-repair response.Genome biology · 2013Article
- Mechanobiology of bone marrow stem cells: from myosin-II forces to compliance of matrix and nucleus in cell forms and fates.Differentiation; research in biological diversity · 2013Review
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genomes are spatially assembled into chromosome territories (CT) within the nucleus of living cells. Recent evidences have suggested associations between three-dimensional organization of CTs and the active gene clusters within neighboring CTs. These gene clusters are part of signaling networks sharing similar transcription factor or other downstream transcription machineries. Hence, presence of such gene clusters of active signaling networks in a cell type may regulate the spatial organization of chromosomes in the nucleus. However, given the probabilistic nature of chromosome positions and complex transcription factor networks (TFNs), quantitative methods to establish their correlation is lacking. In this paper, we use chromosome positions and gene expression profiles in interphase fibroblasts and describe methods to capture the correspondence between their spatial position and expression. In addition, numerical simulations designed to incorporate the interacting TFNs, reveal that the chromosome positions are also optimized for the activity of these networks. These methods were validated for specific chromosome pairs mapped in two distinct transcriptional states of T-Cells (naïve and activated). Taken together, our methods highlight the functional coupling between topology of chromosomes and their respective gene expression patterns.
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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.