ArticleBiophysical journal2021
Differentiating cancer cells reveal early large-scale genome regulation by pericentric domains.
Article in Biophysical journal, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 34 citations in OpenAlex.
- Chromatin Nano-Organization in Peripheral Blood Mononuclear Cells After In-Solution Irradiation with the Beta-Emitter Lu-177.Biomolecules · 2026Article
- Genomic-Thermodynamic Phase Synchronization: Maxwell's Demon-like Regulation of Cell Fate Transition.International journal of molecular sciences · 2025Article
- Role of Nuclear Lamins in the Regulation of the Genome: Focus on CardioLaminopathy.Sub-cellular biochemistry · 2025Review
- Impact of Gold Nanoparticles and Ionizing Radiation on Whole Chromatin Organization as Detected by Single-Molecule Localization Microscopy.International journal of molecular sciences · 2024Article
- PeculiarGenes · 2024Article
- Condensed Matter Systems Exposed to Radiation: Multiscale Theory, Simulations, and Experiment.Chemical reviews · 2024Review
- Drug-resilient Cancer Cell Phenotype Is Acquired via Polyploidization Associated with Early Stress Response Coupled to HIF2α Transcriptional Regulation.Cancer research communications · 2024Article
- From Cell States to Cell Fates: Control of Cell State Transitions.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Microscopic Analysis of Heterochromatin, Euchromatin and Cohesin in Cancer Cell Models and under Anti-Cancer Treatment.Current issues in molecular biology · 2023Article
- Synchronization between Attractors: Genomic Mechanism of Cell-Fate Change.International journal of molecular sciences · 2023Review
- Spatial-Temporal Genome Regulation in Stress-Response and Cell-Fate Change.International journal of molecular sciences · 2023Review
- A comprehensive method to study the DNA's association with lamin and chromatin compaction in intact cell nuclei at super resolution.Nanoscale · 2023Article
- Advanced image-free analysis of the nano-organization of chromatin and other biomolecules by Single Molecule Localization Microscopy (SMLM).Computational and structural biotechnology journal · 2023Article
- Polyploidy and Myc Proto-Oncogenes Promote Stress Adaptation via Epigenetic Plasticity and Gene Regulatory Network Rewiring.International journal of molecular sciences · 2022Review
- Life Entrapped in a Network of Atavistic Attractors: How to Find a Rescue.International journal of molecular sciences · 2022Review
- Review
- Networks and Islands of Genome Nano-architecture and Their Potential Relevance for Radiation Biology : (A Hypothesis and Experimental Verification Hints).Results and problems in cell differentiation · 2022Article
- How Genomes Emerge, Function, and Evolve: Living Systems Emergence-Genotype-Phenotype-Multilism-Genome/Systems Ecology.Results and problems in cell differentiation · 2022Article
- A Unified Genomic Mechanism of Cell-Fate Change.Results and problems in cell differentiation · 2022Article
- Self-organization of whole-gene expression through coordinated chromatin structural transition.Biophysics reviews · 2021Review
Corrections and comments
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Authors and funding
9 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Finding out how cells prepare for fate change during differentiation commitment was our task. To address whether the constitutive pericentromere-associated domains (PADs) may be involved, we used a model system with known transcriptome data, MCF-7 breast cancer cells treated with the ErbB3 ligand heregulin (HRG), which induces differentiation and is used in the therapy of cancer. PAD-repressive heterochromatin (H3K9me3), centromere-associated-protein-specific, and active euchromatin (H3K4me3) antibodies, real-time PCR, acridine orange DNA structural test (AOT), and microscopic image analysis were applied. We found a two-step DNA unfolding after 15-20 and 60 min of HRG treatment, respectively. This behavior was consistent with biphasic activation of the early response genes (c-fos - fosL1/myc) and the timing of two transcriptome avalanches reported in the literature. In control, the average number of PADs negatively correlated with their size by scale-free distribution, and centromere clustering in turn correlated with PAD size, both indicating that PADs may create and modulate a suprachromosomal network by fusing and splitting a constant proportion of the constitutive heterochromatin. By 15 min of HRG treatment, the bursting unraveling of PADs from the nucleolus boundary occurred, coinciding with the first step of H3K4me3 chromatin unfolding, confirmed by AOT. The second step after 60 min of HRG treatment was associated with transcription of long noncoding RNA from PADs and peaking of fosL1/c-myc response. We hypothesize that the bursting of PAD clusters under a critical silencing threshold pushes the first transcription avalanche, whereas the destruction of the PAD network enables genome rewiring needed for differentiation repatterning, mediated by early response bivalent genes.
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