ArticleNucleic acids research2019
Rouse model with transient intramolecular contacts on a timescale of seconds recapitulates folding and fluctuation of yeast chromosomes.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
40 citing papers in PubMed, 87 citations in OpenAlex.
- Loss of SUMOylation drives aberrant PRC1 clustering and 3D genome rewiring independent of H3K27me3.Nucleic acids research · 2026Article
- Article
- Integrated MINFLUX tracking reveals two distinct chromatin dynamics classes across cell types.Nature structural & molecular biology · 2026Article
- Investigating Phase Separation in Genome Folding via Multiscale Computational Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Condensin accelerates long-range intra-chromosomal interactions.Nature communications · 2026Article
- RETRACTED: Kinetic organization of the genome revealed by ultraresolution multiscale live imaging.Science (New York, N.Y.) · 2025Article
- Single nucleosome imaging reveals principles of transient multiscale chromatin reorganization triggered by histone ADP-ribosylation at DNA lesions.Nature communications · 2025Article
- Coarse-grained chromatin dynamics by tracking multiple similarly labeled gene loci.Biophysical journal · 2025Article
- Condensin Accelerates Long-Range Intra-Chromosomal Interactions.bioRxiv : the preprint server for biology · 2025Article
- Insulation between adjacent TADs is controlled by the width of their boundaries through distinct mechanisms.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Transcription regulates the spatio-temporal dynamics of genes through micro-compartmentalization.Nature communications · 2024Article
- Activity-driven chromatin organization during interphase: Compaction, segregation, and entanglement suppression.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Activity-driven chromatin organization during interphase: compaction, segregation, and entanglement suppression.bioRxiv : the preprint server for biology · 2024Article
- The power of weak, transient interactions across biology: A paradigm of emergent behavior.Physica D. Nonlinear phenomena · 2023Article
- Multi-Scale Imaging of the Dynamic Organization of Chromatin.International journal of molecular sciences · 2023Review
- Elasticity control of entangled chromosomes: Crosstalk between condensin complexes and nucleosomes.Biophysical journal · 2023Article
- HP1-driven phase separation recapitulates the thermodynamics and kinetics of heterochromatin condensate formation.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Polymeric nature of tandemly repeated genes enhances assembly of constitutive heterochromatin in fission yeast.Communications biology · 2023Article
- Review
- Epigenetic switching with asymmetric bridging interactions.Biophysical journal · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA folding and dynamics along with major nuclear functions are determined by chromosome structural properties, which remain, thus far, elusive in vivo. Here, we combine polymer modeling and single particle tracking experiments to determine the physico-chemical parameters of chromatin in vitro and in living yeast. We find that the motion of reconstituted chromatin fibers can be recapitulated by the Rouse model using mechanical parameters of nucleosome arrays deduced from structural simulations. Conversely, we report that the Rouse model shows some inconsistencies to analyze the motion and structural properties inferred from yeast chromosomes determined with chromosome conformation capture techniques (specifically, Hi-C). We hence introduce the Rouse model with Transient Internal Contacts (RouseTIC), in which random association and dissociation occurs along the chromosome contour. The parametrization of this model by fitting motion and Hi-C data allows us to measure the kinetic parameters of the contact formation reaction. Chromosome contacts appear to be transient; associated to a lifetime of seconds and characterized by an attractive energy of -0.3 to -0.5 kBT. We suggest attributing this energy to the occurrence of histone tail-DNA contacts and notice that its amplitude sets chromosomes in 'theta' conditions, in which they are poised for compartmentalization and phase separation.
Indexed as
Identifiers
What OpenQuestion holds
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.