Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

Random loop model for long polymers.

Manfred Bohn1, Dieter W Heermann, Roel van Driel

  • 1Institute of Theoretical Physics, University of Heidelberg, Philosophenweg 19, D-69120 Heidelberg, Germany. bohn@tphys.uni-heidelberg.de

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
|February 1, 2008
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Spectral Graph Entropy of Chromatin: A von Neumann Framework for Multiscale Polymer Organization from Hi-C.

The journal of physical chemistry. B·2026
Same author

An experimentally-informed polymer model reveals high resolution organization of genomic loci.

Nature communications·2026
Same author

The role of nucleotide opening dynamics in facilitated target search by DNA-repair proteins.

Biochimica et biophysica acta. Gene regulatory mechanisms·2024
Same author

The environmentally-regulated interplay between local three-dimensional chromatin organisation and transcription of proVWX in E. coli.

Nature communications·2023
Same author

Superstructure Detection in Nucleosome Distribution Shows Common Pattern within a Chromosome and within the Genome.

Life (Basel, Switzerland)·2022
Same author

Inter-nucleosomal potentials from nucleosomal positioning data.

The European physical journal. E, Soft matter·2022
Same journal

Tension on dsDNA bound to ssDNA-RecA filaments may play an important role in driving efficient and accurate homology recognition and strand exchange.

Physical review. E, Statistical, nonlinear, and soft matter physics·2016
Same journal

Publisher's Note: Amplitude-phase coupling drives chimera states in globally coupled laser networks [Phys. Rev. E 91, 040901(R) (2015)].

Physical review. E, Statistical, nonlinear, and soft matter physics·2016
Same journal

Erratum: Shapes of sedimenting soft elastic capsules in a viscous fluid [Phys. Rev. E 92, 033003 (2015)].

Physical review. E, Statistical, nonlinear, and soft matter physics·2016
Same journal

Erratum: Attenuation of excitation decay rate due to collective effect [Phys. Rev. E 90, 022142 (2014)].

Physical review. E, Statistical, nonlinear, and soft matter physics·2016
Same journal

Publisher's Note: Role of connectivity and fluctuations in the nucleation of calcium waves in cardiac cells [Phys. Rev. E 92, 052715 (2015)].

Physical review. E, Statistical, nonlinear, and soft matter physics·2016
Same journal

Publisher's Note: Lattice Boltzmann approach for complex nonequilibrium flows [Phys. Rev. E 92, 043308 (2015)].

Physical review. E, Statistical, nonlinear, and soft matter physics·2016
See all related articles

Chromatin fiber folding in the cell nucleus remains poorly understood. A new polymer model explains how random loops of varying sizes are essential for higher-order chromatin structure and gene regulation.

Area of Science:

  • Molecular Biology
  • Polymer Physics
  • Genomics

Background:

  • Higher-order chromatin fiber folding is crucial for gene regulation within the cell nucleus.
  • Factors like gene density and transcriptional activity influence chromatin folding patterns.
  • Existing models struggle to explain observed chromatin behavior at large scales.

Purpose of the Study:

  • To investigate the higher-order folding motifs of the chromatin fiber.
  • To develop a polymer model explaining the observed plateau in mean square distance at large fiber lengths.
  • To elucidate the role of random looping in chromatin structure and gene regulation.

Main Methods:

  • Development of a polymer model incorporating random looping.
  • Analytical derivation of mean square displacement for chromatin fiber segments.

Related Experiment Videos

  • Numerical simulations involving quenched averaging over random loop configurations (random matrix ensemble).

    • Main Results:

    • The proposed polymer model successfully explains the leveling-off of mean square distance () at chromatin fiber lengths above 5-10 Mb.
    • Random looping, across all scales, is identified as a critical factor for accurately modeling chromatin structure.
    • The model provides an analytical expression for bead displacement, validated by numerical simulations.

    Conclusions:

    • Random looping is a fundamental mechanism driving higher-order chromatin fiber organization.
    • The developed polymer model offers a framework for understanding chromatin folding and its impact on gene regulation.
    • Loops of all sizes are necessary to accurately represent the complex folding of the chromatin fiber in vivo.