Related Experiment Video
Updated: Aug 22, 2025
CRISPR-Mediated Reorganization of Chromatin Loop Structure
Published on: September 14, 2018
3DPolyS-LE: an accessible simulation framework to model the interplay between chromatin and loop extrusion
Todor Gitchev1, Gabriel Zala1, Peter Meister1
1Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, Bern 3012, Switzerland.
Summary:
Recent studies suggest that the loop extrusion activity of Structural Maintenance of Chromosomes complexes is central to proper organization of genomes in vivo. Polymer physics-based modeling of chromosome structure has been instrumental to assess which structures such extrusion can create. Only few laboratories however have the technical and computational expertise to create in silico models combining dynamic features of chromatin and loop extruders. Here, we present 3DPolyS-LE, a self-contained, easy to use modeling and simulation framework allowing non-specialists to ask how specific properties of loop extruders and boundary elements impact on 3D chromosome structure. 3DPolyS-LE also provides algorithms to compare predictions with experimental Hi-C data.
Availability And Implementation:
Software available at https://gitlab.com/togop/3DPolyS-LE; implemented in Python and Fortran 2003 and supported on any Unix-based operating system (Linux and Mac OS).
Supplementary Information:
Supplementary information are available at Bioinformatics online.
More Related Videos
09:17Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
Published on: March 1, 2022
21:55Chromatin Interaction Analysis with Paired-End Tag Sequencing ChIA-PET for Mapping Chromatin Interactions and Understanding Transcription Regulation
Published on: April 30, 2012
Related Concept Videos
02:54Nucleosome Remodeling
Nucleosome remodeling complex
Eukaryotic cells have specialized enzymes called ATP-dependent nucleosome remodeling enzymes. These enzymes...
02:21Chromatin Packaging
The chromatin
In combination with specialized DNA binding protein called Histones, the DNA double helix forms a compact DNA: protein complex called chromatin. The chromatin itself is further compacted into higher-order...
02:05Duplication of Chromatin Structure
The basic unit of the chromatin is the nucleosome, consisting of DNA wrapped around octameric histone proteins and short stretches of linker DNA separating individual nucleosomes. The histone proteins within the nucleosome have their...
02:25Spreading of Chromatin Modifications
Writers
The writer...
01:51Lampbrush Chromosomes
LBCs are made up of two pairs of conjugating homologous chromatids. Each chromatid consists of alternatively positioned regions of condensed-inactive chromatin and loosely placed-active side loops, which can be contracted and extended. The loops...
03:17Inheritance of Chromatin Structures