Back to Search
Start Over
Three-Dimensional Loop Extrusion
- Source :
- Biophys J, Bonato, A & Michieletto, D 2021, ' Three-Dimensional Loop Extrusion ', Biophysical Journal, vol. 120, no. 24, pp. 5544-5552 . https://doi.org/10.1016/j.bpj.2021.11.015
- Publication Year :
- 2021
-
Abstract
- Loop extrusion convincingly describes how certain Structural Maintenance of Chromosome (SMC) proteins mediate the formation of large DNA loops. Yet, most of the existing computational models cannot reconcile recent in vitro observations showing that condensins can traverse each other, bypass large roadblocks and perform steps longer than its own size. To fill this gap, we propose a three-dimensional (3D) "trans-grabbing" model for loop extrusion which not only reproduces the experimental features of loop extrusion by one SMC complex, but also predicts the formation of so-called "Z-loops" via the interaction of two or more SMCs extruding along the same DNA substrate. By performing Molecular Dynamics simulations of this model we discover that the experimentally observed asymmetry in the different types of Z-loops is a natural consequence of the DNA tethering in vitro. Intriguingly, our model predicts this bias to disappear in absence of tethering and a third type of Z-loop, which has not yet been identified in experiments, to appear. Our model naturally explains road-block bypassing and the appearance of steps larger than the SMC size as a consequence of non-contiguous DNA grabbing. Finally, it is the first to our knowledge to address how Z-loops and bypassing might occur in a way that is broadly consistent with existing cis-only 1D loop extrusion models.<br />to appear in biophysical journal
- Subjects :
- Condensin
media_common.quotation_subject
Biophysics
FOS: Physical sciences
Cell Cycle Proteins
Molecular Dynamics Simulation
Condensed Matter - Soft Condensed Matter
Asymmetry
Chromosomes
chemistry.chemical_compound
03 medical and health sciences
Molecular dynamics
0302 clinical medicine
Chromosome (genetic algorithm)
Physics - Biological Physics
Topology (chemistry)
030304 developmental biology
media_common
cond-mat.soft
Physics
0303 health sciences
Computational model
biology
Tethering
Articles
DNA
Loop (topology)
chemistry
Biological Physics (physics.bio-ph)
physics.bio-ph
biology.protein
Soft Condensed Matter (cond-mat.soft)
Extrusion
Biological system
030217 neurology & neurosurgery
Subjects
Details
- Language :
- English
- Database :
- OpenAIRE
- Journal :
- Biophys J, Bonato, A & Michieletto, D 2021, ' Three-Dimensional Loop Extrusion ', Biophysical Journal, vol. 120, no. 24, pp. 5544-5552 . https://doi.org/10.1016/j.bpj.2021.11.015
- Accession number :
- edsair.doi.dedup.....44cd0234d0ddf81d42fcf8899e93d27b