Extrusion of chromatin loops by a composite loop extrusion factor
| Autor: | Ivan V. Surovtsev, Mary Lou P. Bailey, Megan C. King, Jessica F. Williams, Simon G. J. Mochrie, Hao Yan |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
0303 health sciences
Cohesin Statistical Mechanics (cond-mat.stat-mech) Chromosome FOS: Physical sciences musculoskeletal system Article Chromatin 03 medical and health sciences chemistry.chemical_compound Condensin complex 0302 clinical medicine chemistry Biological Physics (physics.bio-ph) Biophysics cardiovascular system Nucleosome Extrusion Chromatin Loop Physics - Biological Physics 030217 neurology & neurosurgery DNA Condensed Matter - Statistical Mechanics 030304 developmental biology |
| Zdroj: | Phys Rev E |
| Popis: | Chromatin loop extrusion by Structural Maintenance of Chromosome (SMC) complexes is thought to underlie intermediate-scale chromatin organization inside cells. Motivated by a number of experiments suggesting that nucleosomes may block loop extrusion by SMCs, such as cohesin and condensin complexes, we introduce and characterize theoretically a composite loop extrusion factor (composite LEF) model. In addition to an SMC complex that creates a chromatin loop by encircling two threads of DNA, this model includes a remodeling complex that relocates or removes nucleosomes as it progresses along the chromatin, and nucleosomes that block SMC translocation along the DNA. Loop extrusion is enabled by SMC motion along nucleosome-free DNA, created in the wake of the remodeling complex, while nucleosome re-binding behind the SMC acts as a ratchet, holding the SMC close to the remodeling complex. We show that, for a wide range of parameter values, this collection of factors constitutes a composite LEF that extrudes loops with a velocity, comparable to the velocity of remodeling complex translocation on chromatin in the absence of SMC, and much faster than loop extrusion by an isolated SMC that is blocked by nucleosomes. Comment: 12 pages, 7 figures |
| Databáze: | OpenAIRE |
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