Encounter times of chromatin loci influenced by polymer decondensation

Physical Review. E
A Amitai, D Holcman

Abstract

The time for a DNA sequence to find its homologous counterpart depends on a long random search inside the cell nucleus. Using polymer models, we compute here the mean first encounter time (MFET) between two sites located on two different polymer chains and confined locally by potential wells. We find that reducing tethering forces acting on the polymers results in local decondensation, and numerical simulations of the polymer model show that these changes are associated with a reduction of the MFET by several orders of magnitude. We derive here new asymptotic formula for the MFET, confirmed by Brownian simulations. We conclude from the present modeling approach that the fast search for homology is mediated by a local chromatin decondensation due to the release of multiple chromatin tethering forces. The present scenario could explain how the homologous recombination pathway for double-stranded DNA repair is controlled by its random search step.

References

Mar 14, 2003·Physical Review Letters·I M Sokolov
Mar 7, 2006·Chromosoma·Ekaterina Revenkova, Rolf Jessberger
Nov 28, 2007·Nature Reviews. Genetics·Adi Barzel, Martin Kupiec
May 21, 2009·Genome Biology·Christine K SchmidtFrank Uhlmann
Mar 9, 2011·The Journal of Cell Biology·Christophe Zimmer, Emmanuelle Fabre
Apr 8, 2011·Current Opinion in Cell Biology·Dieter W Heermann
Apr 10, 2012·Nature Cell Biology·Judith Miné-Hattab, Rodney Rothstein
Jun 9, 2012·Methods : a Companion to Methods in Enzymology·Dieter W HeermannYixue Li
Sep 26, 2012·Physical Review Letters·A AmitaiD Holcman
Jan 3, 2013·The Journal of Chemical Physics·A AmitaiD Holcman
Dec 18, 2013·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·A Amitai, D Holcman
May 16, 2014·Nature Reviews. Molecular Cell Biology·Jörg RenkawitzStefan Jentsch
May 20, 2015·Cold Spring Harbor Perspectives in Biology·Denise Zickler, Nancy Kleckner
Aug 25, 2015·Nature Communications·I BronshteinY Garini
Sep 1, 2015·PLoS Computational Biology·Assaf AmitaiDavid Holcman
Jan 10, 2017·Nature Structural & Molecular Biology·Michael H HauerSusan M Gasser

❮ Previous
Next ❯

Citations

Dec 11, 2019·Biophysical Journal·Jonah A Eaton, Alexandra Zidovska

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.