Encounter times of chromatin loci influenced by polymer decondensation

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. DOI: 10.1103/PhysRevE.97.032417 Repairing DNA double-strand breaks (DSBs) is a key step for cell survival. However, the underlying physical mechanism remains difficult to describe, mostly because it involves multiple molecular steps involving small (nanometer) and large (micrometer) scales. During the homologous recombination (HR) pathway, broken strands perform inside a large portion of the cell nucleus a random search for a homologous DNA template. Once this template is found, it will be used to copy the missing base pairs before repair [1]. As revealed by single-particle trajectories of chromatin [2,3], following a DSB, the broken locus dynamics is modified so that it can scan a larger area of the nucleus. This modification was attributed in part to chromatin decondensation and the release of tethering forces acting locally on the chromatin [4]. These changes could have consequences on the search for a homologous template. We present here polymer modeling and analytical tools to further characterize this search step.We recall that search processes involving two loci located on the same polymers have been investigated in the context of polymer looping [5][6][7][8]. However, much less is known about the mean time for two monomers belonging to two different polymers. The multiple relaxation times associated with the polymer dynamics [9] shows that computing the looping time cannot be obtained by the classical activation escape from a potential well (representing the end-to-end distance energy) [10]. For a long polymer, the mean encounter time is influenced by the slowest internal relaxation times of the polymer [9]. However, it is not clear how these times contribute to the mean encounter time for two monomers located on two different polymers. In addition, in a confined environment, the probability distribution function of monomers varies along the polymer chain [11,12], which again can influence the search time.To account for chromatin reorganization following DSB [4], we study here the random search of two monomers that belongs to two different monomers using the Ro...

The rich inner life of the cell nucleus: dynamic organization, active flows, and emergent rheology

“…Numerous site-specific DNA transactions such as transcription, replication, and DNA repair contribute to chromatin dynamics during the cell cycle, giving rise to chromatin dynamics at different timescales and length scales. Over the past two decades, chromatin dynamics has been investigated by tracking motions of fluorescently tagged nuclear proteins visualizing structures of interest such as nucleosomes (Xu et al 2018 ; Nagashima et al 2019 ; Ashwin et al 2019 ), single genes (Marshall et al 1997 ; Belmont and Straight 1998 ; Levi et al 2005 ; Chuang et al 2006 ; Bronstein et al 2009 ; Weber et al 2012 ; Chen et al 2013 ; Lampo et al 2016 ; Germier et al 2017 ; Amitai and Holcman 2018 ; Khanna et al 2019 ; Vivante et al 2020 ), nuclear proteins, enzymes and machineries (Misteli 2001 ; Carmo-Fonseca et al 2002 ; Darzacq et al 2007 ; Stixová et al 2011 ; Cisse et al 2013 ; Hinde et al 2014 ; Eaton and Zidovska 2020 ), and subchromosomal foci (Bornfleth et al 1999 ; Albiez et al 2006 ), as well as entire chromosome territories (Zink et al 1998 ; Edelmann et al 2001 ). Furthermore, experiments measuring fluorescence recovery after photobleaching (Abney et al 1997 ; Misteli et al 2000 ; Phair and Misteli 2000 ; Kimura and Cook 2001 ) and photoactivation (Mora-Bermúdez et al 2007 ; Wiesmeijer et al 2008 ) of nuclear proteins have revealed their peculiar kinetics.…”

Complex Chromatin Motions for DNA Repair

“…Changes in chromatin mobility are thus a general feature of the cellular response to DSBs affecting the whole genome. Experimental and theoretical studies suggest that changes in chromatin mobility of both damaged and undamaged loci increase the probability of contact between distant loci, thus promoting the kinetics of homologous pairing ( Miné-Hattab and Rothstein, 2012 ; Guerin et al, 2016 ; Miné-Hattab et al, 2017 ; Amitai and Holcman, 2018 ).…”

“…Second, undamaged chromatin also becomes more dynamic during DSB repair, albeit to a lesser extent than repair sites ( Figure 1B ) ( Chiolo et al, 2011 ; Krawczyk et al, 2012 ; Miné-Hattab and Rothstein, 2012 ; Seeber et al, 2013 ; Lottersberger et al, 2015 ; Strecker et al, 2016 ; Herbert et al, 2017 ; Lawrimore et al, 2017 ; Miné-Hattab et al, 2017 ; Caridi et al, 2018a ; Smith et al, 2019 ; Zada et al, 2019 ). The significance of the genome-wide increase in nuclear exploration is still under debate, but this response might increase the frequency of DNA contacts to facilitate homology search ( Gehen et al, 2011 ; Neumann et al, 2012 ; Mine-Hattab and Rothstein, 2013 ; Amitai and Holcman, 2018 ), or reflect chromatin relaxation to promote access for repair ( Kruhlak et al, 2006 ; Ziv et al, 2006 ; Seeber et al, 2013 ; Delabaere and Chiolo, 2016 ). Third, repair sites undergoing HR aggregate into larger units, or “clusters” ( Figure 1C ) ( Lisby et al, 2003 ; Aten et al, 2004 ; Kruhlak et al, 2006 ; Chiolo et al, 2011 , 2013 ; Krawczyk et al, 2012 ; Neumaier et al, 2012 ; Cho et al, 2014 ; Caron et al, 2015 ; Aymard et al, 2017 ; Caridi et al, 2018a ; Schrank et al, 2018 ; Oshidari et al, 2019a ; Waterman et al, 2019 ) (reviewed in Chiolo et al, 2013 ; Guénolé and Legube, 2017 ; Schrank and Gautier, 2019 ), likely to facilitate DSB signaling and resection, e.g., by increasing the local concentration of checkpoint and repair proteins ( Chiolo et al, 2013 ; Schrank et al, 2018 ; Kilic et al, 2019 ; Oshidari et al, 2019a ; Schrank and Gautier, 2019 ).…”

Complex chromatin motions for DNA repair

“…Changes in chromatin mobility are thus a general feature of the cellular response to DSBs affecting the whole genome. Experimental and theoretical studies suggest that changes in chromatin mobility of both damaged and undamaged loci increase the probability of contact between distant loci, thus promoting the kinetics of homologous pairing (Miné-Hattab and Rothstein, 2012;Guerin et al, 2016;Miné-Hattab et al, 2017;Amitai and Holcman, 2018).…”

“…Second, undamaged chromatin also becomes more dynamic during DSB repair, albeit to a lesser extent than repair sites (Figure 1B) (Chiolo et al, 2011;Krawczyk et al, 2012;Miné-Hattab and Rothstein, 2012;Seeber et al, 2013;Lottersberger et al, 2015;Strecker et al, 2016;Herbert et al, 2017;Lawrimore et al, 2017;Miné-Hattab et al, 2017;Caridi et al, 2018a;Smith et al, 2019;Zada et al, 2019). The significance of the genome-wide increase in nuclear exploration is still under debate, but this response might increase the frequency of DNA contacts to facilitate homology search (Gehen et al, 2011;Neumann et al, 2012;Mine-Hattab and Rothstein, 2013;Amitai and Holcman, 2018), or reflect chromatin relaxation to promote access for repair (Kruhlak et al, 2006;Ziv et al, 2006;Seeber et al, 2013;Delabaere and Chiolo, 2016). Third, repair sites undergoing HR aggregate into larger units, or "clusters" (Figure 1C) (Lisby et al, 2003;Aten et al, 2004;Kruhlak et al, 2006;Chiolo et al, 2011Chiolo et al, , 2013Krawczyk et al, 2012;Neumaier et al, 2012;Cho et al, 2014;Caron et al, 2015;Aymard et al, 2017;Caridi et al, 2018a;Schrank et al, 2018;Oshidari et al, 2019a;Waterman et al, 2019) (reviewed in Chiolo et al, ...…”