TY - JOUR T1 - Two loci single particle trajectories analysis: constructing a first passage time statistics of local chromatin exploration JF - bioRxiv DO - 10.1101/135012 SP - 135012 AU - O. Shukron AU - D. Holcman Y1 - 2017/01/01 UR - http://biorxiv.org/content/early/2017/05/06/135012.abstract N2 - Stochastic single particle trajectories are used to explore the local chromatin organization. We present here a statistical analysis of the first contact time distributions between two tagged loci recorded experimentally. First, we extract the association and dissociation times from data for various genomic distances between loci and we show that the looping time occurs in confined nanometer regions. Second, we characterize the looping time distribution for two loci in the presence of multiple DNA damages. Finally, we construct a polymer model that accounts for the local chromatin organization before and after a double-stranded DNA break (DSB) to estimate the level of chromatin decompaction. This novel passage time statistics method allows extracting transient dynamic at scales from one to few hundreds of nanometers, predicts the local changes in the number of binding molecules following DSB and can be used to better characterize the local dynamic of the chromatin.Author summary Extracting local properties of the chromatin from temporal tracking of a tagged genomic section remains a challenging task. In this work, we analyze empirical trajectories of two tagged loci, simultaneously tracked over time and positioned at various genomic distance apart. The correlated motion of two loci provides complementary information compared to single ones, contained in the distribution of their recurrence encounter times. We show here how to construct such distribution from empirical data. In particular, We find that this distribution is affected after the induction of damages by Zeocin drugs (causing double strand DNA breaks) and report the changes in the local chromatin environment exploration. Finally, we examine the local chromatin remodeling following a double strand breaks, by using simulation of a randomly cross linked polymer model. We show that only small a small percentage of cross-linker molecules are removed following damages. The analysis presented in this work could be extended to multiple tagged loci. ER -