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Two loci single particle trajectories analysis: constructing a first passage time statistics of local chromatin exploration

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...

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Detalles Bibliográficos
Autores principales: Shukron, Ofir, Hauer, Michael, Holcman, David
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5583259/
https://www.ncbi.nlm.nih.gov/pubmed/28871173
http://dx.doi.org/10.1038/s41598-017-10842-9
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author Shukron, Ofir
Hauer, Michael
Holcman, David
author_facet Shukron, Ofir
Hauer, Michael
Holcman, David
author_sort Shukron, Ofir
collection PubMed
description 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 varying from one to few hundreds of nanometers, it predicts the local changes in the number of binding molecules following DSB and can be used to characterize the local dynamic of the chromatin.
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spelling pubmed-55832592017-09-06 Two loci single particle trajectories analysis: constructing a first passage time statistics of local chromatin exploration Shukron, Ofir Hauer, Michael Holcman, David Sci Rep Article 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 varying from one to few hundreds of nanometers, it predicts the local changes in the number of binding molecules following DSB and can be used to characterize the local dynamic of the chromatin. Nature Publishing Group UK 2017-09-04 /pmc/articles/PMC5583259/ /pubmed/28871173 http://dx.doi.org/10.1038/s41598-017-10842-9 Text en © The Author(s) 2017 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Shukron, Ofir
Hauer, Michael
Holcman, David
Two loci single particle trajectories analysis: constructing a first passage time statistics of local chromatin exploration
title Two loci single particle trajectories analysis: constructing a first passage time statistics of local chromatin exploration
title_full Two loci single particle trajectories analysis: constructing a first passage time statistics of local chromatin exploration
title_fullStr Two loci single particle trajectories analysis: constructing a first passage time statistics of local chromatin exploration
title_full_unstemmed Two loci single particle trajectories analysis: constructing a first passage time statistics of local chromatin exploration
title_short Two loci single particle trajectories analysis: constructing a first passage time statistics of local chromatin exploration
title_sort two loci single particle trajectories analysis: constructing a first passage time statistics of local chromatin exploration
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5583259/
https://www.ncbi.nlm.nih.gov/pubmed/28871173
http://dx.doi.org/10.1038/s41598-017-10842-9
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