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Transient chromatin properties revealed by polymer models and stochastic simulations constructed from Chromosomal Capture data
Chromatin organization can be probed by Chromosomal Capture (5C) data, from which the encounter probability (EP) between genomic sites is presented in a large matrix. This matrix is averaged over a large cell population, revealing diagonal blocks called Topological Associating Domains (TADs) that re...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5393903/ https://www.ncbi.nlm.nih.gov/pubmed/28369076 http://dx.doi.org/10.1371/journal.pcbi.1005469 |
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author | Shukron, Ofir Holcman, David |
author_facet | Shukron, Ofir Holcman, David |
author_sort | Shukron, Ofir |
collection | PubMed |
description | Chromatin organization can be probed by Chromosomal Capture (5C) data, from which the encounter probability (EP) between genomic sites is presented in a large matrix. This matrix is averaged over a large cell population, revealing diagonal blocks called Topological Associating Domains (TADs) that represent a sub-chromatin organization. To study the relation between chromatin organization and gene regulation, we introduce a computational procedure to construct a bead-spring polymer model based on the EP matrix. The model permits exploring transient properties constrained by the statistics of the 5C data. To construct the polymer model, we proceed in two steps: first, we introduce a minimal number of random connectors inside restricted regions to account for diagonal blocks. Second, we account for long-range frequent specific genomic interactions. Using the constructed polymer, we compute the first encounter time distribution and the conditional probability of three key genomic sites. By simulating single particle trajectories of loci located on the constructed polymers from 5C data, we found a large variability of the anomalous exponent, used to interpret live cell imaging trajectories. The present polymer construction provides a generic tool to study steady-state and transient properties of chromatin constrained by some physical properties embedded in 5C data. |
format | Online Article Text |
id | pubmed-5393903 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-53939032017-05-15 Transient chromatin properties revealed by polymer models and stochastic simulations constructed from Chromosomal Capture data Shukron, Ofir Holcman, David PLoS Comput Biol Research Article Chromatin organization can be probed by Chromosomal Capture (5C) data, from which the encounter probability (EP) between genomic sites is presented in a large matrix. This matrix is averaged over a large cell population, revealing diagonal blocks called Topological Associating Domains (TADs) that represent a sub-chromatin organization. To study the relation between chromatin organization and gene regulation, we introduce a computational procedure to construct a bead-spring polymer model based on the EP matrix. The model permits exploring transient properties constrained by the statistics of the 5C data. To construct the polymer model, we proceed in two steps: first, we introduce a minimal number of random connectors inside restricted regions to account for diagonal blocks. Second, we account for long-range frequent specific genomic interactions. Using the constructed polymer, we compute the first encounter time distribution and the conditional probability of three key genomic sites. By simulating single particle trajectories of loci located on the constructed polymers from 5C data, we found a large variability of the anomalous exponent, used to interpret live cell imaging trajectories. The present polymer construction provides a generic tool to study steady-state and transient properties of chromatin constrained by some physical properties embedded in 5C data. Public Library of Science 2017-04-03 /pmc/articles/PMC5393903/ /pubmed/28369076 http://dx.doi.org/10.1371/journal.pcbi.1005469 Text en © 2017 Shukron, Holcman http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Shukron, Ofir Holcman, David Transient chromatin properties revealed by polymer models and stochastic simulations constructed from Chromosomal Capture data |
title | Transient chromatin properties revealed by polymer models and stochastic simulations constructed from Chromosomal Capture data |
title_full | Transient chromatin properties revealed by polymer models and stochastic simulations constructed from Chromosomal Capture data |
title_fullStr | Transient chromatin properties revealed by polymer models and stochastic simulations constructed from Chromosomal Capture data |
title_full_unstemmed | Transient chromatin properties revealed by polymer models and stochastic simulations constructed from Chromosomal Capture data |
title_short | Transient chromatin properties revealed by polymer models and stochastic simulations constructed from Chromosomal Capture data |
title_sort | transient chromatin properties revealed by polymer models and stochastic simulations constructed from chromosomal capture data |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5393903/ https://www.ncbi.nlm.nih.gov/pubmed/28369076 http://dx.doi.org/10.1371/journal.pcbi.1005469 |
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