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3DPolyS-LE: an accessible simulation framework to model the interplay between chromatin and loop extrusion
SUMMARY: Recent studies suggest that the loop extrusion activity of Structural Maintenance of Chromosomes complexes is central to proper organization of genomes in vivo. Polymer physics-based modeling of chromosome structure has been instrumental to assess which structures such extrusion can create....
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9750120/ https://www.ncbi.nlm.nih.gov/pubmed/36355469 http://dx.doi.org/10.1093/bioinformatics/btac705 |
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author | Gitchev, Todor Zala, Gabriel Meister, Peter Jost, Daniel |
author_facet | Gitchev, Todor Zala, Gabriel Meister, Peter Jost, Daniel |
author_sort | Gitchev, Todor |
collection | PubMed |
description | SUMMARY: Recent studies suggest that the loop extrusion activity of Structural Maintenance of Chromosomes complexes is central to proper organization of genomes in vivo. Polymer physics-based modeling of chromosome structure has been instrumental to assess which structures such extrusion can create. Only few laboratories however have the technical and computational expertise to create in silico models combining dynamic features of chromatin and loop extruders. Here, we present 3DPolyS-LE, a self-contained, easy to use modeling and simulation framework allowing non-specialists to ask how specific properties of loop extruders and boundary elements impact on 3D chromosome structure. 3DPolyS-LE also provides algorithms to compare predictions with experimental Hi-C data. AVAILABILITY AND IMPLEMENTATION: Software available at https://gitlab.com/togop/3DPolyS-LE; implemented in Python and Fortran 2003 and supported on any Unix-based operating system (Linux and Mac OS). SUPPLEMENTARY INFORMATION: Supplementary information are available at Bioinformatics online. |
format | Online Article Text |
id | pubmed-9750120 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-97501202022-12-15 3DPolyS-LE: an accessible simulation framework to model the interplay between chromatin and loop extrusion Gitchev, Todor Zala, Gabriel Meister, Peter Jost, Daniel Bioinformatics Applications Note SUMMARY: Recent studies suggest that the loop extrusion activity of Structural Maintenance of Chromosomes complexes is central to proper organization of genomes in vivo. Polymer physics-based modeling of chromosome structure has been instrumental to assess which structures such extrusion can create. Only few laboratories however have the technical and computational expertise to create in silico models combining dynamic features of chromatin and loop extruders. Here, we present 3DPolyS-LE, a self-contained, easy to use modeling and simulation framework allowing non-specialists to ask how specific properties of loop extruders and boundary elements impact on 3D chromosome structure. 3DPolyS-LE also provides algorithms to compare predictions with experimental Hi-C data. AVAILABILITY AND IMPLEMENTATION: Software available at https://gitlab.com/togop/3DPolyS-LE; implemented in Python and Fortran 2003 and supported on any Unix-based operating system (Linux and Mac OS). SUPPLEMENTARY INFORMATION: Supplementary information are available at Bioinformatics online. Oxford University Press 2022-11-10 /pmc/articles/PMC9750120/ /pubmed/36355469 http://dx.doi.org/10.1093/bioinformatics/btac705 Text en © The Author(s) 2022. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Applications Note Gitchev, Todor Zala, Gabriel Meister, Peter Jost, Daniel 3DPolyS-LE: an accessible simulation framework to model the interplay between chromatin and loop extrusion |
title | 3DPolyS-LE: an accessible simulation framework to model the interplay between chromatin and loop extrusion |
title_full | 3DPolyS-LE: an accessible simulation framework to model the interplay between chromatin and loop extrusion |
title_fullStr | 3DPolyS-LE: an accessible simulation framework to model the interplay between chromatin and loop extrusion |
title_full_unstemmed | 3DPolyS-LE: an accessible simulation framework to model the interplay between chromatin and loop extrusion |
title_short | 3DPolyS-LE: an accessible simulation framework to model the interplay between chromatin and loop extrusion |
title_sort | 3dpolys-le: an accessible simulation framework to model the interplay between chromatin and loop extrusion |
topic | Applications Note |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9750120/ https://www.ncbi.nlm.nih.gov/pubmed/36355469 http://dx.doi.org/10.1093/bioinformatics/btac705 |
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