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Identification of alternative topological domains in chromatin
Chromosome conformation capture experiments have led to the discovery of dense, contiguous, megabase-sized topological domains that are similar across cell types and conserved across species. These domains are strongly correlated with a number of chromatin markers and have since been included in a n...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4019371/ https://www.ncbi.nlm.nih.gov/pubmed/24868242 http://dx.doi.org/10.1186/1748-7188-9-14 |
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author | Filippova, Darya Patro, Rob Duggal, Geet Kingsford, Carl |
author_facet | Filippova, Darya Patro, Rob Duggal, Geet Kingsford, Carl |
author_sort | Filippova, Darya |
collection | PubMed |
description | Chromosome conformation capture experiments have led to the discovery of dense, contiguous, megabase-sized topological domains that are similar across cell types and conserved across species. These domains are strongly correlated with a number of chromatin markers and have since been included in a number of analyses. However, functionally-relevant domains may exist at multiple length scales. We introduce a new and efficient algorithm that is able to capture persistent domains across various resolutions by adjusting a single scale parameter. The ensemble of domains we identify allows us to quantify the degree to which the domain structure is hierarchical as opposed to overlapping, and our analysis reveals a pronounced hierarchical structure in which larger stable domains tend to completely contain smaller domains. The identified novel domains are substantially different from domains reported previously and are highly enriched for insulating factor CTCF binding and histone marks at the boundaries. |
format | Online Article Text |
id | pubmed-4019371 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-40193712014-05-27 Identification of alternative topological domains in chromatin Filippova, Darya Patro, Rob Duggal, Geet Kingsford, Carl Algorithms Mol Biol Research Chromosome conformation capture experiments have led to the discovery of dense, contiguous, megabase-sized topological domains that are similar across cell types and conserved across species. These domains are strongly correlated with a number of chromatin markers and have since been included in a number of analyses. However, functionally-relevant domains may exist at multiple length scales. We introduce a new and efficient algorithm that is able to capture persistent domains across various resolutions by adjusting a single scale parameter. The ensemble of domains we identify allows us to quantify the degree to which the domain structure is hierarchical as opposed to overlapping, and our analysis reveals a pronounced hierarchical structure in which larger stable domains tend to completely contain smaller domains. The identified novel domains are substantially different from domains reported previously and are highly enriched for insulating factor CTCF binding and histone marks at the boundaries. BioMed Central 2014-05-03 /pmc/articles/PMC4019371/ /pubmed/24868242 http://dx.doi.org/10.1186/1748-7188-9-14 Text en Copyright © 2014 Filippova et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Filippova, Darya Patro, Rob Duggal, Geet Kingsford, Carl Identification of alternative topological domains in chromatin |
title | Identification of alternative topological domains in chromatin |
title_full | Identification of alternative topological domains in chromatin |
title_fullStr | Identification of alternative topological domains in chromatin |
title_full_unstemmed | Identification of alternative topological domains in chromatin |
title_short | Identification of alternative topological domains in chromatin |
title_sort | identification of alternative topological domains in chromatin |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4019371/ https://www.ncbi.nlm.nih.gov/pubmed/24868242 http://dx.doi.org/10.1186/1748-7188-9-14 |
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