OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries

The spatial organization of chromatin in the nucleus has been implicated in regulating gene expression. Maps of high-frequency interactions between different segments of chromatin have revealed topologically associating domains (TADs), within which most of the regulatory interactions are thought to...

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Detalles Bibliográficos
Autores principales: An, Lin, Yang, Tao, Yang, Jiahao, Nuebler, Johannes, Xiang, Guanjue, Hardison, Ross C., Li, Qunhua, Zhang, Yu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6918570/
https://www.ncbi.nlm.nih.gov/pubmed/31847870
http://dx.doi.org/10.1186/s13059-019-1893-y
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author An, Lin
Yang, Tao
Yang, Jiahao
Nuebler, Johannes
Xiang, Guanjue
Hardison, Ross C.
Li, Qunhua
Zhang, Yu
author_facet An, Lin
Yang, Tao
Yang, Jiahao
Nuebler, Johannes
Xiang, Guanjue
Hardison, Ross C.
Li, Qunhua
Zhang, Yu
author_sort An, Lin
collection PubMed
description The spatial organization of chromatin in the nucleus has been implicated in regulating gene expression. Maps of high-frequency interactions between different segments of chromatin have revealed topologically associating domains (TADs), within which most of the regulatory interactions are thought to occur. TADs are not homogeneous structural units but appear to be organized into a hierarchy. We present OnTAD, an optimized nested TAD caller from Hi-C data, to identify hierarchical TADs. OnTAD reveals new biological insights into the role of different TAD levels, boundary usage in gene regulation, the loop extrusion model, and compartmental domains. OnTAD is available at https://github.com/anlin00007/OnTAD.
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spelling pubmed-69185702019-12-20 OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries An, Lin Yang, Tao Yang, Jiahao Nuebler, Johannes Xiang, Guanjue Hardison, Ross C. Li, Qunhua Zhang, Yu Genome Biol Method The spatial organization of chromatin in the nucleus has been implicated in regulating gene expression. Maps of high-frequency interactions between different segments of chromatin have revealed topologically associating domains (TADs), within which most of the regulatory interactions are thought to occur. TADs are not homogeneous structural units but appear to be organized into a hierarchy. We present OnTAD, an optimized nested TAD caller from Hi-C data, to identify hierarchical TADs. OnTAD reveals new biological insights into the role of different TAD levels, boundary usage in gene regulation, the loop extrusion model, and compartmental domains. OnTAD is available at https://github.com/anlin00007/OnTAD. BioMed Central 2019-12-18 /pmc/articles/PMC6918570/ /pubmed/31847870 http://dx.doi.org/10.1186/s13059-019-1893-y Text en © The Author(s). 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided 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 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 Method
An, Lin
Yang, Tao
Yang, Jiahao
Nuebler, Johannes
Xiang, Guanjue
Hardison, Ross C.
Li, Qunhua
Zhang, Yu
OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries
title OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries
title_full OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries
title_fullStr OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries
title_full_unstemmed OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries
title_short OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries
title_sort ontad: hierarchical domain structure reveals the divergence of activity among tads and boundaries
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6918570/
https://www.ncbi.nlm.nih.gov/pubmed/31847870
http://dx.doi.org/10.1186/s13059-019-1893-y
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