DeTOKI identifies and characterizes the dynamics of chromatin TAD-like domains in a single cell

Topologically associating domains (TAD) are a key structure of the 3D mammalian genomes. However, the prevalence and dynamics of TAD-like domains in single cells remain elusive. Here we develop a new algorithm, named deTOKI, to decode TAD-like domains with single-cell Hi-C data. By non-negative matr...

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Detalles Bibliográficos
Autores principales: Li, Xiao, Zeng, Guangjie, Li, Angsheng, Zhang, Zhihua
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Software
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8314462/
https://www.ncbi.nlm.nih.gov/pubmed/34311744
http://dx.doi.org/10.1186/s13059-021-02435-7
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author Li, Xiao
Zeng, Guangjie
Li, Angsheng
Zhang, Zhihua
author_facet Li, Xiao
Zeng, Guangjie
Li, Angsheng
Zhang, Zhihua
author_sort Li, Xiao
collection PubMed
description Topologically associating domains (TAD) are a key structure of the 3D mammalian genomes. However, the prevalence and dynamics of TAD-like domains in single cells remain elusive. Here we develop a new algorithm, named deTOKI, to decode TAD-like domains with single-cell Hi-C data. By non-negative matrix factorization, deTOKI seeks regions that insulate the genome into blocks with minimal chance of clustering. deTOKI outperforms competing tools and reliably identifies TAD-like domains in single cells. Finally, we find that TAD-like domains are not only prevalent, but also subject to tight regulation in single cells. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-021-02435-7.
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spelling pubmed-83144622021-07-28 DeTOKI identifies and characterizes the dynamics of chromatin TAD-like domains in a single cell Li, Xiao Zeng, Guangjie Li, Angsheng Zhang, Zhihua Genome Biol Software Topologically associating domains (TAD) are a key structure of the 3D mammalian genomes. However, the prevalence and dynamics of TAD-like domains in single cells remain elusive. Here we develop a new algorithm, named deTOKI, to decode TAD-like domains with single-cell Hi-C data. By non-negative matrix factorization, deTOKI seeks regions that insulate the genome into blocks with minimal chance of clustering. deTOKI outperforms competing tools and reliably identifies TAD-like domains in single cells. Finally, we find that TAD-like domains are not only prevalent, but also subject to tight regulation in single cells. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-021-02435-7. BioMed Central 2021-07-27 /pmc/articles/PMC8314462/ /pubmed/34311744 http://dx.doi.org/10.1186/s13059-021-02435-7 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis 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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Software
Li, Xiao
Zeng, Guangjie
Li, Angsheng
Zhang, Zhihua
DeTOKI identifies and characterizes the dynamics of chromatin TAD-like domains in a single cell
title DeTOKI identifies and characterizes the dynamics of chromatin TAD-like domains in a single cell
title_full DeTOKI identifies and characterizes the dynamics of chromatin TAD-like domains in a single cell
title_fullStr DeTOKI identifies and characterizes the dynamics of chromatin TAD-like domains in a single cell
title_full_unstemmed DeTOKI identifies and characterizes the dynamics of chromatin TAD-like domains in a single cell
title_short DeTOKI identifies and characterizes the dynamics of chromatin TAD-like domains in a single cell
title_sort detoki identifies and characterizes the dynamics of chromatin tad-like domains in a single cell
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8314462/
https://www.ncbi.nlm.nih.gov/pubmed/34311744
http://dx.doi.org/10.1186/s13059-021-02435-7
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AT liangsheng detokiidentifiesandcharacterizesthedynamicsofchromatintadlikedomainsinasinglecell
AT zhangzhihua detokiidentifiesandcharacterizesthedynamicsofchromatintadlikedomainsinasinglecell

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