Using linkage logic theory to control dynamics of a gene regulatory network of a chordate embryo

Abstract Linkage logic theory provides a mathematical criterion to control network dynamics by manipulating activities of a subset of network nodes, which are collectively called a feedback vertex set (FVS). Because many biological functions emerge from dynamics of biological networks, this theory p...

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Autores principales:	Kenji Kobayashi, Kazuki Maeda, Miki Tokuoka, Atsushi Mochizuki, Yutaka Satou
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/03c261f681d44817b685e5c21ddd51ec
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spelling	oai:doaj.org-article:03c261f681d44817b685e5c21ddd51ec2021-12-02T14:03:45ZUsing linkage logic theory to control dynamics of a gene regulatory network of a chordate embryo10.1038/s41598-021-83045-y2045-2322https://doaj.org/article/03c261f681d44817b685e5c21ddd51ec2021-02-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-83045-yhttps://doaj.org/toc/2045-2322Abstract Linkage logic theory provides a mathematical criterion to control network dynamics by manipulating activities of a subset of network nodes, which are collectively called a feedback vertex set (FVS). Because many biological functions emerge from dynamics of biological networks, this theory provides a promising tool for controlling biological functions. By manipulating the activity of FVS molecules identified in a gene regulatory network (GRN) for fate specification of seven tissues in ascidian embryos, we previously succeeded in reproducing six of the seven cell types. Simultaneously, we discovered that the experimentally reconstituted GRN lacked information sufficient to reproduce muscle cells. Here, we utilized linkage logic theory as a tool to find missing edges in the GRN. Then, we identified a FVS from an updated version of the GRN and confirmed that manipulating the activity of this FVS was sufficient to induce all seven cell types, even in a multi-cellular environment. Thus, linkage logic theory provides tools to find missing edges in experimentally reconstituted networks, to determine whether reconstituted networks contain sufficient information to fulfil expected functions, and to reprogram cell fate.Kenji KobayashiKazuki MaedaMiki TokuokaAtsushi MochizukiYutaka SatouNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Kenji Kobayashi Kazuki Maeda Miki Tokuoka Atsushi Mochizuki Yutaka Satou Using linkage logic theory to control dynamics of a gene regulatory network of a chordate embryo
description	Abstract Linkage logic theory provides a mathematical criterion to control network dynamics by manipulating activities of a subset of network nodes, which are collectively called a feedback vertex set (FVS). Because many biological functions emerge from dynamics of biological networks, this theory provides a promising tool for controlling biological functions. By manipulating the activity of FVS molecules identified in a gene regulatory network (GRN) for fate specification of seven tissues in ascidian embryos, we previously succeeded in reproducing six of the seven cell types. Simultaneously, we discovered that the experimentally reconstituted GRN lacked information sufficient to reproduce muscle cells. Here, we utilized linkage logic theory as a tool to find missing edges in the GRN. Then, we identified a FVS from an updated version of the GRN and confirmed that manipulating the activity of this FVS was sufficient to induce all seven cell types, even in a multi-cellular environment. Thus, linkage logic theory provides tools to find missing edges in experimentally reconstituted networks, to determine whether reconstituted networks contain sufficient information to fulfil expected functions, and to reprogram cell fate.
format	article
author	Kenji Kobayashi Kazuki Maeda Miki Tokuoka Atsushi Mochizuki Yutaka Satou
author_facet	Kenji Kobayashi Kazuki Maeda Miki Tokuoka Atsushi Mochizuki Yutaka Satou
author_sort	Kenji Kobayashi
title	Using linkage logic theory to control dynamics of a gene regulatory network of a chordate embryo
title_short	Using linkage logic theory to control dynamics of a gene regulatory network of a chordate embryo
title_full	Using linkage logic theory to control dynamics of a gene regulatory network of a chordate embryo
title_fullStr	Using linkage logic theory to control dynamics of a gene regulatory network of a chordate embryo
title_full_unstemmed	Using linkage logic theory to control dynamics of a gene regulatory network of a chordate embryo
title_sort	using linkage logic theory to control dynamics of a gene regulatory network of a chordate embryo
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/03c261f681d44817b685e5c21ddd51ec
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_version_	1718392062210998272

Using linkage logic theory to control dynamics of a gene regulatory network of a chordate embryo

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