Controlling Cell Fate Specification System by Key Genes Determined from Network Structure

IScience
Kenji KobayashiYutaka Satou

Abstract

Network structures describing regulation between biomolecules have been determined in many biological systems. Dynamics of molecular activities based on such networks are considered to be the origin of many biological functions. Recently, it has been proved mathematically that key nodes for controlling dynamics in networks are identified from network structure alone. Here, we applied this theory to a gene regulatory network for the cell fate specification of seven tissues in the ascidian embryo and found that this network, which consisted of 92 factors, had five key molecules. By controlling the activities of these key molecules, the specific gene expression of six of seven tissues observed in the embryo was successfully reproduced. Since this method is applicable to all nonlinear dynamic systems, we propose this method as a tool for controlling gene regulatory networks and reprogramming cell fates.

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Citations

Jan 18, 2019·Physical Biology·Jorge Gómez Tejeda ZañudoRéka Albert
Sep 4, 2020·Bioinformatics·Lauren MarazziPaola Vera-Licona
Aug 21, 2021·Frontiers in Cell and Developmental Biology·Pina MarottaAnnamaria Locascio

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Methods Mentioned

BETA
gene knockdown
PCR
antisense oligonucleotides
RNA-seq

Software Mentioned

FVS

Related Concepts

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Cell Fate Specification

Cell fate specification is determined by complex signal transduction pathways including Notch and the Sonic hedgehog signaling pathway. Here is the latest research on regulation of cell fate determination.