Three topological features of regulatory networks control life-essential and specialized subsystems.

Autor: Wolf IR; Department of Bioprocess and Biotechnology, School of Agriculture, São Paulo State University (UNESP), Botucatu, São Paulo, 18610-034, Brazil., Simões RP; Department of Bioprocess and Biotechnology, School of Agriculture, São Paulo State University (UNESP), Botucatu, São Paulo, 18610-034, Brazil.; Medical School, Sao Paulo State University (UNESP), Botucatu, São Paulo, 18618-687, Brazil., Valente GT; Department of Bioprocess and Biotechnology, School of Agriculture, São Paulo State University (UNESP), Botucatu, São Paulo, 18610-034, Brazil. valentegt@gmail.com.; Max-Planck-Institut für Herz- und Lungenforschung, Max Planck Institute, 61231, Bad Nauheim, Hessen, Germany. valentegt@gmail.com.
Jazyk: angličtina
Zdroj: Scientific reports [Sci Rep] 2021 Dec 20; Vol. 11 (1), pp. 24209. Date of Electronic Publication: 2021 Dec 20.
DOI: 10.1038/s41598-021-03625-w
Abstrakt: Gene regulatory networks (GRNs) play key roles in development, phenotype plasticity, and evolution. Although graph theory has been used to explore GRNs, associations amongst topological features, transcription factors (TFs), and systems essentiality are poorly understood. Here we sought the relationship amongst the main GRN topological features that influence the control of essential and specific subsystems. We found that the K nn , page rank, and degree are the most relevant GRN features: the ones are conserved along the evolution and are also relevant in pluripotent cells. Interestingly, life-essential subsystems are governed mainly by TFs with intermediary K nn and high page rank or degree, whereas specialized subsystems are mainly regulated by TFs with low K nn . Hence, we suggest that the high probability of TFs be toured by a random signal, and the high probability of the signal propagation to target genes ensures the life-essential subsystems' robustness. Gene/genome duplication is the main evolutionary process to rise K nn as the most relevant feature. Herein, we shed light on unexplored topological GRN features to assess how they are related to subsystems and how the duplications shaped the regulatory systems along the evolution. The classification model generated can be found here: https://github.com/ivanrwolf/NoC/ .
(© 2021. The Author(s).)
Databáze: MEDLINE
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