Topological basis of signal integration in the transcriptional-regulatory network of the yeast, Saccharomyces cerevisiae

Chuang Wu,Illés J Farkas,Ivet Bahar,Chakra Chennubhotla,Zoltán N Oltvai

doi:10.1186/1471-2105-7-478

Chuang Wu, Illés J Farkas + Show 3 more

Open Access

https://doi.org/10.1186/1471-2105-7-478

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Abstract

BackgroundSignal recognition and information processing is a fundamental cellular function, which in part involves comprehensive transcriptional regulatory (TR) mechanisms carried out in response to complex environmental signals in the context of the cell's own internal state. However, the network topological basis of developing such integrated responses remains poorly understood.ResultsBy studying the TR network of the yeast Saccharomyces cerevisiae we show that an intermediate layer of transcription factors naturally segregates into distinct subnetworks. In these topological units transcription factors are densely interlinked in a largely hierarchical manner and respond to external signals by utilizing a fraction of these subnets.ConclusionAs transcriptional regulation represents the 'slow' component of overall information processing, the identified topology suggests a model in which successive waves of transcriptional regulation originating from distinct fractions of the TR network control robust integrated responses to complex stimuli.

Highlights

Signal recognition and information processing is a fundamental cellular function, which in part involves comprehensive transcriptional regulatory (TR) mechanisms carried out in response to complex environmental signals in the context of the cell's own internal state
We show that regulatory interactions among an intermediate layer of transcription factors is a key determinant of information transfer within the S. cerevisiae TR network, and that this layer naturally segregates into distinct, sparsely communicating subnets in which TFs are densely interlinked in a hierarchical manner
In the S. cerevisiae TR network each TF regulates a limited number of target genes, with an average number of 34.3

Summary

Introduction

Signal recognition and information processing is a fundamental cellular function, which in part involves comprehensive transcriptional regulatory (TR) mechanisms carried out in response to complex environmental signals in the context of the cell's own internal state. Living cells continuously process information about their environment, and based on this information and their own internal state mount appropriate responses to these signals. This information processing is carried out by various regulatory networks functioning in a highly crowded, viscous cellular interior, with characteristic times spanning several orders of magnitude. It is evident that the TR network is utilized in a condition-specific manner [12], perhaps through the activation of distinct, signal-specific subnetworks [13] In spite of these advances the principles along which regulatory networks process signals, encode the relevant signals at different layers of the network, and integrate them with other signals remain poorly understood

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