DOI: 10.1101/479857Nov 28, 2018Paper

Limits to a classic paradigm: Most transcription factors regulate genes in multiple biological processes

BioRxiv : the Preprint Server for Biology
Daniela Ledezma-TejeidaJulio Collado-Vides

Abstract

Transcription factors (TFs) are important drivers of cellular decision-making. When bacteria encounter a change in the environment, transcription factors alter the expression of a defined set of genes in order to adequately respond. It is commonly assumed that genes regulated by the same TF should be involved in the same biological process. Examples of this are methods that rely on coregulation to infer function of not yet annotated genes. We have previously shown that only 21% of TFs regulate functionally homogeneous genes based on the proximity of their catalyzed reactions in the metabolic network. Here, we provide more evidence to support the claim that a one TF/one process relationship is not a general property. We show that the observed functional heterogeneity of regulons is not a result of the quality of the annotation of regulatory interactions, or the absence of protein-metabolite interactions, and is also present when function is defined by Gene Ontology terms. Furthermore, the observed functional heterogeneity is different from the one expected by chance, supporting the notion that it is a biological property. To further explore the relationship between transcriptional regulation and metabolism, we analyze 5 other ty...Continue Reading

Related Concepts

Decision Making
Environment
Genes
Metabolism
Transcription Factor
Inference
Paradigm
Drug Interactions
Metabolite
Homogeneous Organ

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