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Sequential rather than coincident molecular mechanisms govern the combinatorial control logic underlying pathogen-responsive gene expression programs

ABSTRACT: Combinatorial control of gene expression is presumed to be mediated by molecular interactions between coincident transcription factors (TFs). While information on the genome-wide locations of TFs is available, the genes they regulate and whether they function combinatorially often remain open questions. Here, we developed a mechanistic, rather than statistical, modeling approach to elucidate TF control logic from gene expression data. Applying this approach to hundreds of genes in 85 datasets measuring the transcriptional responses of murine fibroblasts and macrophages to cytokines and pathogens, we found that stimulus-responsive TFs generally function sequentially in logical OR gates or singly. Logical AND gates were found between NFB-responsive mRNA synthesis and MAPKp38-responsive control of mRNA half-life, but not between temporally coincident TFs. Our analyses identified the functional target genes of each of the pathogen-responsive TFs and prompts a revision of the conceptual underpinnings of combinatorial control of gene expression to include sequentially acting molecular mechanisms that govern mRNA synthesis and decay.

ORGANISM(S): Mus musculus

PROVIDER: GSE35521 | GEO | 2017/02/01

SECONDARY ACCESSION(S): PRJNA152241

REPOSITORIES: GEO

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Mus musculus

Project description:Sequential rather than coincident molecular mechanisms govern the combinatorial control logic underlying pathogen-responsive gene expression programs

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