Journal
CELL SYSTEMS
Volume 4, Issue 3, Pages 330-343Publisher
CELL PRESS
DOI: 10.1016/j.cels.2017.01.012
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Funding
- NIH [P50 GM085763, P50 AR063020, U01 AI124319, R01 AI127864, R01 GM117134]
- Department of Defense Breast Cancer Predoctoral Training Fellowship
- Cancer Research Institute postdoctoral fellowship
- Quantitative and Computational Biosciences (QCB) Collaboratory Fellowship
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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 NF-kB-responsive mRNA synthesis and MAPKp38responsive 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 prompt a revision of the conceptual underpinnings of combinatorial control of gene expression to include sequentially acting molecular mechanisms that govern mRNA synthesis and decay.
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