Institute of Fundamental Technological Research
Polish Academy of Sciences

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Christopher Clark


Recent publications
1.  Bagnall J., Rowe W., Alachkar N., Roberts J., England H., Clark C., Platt M., Jackson Dean A., Muldoon M., Paszek P., Gene-Specific Linear Trends Constrain Transcriptional Variability of the Toll-like Receptor Signaling, Cell Systems, ISSN: 2405-4712, DOI: 10.1016/j.cels.2020.08.007, Vol.11, No.3, pp.300-314, 2020

Abstract:
Single-cell gene expression is inherently variable, but how this variability is controlled in response to stimulation remains unclear. Here, we use single-cell RNA-seq and single-molecule mRNA counting (smFISH) to study inducible gene expression in the immune toll-like receptor system. We show that mRNA counts of tumor necrosis factor α conform to a standard stochastic switch model, while transcription of interleukin-1β involves an additional regulatory step resulting in increased heterogeneity. Despite different modes of regulation, systematic analysis of single-cell data for a range of genes demonstrates that the variability in transcript count is linearly constrained by the mean response over a range of conditions. Mathematical modeling of smFISH counts and experimental perturbation of chromatin state demonstrates that linear constraints emerge through modulation of transcriptional bursting along with gene-specific relationships. Overall, our analyses demonstrate that the variability of the inducible single-cell mRNA response is constrained by transcriptional bursting.

Keywords:
cellular heterogeneity, transcriptional bursting, stochastic gene expression, toll-like receptor, single-cell transcriptomics, stochastic modeling, TNF-α, IL-1β

Affiliations:
Bagnall J. - other affiliation
Rowe W. - other affiliation
Alachkar N. - other affiliation
Roberts J. - other affiliation
England H. - other affiliation
Clark C. - other affiliation
Platt M. - other affiliation
Jackson Dean A. - other affiliation
Muldoon M. - other affiliation
Paszek P. - other affiliation

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