Abstract
Signals often ultimately affect the transcription of genes, and often, two different signals can affect the transcription of the same gene. In such cases, it is natural to ask how the combined transcriptional response compares to the individual responses. Mechanistic models can predict a range of combined responses, with the most commonly applied models predicting additive or multiplicative responses, but systematic genome-wide evaluation of these predictions are not available. Here, we performed a comprehensive analysis of the transcriptional response of human MCF-7 cells to two different signals (retinoic acid and TGF-β), applied individually and in combination. We found that the combined responses exhibited a range of behaviors, but clearly favored both additive and multiplicative combined transcriptional responses. We also performed paired chromatin accessibility measurements to measure putative transcription factor occupancy at regulatory elements near these genes. We found that increases in chromatin accessibility were largely additive, meaning that the combined accessibility response was the sum of the accessibility responses to each signal individually. We found some association between super-additivity of accessibility and multiplicative or super-multiplicative combined transcriptional responses, while sub-additivity of accessibility associated with additive transcriptional responses. Our findings suggest that mechanistic models of combined transcriptional regulation must be able to reproduce a range of behaviors.
Competing Interest Statement
AR receives royalties related to Stellaris RNA FISH probes. All other authors declare no competing interests.
Footnotes
We revised the manuscript in response to the reviews that were shared by eLife's preprint review service. Highlights of our revision include (1) A greatly expanded analysis of the c-value distribution, showing more rigorously that there are indeed two peaks that correspond to additive and multiplicative behavior. (2) An analysis of cross-activation between the two signals using new immunofluorescence data, showing minimal cross-activation. (3) More explanatory diagrams and equations throughout the manuscript, as suggested by the reviewers.
