Graham D. Johnson, Alejandro Barrera, Ian C. McDowell, Anthony M. D’Ippolito, William H. Majoros et al.
Environmental stimuli commonly act via changes in gene regulation. Human-genome-scale assays to measure such responses are indirect or require knowledge of the transcription factors (TFs) involved. Here, we present the use of human genome-wide high-throughput reporter assays to measure environmentally-responsive regulatory element activity. We focus on responses to glucocorticoids (GCs), an important class of pharmaceuticals and a paradigmatic genomic response model. We assay GC-responsive regulatory activity across >10^8 unique DNA fragments, covering the human genome at >50×. Those assays directly detected thousands of GC-responsive regulatory elements genome-wide. We then validate those findings with measurements of transcription factor occupancy, histone modifications, chromatin accessibility, and gene expression. We also detect allele-specific environmental responses. Notably, the assays did not require knowledge of GC response mechanisms. Thus, this technology can be used to agnostically quantify genomic responses for which the underlying mechanism remains unknown.
Graham D. Johnson, Alejandro Barrera, Ian C. McDowell, Anthony M. D’Ippolito, William H. Majoros, Christopher M. Vockley, Xingyan Wang, Andrew S. Allen, Timothy E. Reddy. Human genome-wide measurement of drug-responsive regulatory activity. 2018-12-21. https://doi.org/10.1038/s41467-018-07607-x
The GM12878-derived whole-genome STARR-seq plasmid library was transfected into A549 cells and assayed after the vehicle-control 0 h condition across five biological replicate plates. The table contains the public union of MACS2-called baseline active regions; differential drug-response statistics are not defined for this control.
The GM12878-derived whole-genome STARR-seq plasmid library was transfected into A549 cells and assayed after 100 nM dexamethasone exposure for 12 h across five biological replicate plates. The table contains published induced and repressed dex-responsive elements (DREs) passing the paper's FDR threshold.
The GM12878-derived whole-genome STARR-seq plasmid library was transfected into A549 cells and assayed after 100 nM dexamethasone exposure for 4 h across five biological replicate plates. The table contains published induced and repressed dex-responsive elements (DREs) passing the paper's FDR threshold.
The GM12878-derived whole-genome STARR-seq plasmid library was transfected into A549 cells and assayed after 100 nM dexamethasone exposure for 1 h across five biological replicate plates. The table contains published induced and repressed dex-responsive elements (DREs) passing the paper's FDR threshold.
The GM12878-derived whole-genome STARR-seq plasmid library was transfected into A549 cells and assayed after 100 nM dexamethasone exposure for 8 h across five biological replicate plates. The table contains published induced and repressed dex-responsive elements (DREs) passing the paper's FDR threshold.
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