Multiplex profiling of developmental enhancers with quantitative, single-cell expression reporters [plasmid_libraries_subassembly]

The inability to scalably and precisely measure the cell-type-specific activity of developmental enhancers is a bottleneck in genomics. To address this, we developed a “dual RNA”' system that decouples the detection and quantification tasks inherent to multiplex single-cell reporter assays. Together with RNA barcode circularization, the resulting single-cell quantitative expression reporters (scQers) facilitate the robust detection of which reporter(s) are present in which single cells, thereby providing high contrast readouts analogous to classic in situ assays but entirely from sequencing. Our dual RNA strategy extends the range of expression measurement into a regime fundamentally inaccessible with traditional multiplex reporter systems, yielding an accurate readout of mRNA levels spanning four orders of magnitude and a precision approaching the limit set by Poisson (shot) noise. As a proof-of-concept experiment, we profile over two hundred putative developmental cis-regulatory elements (CREs) for cell-type-specific activity in a multicellular in vitro model of early mammalian development, identifying dozens of active elements, ten of which function in an autonomous, cell-type-specific manner. These include constituents of the canonical Sox2 control region, exclusively active in pluripotent cells, multiple parietal endoderm-specific enhancers, including at the Foxa2 and Gata4 loci, and a compact pleiotropic enhancer at the Lamc1 locus. Looking forward, we envision that scQers will be broadly useful in developmental systems to quantitatively profile the activity of native, perturbed, or synthetic enhancers at scale, with high sensitivity and at single cell resolution. Subassembly of plasmid barcoded reporter libraries. Experient type (submitter-provided): barcode association for library construction