Multiplex profiling of developmental enhancers with quantitative, single-cell expression reporters [bulkMPRA(promoters, cells v2)]
The inability to scalably and precisely measure the activity of developmental enhancers in multicellular systems is a bottleneck in genomics. Here, we develop a dual RNA cassette that decouples the detection and quantification tasks inherent to multiplex single-cell reporter assays. The resulting measurement of reporter expression is accurate over multiple orders of magnitude, with a precision approaching the limit set by Poisson counting noise. Together with RNA barcode circularization, these scalable single-cell quantitative expression reporters (scQers) provide high-contrast readouts, analogous to classic in situ assays, but entirely from sequencing. Screening >200 putative enhancers in a multicellular in vitro model of early mammalian development, we identified thirteen (eight previously uncharacterized) autonomous and cell-type-specific elements, such as constituents of the Sox2 control region exclusively active in pluripotent cells, endoderm-specific enhancers, including near Foxa2 and Gata4, and a compact pleiotropic enhancer at the Lamc1 locus. We further demonstrate that synthetic enhancer pairs generate cognate two-cell-type activity profiles and assess gain/loss-of-function multicellular expression phenotypes from enhancer variants with perturbed transcription factor binding sites. scQers can be applied in developmental systems to quantitatively characterise native, perturbed, and synthetic enhancers at scale, with high sensitivity and at single-cell resolution. Overall design: Bulk MPRA from K562 & HEK293T bottlenecked populations with genome-integrated MPRA reporters (promoter series).