Multiplex profiling of developmental enhancers with quantitative, single-cell expression reporters
Year: 2022
Type: preprint
Abstract: 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, resulting in accurate measurement of reporter expression over a >10,000-fold range of activity with a precision approaching the limit set by Poisson counting noise. Together with RNA barcode circularization, these s ingle- c ell q uantitative e xpression r eporters (scQers) provide high-contrast readouts analogous to classic in situ assays, but entirely from sequencing. Screening >200 enhancers in a multicellular in vitro model of early mammalian development, we identified numerous autonomous and cell-type-specific elements, including 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. scQers can be mobilized in developmental systems to quantitatively characterize native, perturbed, and synthetic enhancers at scale, with high sensitivity and at single-cell resolution.
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
Awards: Optimization of a massively parallel genome editing approach to link regulatory elements to their target genes during mouse germ layer formation, G3768157195, Characterizing the comprehensive gene regulatory basis of autoimmunity., Massively parallel characterization of variants and elements impacting transcriptional regulation in dynamic cellular systems, Versatile, exponentially scalable methods for single cell molecular profiling, Cardiovascular Research Training Program
OpenAlex ID: W4312097592