%0 Journal Article %A Siqi Zhao %A Clarice KY Hong %A David M Granas %A Barak A Cohen %T A single-cell massively parallel reporter assay detects cell type specific cis-regulatory activity %D 2021 %R 10.1101/2021.11.11.468308 %J bioRxiv %P 2021.11.11.468308 %X We developed a single-cell massively parallel reporter assay (scMPRA) to measure the activity of libraries of cis-regulatory sequences (CRSs) across multiple cell-types simultaneously. As a proof of concept, we assayed a library of core promoters in a mixture of HEK293 and K562 cells and showed that scMPRA is a reproducible, highly parallel, single-cell reporter gene assay. Our results show that housekeeping promoters and CpG island promoters have lower activity in K562 cells relative to HEK293, which likely reflects developmental differences between the cell lines. Within K562 cells, scMPRA identified a subset of developmental promoters that are upregulated in the CD34+/CD38− sub-state, confirming this state as more “stem-like.” Finally, we deconvolved the intrinsic and extrinsic components of promoter cell-to-cell variability and found that developmental promoters have a higher proportion of extrinsic noise compared to housekeeping promoters, which may reflect the responsiveness of developmental promoters to the cellular environment. We anticipate scMPRA will be widely applicable for studying the role of CRSs across diverse cell types.Competing Interest StatementS.Z. and B.A.C. are inventors on a pending patent filed by Washington University in St. Louis which may encompass the methods, reagents, and data disclosed in this manuscript. B.A.C is on the scientific advisory board of Patch Biosciences. %U https://www.biorxiv.org/content/biorxiv/early/2021/11/12/2021.11.11.468308.full.pdf