A single-cell massively parallel reporter assay detects cell-type-specific gene regulation

Massively parallel reporter gene assays are key tools in regulatory genomics but cannot be used to identify cell-type-specific regulatory elements without performing assays serially across different cell types. To address this problem, 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. 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 that detects cell-type-specific cis-regulatory activity. We then measured a library of promoter variants across multiple cell types in live mouse retinas and showed that subtle genetic variants can produce cell-type-specific effects on cis-regulatory activity. We anticipate that scMPRA will be widely applicable for studying the role of CRSs across diverse cell types.

Automated summary

Massively parallel reporter gene assays are essential for regulatory genomics but lack the ability to identify cell-type-specific regulatory elements without sequential assays. To overcome this, a single-cell massively parallel reporter assay (scMPRA) was developed to simultaneously measure the activity of libraries of cis-regulatory sequences (CRSs) across multiple cell types. The scMPRA was shown to be reproducible and capable of detecting cell-type-specific cis-regulatory activity using a library of core promoters in HEK293 and K562 cells. Furthermore, scMPRA was used to measure promoter variants in live mouse retinas, revealing that subtle genetic variations can result in cell-type-specific effects on cis-regulatory activity. The scMPRA is expected to have wide applications in studying CRSs in different cell types.