Self-reporting transposons enable simultaneous readout of gene expression and transcription factor binding in single cells

In situ assays of transcription factor (TF) binding are confounded by cellular heterogeneity and represent averaged profiles in complex tissues. Single cell RNA-seq (scRNA-seq) is capable of resolving different cell types based on gene expression profiles, but no technology exists to directly link specific cell types to the binding pattern of TFs in those cell types. Here, we present self-reporting transposons (SRTs) and their use in single cell calling cards (scCC), a novel assay for simultaneously capturing gene expression profiles and mapping TF binding sites in single cells. First, we show how the genomic locations of SRTs can be recovered from mRNA. Next, we demonstrate that SRTs deposited by the piggyBac transposase can be used to map the genome-wide localization of the TFs SP1, through a direct fusion of the two proteins, and BRD4, through its native affinity for piggyBac. We then present the scCC method, which maps SRTs from scRNA-seq libraries, thus enabling concomitant identification of cell types and TF binding sites in those same cells. As a proof-of-concept, we use scCC to map the binding of BRD4 and three additional TFs in cultured cells. We then apply this technique to discover bromodomain-dependent cell state dynamics in K562 cells. Finally, we map BRD4 binding sites in the mouse cortex at single cell resolution, thus establishing a new technique for studying TF biology in situ. 1 bulk DNA calling card library, 8 bulk RNA calling card libraries, 9 single cell RNA-seq libraries, 9 single cell calling card libraries