Self-Reporting Transposons Enable Simultaneous Readout of Gene Expression and Transcription Factor Binding in Single Cells

Cell. 2020 Aug 20;182(4):992-1008.e21. doi: 10.1016/j.cell.2020.06.037. Epub 2020 Jul 24.


Cellular heterogeneity confounds in situ assays of transcription factor (TF) binding. Single-cell RNA sequencing (scRNA-seq) deconvolves cell types from gene expression, but no technology links cell identity to TF binding sites (TFBS) in those cell types. We present self-reporting transposons (SRTs) and use them in single-cell calling cards (scCC), a novel assay for simultaneously measuring gene expression and mapping TFBS in single cells. The genomic locations of SRTs are recovered from mRNA, and SRTs deposited by exogenous, TF-transposase fusions can be used to map TFBS. We then present scCC, which map SRTs from scRNA-seq libraries, simultaneously identifying cell types and TFBS in those same cells. We benchmark multiple TFs with this technique. Next, we use scCC to discover BRD4-mediated cell-state transitions in K562 cells. Finally, we map BRD4 binding sites in the mouse cortex at single-cell resolution, establishing a new method for studying TF biology in situ.

Keywords: bromodomains; calling cards; cell state; mouse cortex; single cell; transcription factors; transposons.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Binding Sites
  • Cell Cycle Proteins / metabolism
  • Cell Line, Tumor
  • Cerebral Cortex / metabolism
  • Chromatin Immunoprecipitation
  • DNA Transposable Elements / genetics*
  • Gene Expression
  • Hepatocyte Nuclear Factor 3-beta / genetics
  • Hepatocyte Nuclear Factor 3-beta / metabolism
  • Humans
  • Mice
  • Protein Binding
  • Sequence Analysis, RNA
  • Single-Cell Analysis / methods*
  • Sp1 Transcription Factor / genetics
  • Sp1 Transcription Factor / metabolism
  • Transcription Factors / genetics
  • Transcription Factors / metabolism*


  • BRD4 protein, human
  • Cell Cycle Proteins
  • DNA Transposable Elements
  • FOXA2 protein, human
  • Sp1 Transcription Factor
  • Transcription Factors
  • Hepatocyte Nuclear Factor 3-beta