C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution

Nat Commun. 2019 Jan 21;10(1):360. doi: 10.1038/s41467-018-08126-5.


Single-cell transcriptomic profiling is a powerful tool to explore cellular heterogeneity. However, most of these methods focus on the 3'-end of polyadenylated transcripts and provide only a partial view of the transcriptome. We introduce C1 CAGE, a method for the detection of transcript 5'-ends with an original sample multiplexing strategy in the C1TM microfluidic system. We first quantifiy the performance of C1 CAGE and find it as accurate and sensitive as other methods in the C1 system. We then use it to profile promoter and enhancer activities in the cellular response to TGF-β of lung cancer cells and discover subpopulations of cells differing in their response. We also describe enhancer RNA dynamics revealing transcriptional bursts in subsets of cells with transcripts arising from either strand in a mutually exclusive manner, validated using single molecule fluorescence in situ hybridization.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • A549 Cells
  • Animals
  • Cell Line
  • Enhancer Elements, Genetic*
  • Fibroblasts / cytology
  • Fibroblasts / drug effects
  • Fibroblasts / metabolism*
  • Gene Expression Profiling
  • Humans
  • In Situ Hybridization, Fluorescence
  • Mice
  • Microfluidic Analytical Techniques
  • Promoter Regions, Genetic
  • RNA, Messenger / genetics*
  • RNA, Messenger / metabolism
  • Sequence Analysis, RNA
  • Single-Cell Analysis / instrumentation
  • Single-Cell Analysis / methods*
  • Transcription Initiation Site*
  • Transcriptome*
  • Transforming Growth Factor beta / pharmacology


  • RNA, Messenger
  • Transforming Growth Factor beta