NET-CAGE characterizes the dynamics and topology of human transcribed cis-regulatory elements

Nat Genet. 2019 Sep;51(9):1369-1379. doi: 10.1038/s41588-019-0485-9. Epub 2019 Sep 2.


Promoters and enhancers are key cis-regulatory elements, but how they operate to generate cell type-specific transcriptomes is not fully understood. We developed a simple and robust method, native elongating transcript-cap analysis of gene expression (NET-CAGE), to sensitively detect 5' ends of nascent RNAs in diverse cells and tissues, including unstable transcripts such as enhancer-derived RNAs. We studied RNA synthesis and degradation at the transcription start site level, characterizing the impact of differential promoter usage on transcript stability. We quantified transcription from cis-regulatory elements without the influence of RNA turnover, and show that enhancer-promoter pairs are generally activated simultaneously on stimulation. By integrating NET-CAGE data with chromatin interaction maps, we show that cis-regulatory elements are topologically connected according to their cell type specificity. We identified new enhancers with high sensitivity, and delineated primary locations of transcription within super-enhancers. Our NET-CAGE dataset derived from human and mouse cells expands the FANTOM5 atlas of transcribed enhancers, with broad applicability to biomedical research.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • 5' Untranslated Regions / genetics*
  • Computational Biology / methods*
  • Enhancer Elements, Genetic*
  • Gene Expression Profiling
  • Gene Expression Regulation*
  • HeLa Cells
  • Hep G2 Cells
  • Humans
  • MCF-7 Cells
  • Promoter Regions, Genetic*
  • RNA / genetics*
  • Transcription Initiation Site
  • Transcription, Genetic*
  • Transcriptome


  • 5' Untranslated Regions
  • RNA