TT‐seq captures enhancer landscapes immediately after T‐cell stimulation

Abstract

To monitor transcriptional regulation in human cells, rapid changes in enhancer and promoter activity must be captured with high sensitivity and temporal resolution. Here, we show that the recently established protocol TT‐seq (“transient transcriptome sequencing”) can monitor rapid changes in transcription from enhancers and promoters during the immediate response of T cells to ionomycin and phorbol 12‐myristate 13‐acetate (PMA). TT‐seq maps eRNAs and mRNAs every 5 min after T‐cell stimulation with high sensitivity and identifies many new primary response genes. TT‐seq reveals that the synthesis of 1,601 eRNAs and 650 mRNAs changes significantly within only 15 min after stimulation, when standard RNA‐seq does not detect differentially expressed genes. Transcription of enhancers that are primed for activation by nucleosome depletion can occur immediately and simultaneously with transcription of target gene promoters. Our results indicate that enhancer transcription is a good proxy for enhancer regulatory activity in target gene activation, and establish TT‐seq as a tool for monitoring the dynamics of enhancer landscapes and transcription programs during cellular responses and differentiation. image Transient transcriptome sequencing (TT‐seq) maps the dynamic landscape of enhancer transcription with great sensitivity and temporal resolution during the immediate T‐cell response. Changes in transcription from enhancers and promoters occur simultaneously within minutes. TT‐seq is used to analyze the immediate T‐cell response and maps eRNAs and mRNAs with high sensitivity. TT‐seq identifies many new primary response genes. Changes in transcription from enhancers and target promoters occur simultaneously within minutes. Transcription from promoters and enhancers is correlated and distance‐dependent.