title: 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.
authors.affiliation: Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
authors.forename: Margaux
authors.identifier: 0000-0001-8761-4539
authors.initials: M
authors.lastname: Michel
authors.affiliation: Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
authors.forename: Carina
authors.identifier: 0000-0001-7843-3293
authors.initials: C
authors.lastname: Demel
authors.affiliation: Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany.
authors.forename: Benedikt
authors.initials: B
authors.lastname: Zacher
authors.affiliation: Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
authors.forename: Björn
authors.initials: B
authors.lastname: Schwalb
authors.affiliation: Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Krebs
authors.affiliation: Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany.
authors.forename: Helmut
authors.initials: H
authors.lastname: Blum
authors.affiliation: Department of Informatics, Technische Universität München, Garching, Germany gagneur@in.tum.de patrick.cramer@mpibpc.mpg.de.
authors.forename: Julien
authors.identifier: 0000-0002-8924-8365
authors.initials: J
authors.lastname: Gagneur
authors.affiliation: Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany gagneur@in.tum.de patrick.cramer@mpibpc.mpg.de.
authors.forename: Patrick
authors.identifier: 0000-0001-5454-7755
authors.initials: P
authors.lastname: Cramer
mesh_terms: D020029:Base Pairing; D004742:Enhancer Elements, Genetic; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation / Q000187:drug effects; D006801:Humans; D015759:Ionomycin / Q000494:pharmacology*; D019169:Jurkat Cells; D012313:RNA / Q000032:analysis; D017423:Sequence Analysis, RNA / Q000379:methods*; D013601:T-Lymphocytes / Q000187:drug effects*; D013755:Tetradecanoylphorbol Acetate / Q000494:pharmacology*; D014158:Transcription, Genetic / Q000187:drug effects; D015533:Transcriptional Activation
chemical_list: D015759:Ionomycin; D012313:RNA; D013755:Tetradecanoylphorbol Acetate
keywords: T‐cell response; enhancers; functional genomics; promoters; transcriptome analysis