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Journal Article

TT-seq captures enhancer landscapes immediately after T-cell stimulation.

MPS-Authors
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Michel,  M.
Department of Molecular Biology, MPI for Biophysical Chemistry, Max Planck Society;

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Demel,  C.
Department of Molecular Biology, MPI for Biophysical Chemistry, Max Planck Society;

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Schwalb,  B.
Department of Molecular Biology, MPI for Biophysical Chemistry, Max Planck Society;

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Cramer,  P.
Department of Molecular Biology, MPI for Biophysical Chemistry, Max Planck Society;

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Fulltext (public)

2406677.pdf
(Publisher version), 2MB

Supplementary Material (public)

2406677_Suppl_1.pdf
(Supplementary material), 4MB

2406677_Suppl_2.pdf
(Supplementary material), 2MB

2406677_Suppl_3.xls
(Supplementary material), 6MB

2406677_Suppl_4.xls
(Supplementary material), 3MB

2406677_Suppl_5.xls
(Supplementary material), 41KB

2406677_Suppl_6.xlsx
(Supplementary material), 659KB

Citation

Michel, M., Demel, C., Zacher, B., Schwalb, B., Krebs, S., Blum, H., et al. (2017). TT-seq captures enhancer landscapes immediately after T-cell stimulation. Molecular Systems Biology, 13(3): 920. doi:10.15252/msb.20167507.


Cite as: http://hdl.handle.net/11858/00-001M-0000-002C-A0A4-B
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.