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Science. 2018 May 18;360(6390):800-805. doi: 10.1126/science.aao2793. Epub 2018 Apr 5.

SLAM-seq defines direct gene-regulatory functions of the BRD4-MYC axis.

Author information

1
Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria.
2
Boehringer Ingelheim-Regional Center Vienna GmbH and Company KG, 1121 Vienna, Austria.
3
Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna and Medical University of Vienna, 1030 Vienna, Austria.
4
Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), VBC, 1030 Vienna, Austria.
5
Vienna Biocenter Core Facilities (VBCF), 1030 Vienna, Austria.
6
Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), VBC, 1030 Vienna, Austria. johannes.zuber@imp.ac.at stefan.ameres@imba.oeaw.ac.at.
7
Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria. johannes.zuber@imp.ac.at stefan.ameres@imba.oeaw.ac.at.
8
Medical University of Vienna, VBC, 1030 Vienna, Austria.

Abstract

Defining direct targets of transcription factors and regulatory pathways is key to understanding their roles in physiology and disease. We combined SLAM-seq [thiol(SH)-linked alkylation for the metabolic sequencing of RNA], a method for direct quantification of newly synthesized messenger RNAs (mRNAs), with pharmacological and chemical-genetic perturbation in order to define regulatory functions of two transcriptional hubs in cancer, BRD4 and MYC, and to interrogate direct responses to BET bromodomain inhibitors (BETis). We found that BRD4 acts as general coactivator of RNA polymerase II-dependent transcription, which is broadly repressed upon high-dose BETi treatment. At doses triggering selective effects in leukemia, BETis deregulate a small set of hypersensitive targets including MYC. In contrast to BRD4, MYC primarily acts as a selective transcriptional activator controlling metabolic processes such as ribosome biogenesis and de novo purine synthesis. Our study establishes a simple and scalable strategy to identify direct transcriptional targets of any gene or pathway.

PMID:
29622725
PMCID:
PMC6409205
DOI:
10.1126/science.aao2793
[Indexed for MEDLINE]
Free PMC Article

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