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

Matthias Muhar, Anja Ebert, Tobias Neumann, Christian Umkehrer, Julian Jude, Corinna Wieshofer, Philipp Rescheneder, Jesse J. Lipp, Veronica A. Herzog, Brian Reichholf, David A. Cisneros, Thomas Hoffmann, Moritz F. Schlapansky, Pooja Bhat, Arndt von Haeseler, Thomas Köcher, Anna C. Obenauf, Johannes Popow, Stefan L. Ameres*, Johannes Zuber*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

234 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)800-805
Number of pages6
JournalScience
Volume360
Issue number6390
Early online date05 Apr 2018
DOIs
Publication statusPublished - 18 May 2018
Externally publishedYes

Keywords

  • Humans
  • *Genes, Regulator
  • Antineoplastic Agents/*pharmacology/therapeutic use
  • Dose-Response Relationship, Drug
  • Gene Expression Regulation, Leukemic/*drug effects
  • Leukemia, Myeloid/*drug therapy/genetics
  • Molecular Targeted Therapy
  • Nuclear Proteins/genetics/*metabolism
  • Proteins/*antagonists & inhibitors
  • Proto-Oncogene Proteins c-myc/genetics/*metabolism
  • Purines/biosynthesis
  • Ribosomes/metabolism
  • RNA, Messenger/biosynthesis/genetics
  • Sequence Analysis, RNA
  • Transcription Factors/genetics/*metabolism
  • Transcription, Genetic
  • Cell Cycle Proteins

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