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

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

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.

Grafik Top
Authors
  • Muhar, Matthias
  • Ebert, Anna
  • Neumann, Tobias
  • Umkehrer, Christian
  • Jude, Julian Georg
  • Wieshofer, Corinna
  • Rescheneder, Philipp
  • Lipp, Jesse J.
  • Herzog, Veronika A.
  • Reichholf, Brian
  • Cisneros, David A.
  • Hoffmann, Thomas
  • Schlapansky, Moritz F.
  • Bhat, Pooja
  • von Haeseler, Arndt
  • Köcher, Thomas
  • Obenauf, Anna C.
  • Popow, Johann
  • Ameres, Stefan L.
  • Zuber, Johannes
Grafik Top
Shortfacts
Category
Journal Paper
Divisions
Bioinformatics and Computational Biology
Journal or Publication Title
Science
ISSN
0036-8075
Publisher
American Association for the Advancement of Science
Place of Publication
Washington, D.C.
Page Range
pp. 800-805
Number
6390
Volume
360
Date
18 May 2018
Export
Grafik Top