SLAM seq defines direct gene regulatory functions of the BRD4 MYC axis
Profiling transcription a SLAM dunk Identification of the direct target genes of transcription factors could shed light on how healthy cells become malignant. Muhar et al. applied a modified version of a transcript mapping method called SLAM seq to identify the target genes of two transcriptional regulators of major interest in cancer research (see the Perspective by Sabo and Amati) The MYC oncoprotein selectively activates transcription of just a few genes, primarily those involved in basic cell metabolism. In contrast, BRD4, a bromodomain containing protein that is being targeted for cancer therapy, activates transcription of many genes. Science, this issue p. 800; see also p. 713 An mRNA mapping method identifies the direct gene targets of two transcriptional regulators implicated in cancer. 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.
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