Science https://doi.org/10.1126/science.aao2793 (2018)

Deciphering direct transcriptional responses to cell perturbations is challenging because of vast differences in mRNA and protein turnover. One method that can potentially address this concern is SLAM-seq, which enables the direct quantification of newly synthesized mRNAs. In this approach, the nucleotide analog 4-thiouridine is incorporated during RNA synthesis and then alkylated by iodoacetamide, which can be detected by reverse-transcriptase-induced thymine-to-cytosine changes in mRNA 3′-end sequencing. Muhar et al. applied SLAM-seq in combination with the auxin-inducible degradation system or small-molecule inhibition to determine whether rapid loss of the transcriptional regulators MYC or BRD4 resulted in global or specific loss in downstream gene expression. Performing SLAM-seq following degradation or inhibition of BRD4 revealed global downregulation of transcription owing to alterations in Pol II–mediated promoter-proximal pause release. In contrast, loss of MYC led to a selective decrease in transcription of genes involved in protein and nucleotide synthesis. Taken together, the combination of SLAM-seq with small-molecule-mediated inhibition or degradation may provide an effective approach to measure global and specific transcriptional responses to cellular perturbations.