The CDK7 Inhibitor THZ1 Alters RNA Polymerase Dynamics at the 5' and 3' Ends of Genes

The t(8;21) is one of the most frequent chromosomal translocations associated with acute myeloid leukemia (AML). We found that t(8;21) AML were extremely sensitive to THZ1, which triggered apoptosis after only 4 hr. We used precision nuclear run-on transcription sequencing (PROseq) to define the global effects of THZ1 and other CDK inhibitors on RNA polymerase II dynamics. Inhibition of CDK7 using THZ1 caused wide-spread loss of promoter-proximal paused RNA polymerase. This loss of 5' pausing was associated with accumulation of polymerases in the body of a large number of genes. However, there were modest effects on genes regulated by “super-enhancers”. At the 3' ends of genes, treatment with THZ1 suppressed RNA polymerase “read through” at the end of the last exon, which resembled a phenotype associated with a mutant RNA polymerase with slower elongation rates. Consistent with this hypothesis, polyA site-sequencing (PolyA-seq) did not detect differences in polyA sites after THZ1 treatment. PROseq analysis after short treatments with THZ1 suggested that these 3' effects were due to altered CDK7 activity at the 5' end of long genes, and were likely to be due to slower rates of elongation. Overall design: Kasumi-1 cells were treated with DMSO, 400nM flavopiridol (FVP), 25nM dinaciclib (Dina), 5uM PHA-767491 (PHA), 400nM THZ1 and 5uM palbociclib (Palbo) for 1hr and PROseq and RNAseq were performed to study changes in transcription and gene expression. Kasumi-1 cells were treated with 400nM THZ1 for 0, 15, 30,60 and 120 minutes and PROseq was performed. RNAseq was performed for 0 and 2hr THZ1 treated samples. Two biological replicates were included for each time point.