Abstract Cyclin-dependent kinases (CDKs) with primary roles in transcription regulation are emerging as tractable therapeutic targets in cancers driven by the aberrant expression of oncogenic transcription factors. Our goal is to disrupt the myriad and pleomorphic features of oncogenic MYC through inhibiting CDKs involved in its transcriptional amplifier role. CDK7 participates in transcription initiation by phosphorylating the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II and also functions as a CDK-activating kinase, while CDK12 functions in transcription elongation and RNA processing. Using a novel covalent CDK7 inhibitor, THZ1, we demonstrated striking activity and selectivity in neuroblastoma (NB) cells driven by high MYCN expression. This response translated to significant tumor regression in a mouse model of high-risk NB, without introducing discernible toxicity. We determined that this effect was associated with global inhibition of MYCN-dependent transcriptional amplification. THZ1 led to preferential downregulation of Pol II occupancy at super-enhancer-associated genes, including MYCN and other master transcription factors critical to neuronal development such as PHOX2B, GATA2, and DBH. Similarly, inhibition of CDK12 activity using a novel, first-in-class small molecule inhibitor, THZ-5-31-1, resulted in potent antitumor activity in MYCN-overexpressing NB cells. THZ-5-31-1 doses sufficient to induce PARP cleavage did not lead to significant inhibition of global transcription elongation. Rather, cytotoxicity was associated with preferential downregulation of RNA processing factors and a higher percentage of immature mRNA transcripts. Together, these results suggest that transcriptional CDK inhibitors, by affecting different aspects of the transcription machinery, may inhibit the growth of cancers driven by oncogenic transcription factors such as MYC. Citation Format: Malgorzata Krajewska, Nathan F. Moore, Edmond Chipumuro, Tinghu Zhang, Eugenio Marco, Clark Hatheway, Bandana Sharma, Nicholas Kwiatkowski, Guo-Cheng Yuan, Richard A. Young, Nathanael S. Gray, Rani E. George. Targeting super-enhancer driven oncogene transcription through cyclin-dependent kinase inhibitors. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Sep 24-27, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2016;76(2 Suppl):Abstract nr PR04.