Poster #52: Ayna Mammedova MS

CDK9 and CDK12 Inhibition Drive Chromatin Relaxation and Transposable Element Reactivation Through Distinct, Gene-Length-Dependent Mechanisms

Mammedova A, MS; Ghelfi M, PhD; Calendo G, MS; Issa JP, MD Affiliations: Coriell Institute for Medical Research, Camden, NJ, USA

CDK9 and CDK12 are transcriptional CDKs that support RNA Polymerase II elongation and are clinically effective anticancer targets, yet how their inhibition reshapes chromatin and gene expression remains unclear, particularly in an epigenetic context. To address this, we used YB5, a SW48-derived colon cancer cell line carrying a silenced, hypermethylated GFP reporter that serves as a sensitive readout of chromatin relaxation. Treating YB5 cells with CDK12-targeting agents (the degrader BSJ-4-116 and inhibitor THZ531) or CDK9 inhibitors (BAY1143572 and AZD4573) over a 2–48h time course, we found that all four drugs reactivated GFP, but AZD4573 drove greater reactivation than other agents. RNA-seq showed that this chromatin opening was accompanied by a shared transcriptional signature: global gene downregulation paired with derepression of transposable elements, primarily LTRs and SINEs. CDK12-targeting agents, especially THZ531, preferentially silenced long genes while sparing or upregulating short, growth-associated programs such as MYC targets. Given that 61% of SINEs are located within introns, we hypothesize that SINE reactivation reflects both a chromatin relaxation effect and a transcriptional/elongation effect. CUT&Tag profiling of BSJ-4-116-treated cells showed that by 24h, promoter-proximal Pol II Ser2P was selectively lost at long genes, consistent with RNA Polymerase II stalling within the first 5-10kb of transcription. This early stalling would expose proximal intronic SINEs as unspliced, intron-retained transcripts, independent of any change in local chromatin accessibility. Together, these findings suggest that CDK9 and CDK12 inhibition upregulate transposable elements through a combination of general chromatin opening and gene-length-dependent transcriptional truncation, with distinct contributions from each mechanism.