Jonathan Rubin

Transcriptional regulation plays a crucial role in normal cellular function, including response to stress or developmental cues. Transcription is largely governed through transcription factor (TF) binding to genomic DNA, in regions called enhancers and promoters. The Mediator complex is a global regulator of transcription that acts as a bridge connecting enhancer-bound TFs to the promoter-bound RNA polymerase II enzyme. I am interested in how Mediator and Mediator-associated kinases influence transcriptional regulation. Mediator kinases (CDK8 and CDK19) can reversibly bind to Mediator, and the function of their kinase activity specifically on transcriptional regulation remains unclear. Using GRO-Seq, a high throughput sequencing method that measures nascent transcription, and Cortistatin A, a specific and potent inhibitor of Mediator kinase activity, I plan to determine the role of Mediator kinases in transcription and on signaling pathways under specific cellular contexts. Additionally, I am interested in determining functional TF-enhancer binding events and developing computational tools to better analyze GRO-Seq datasets.

Publications:

Fant, CB; Levandowski, CB; Gupta, K; Maas, ZL; Moir, JT; Rubin, JD; Sawyer, A; Esbin, M; Rimel, JK; Luyties, O; Marr, MT; Berger, I; Dowell, RD; Taatjes, DJ. TFIID enables RNA polymerase II promoter-proximal pausing. Mol Cell 2020, 78: In Press. (May 21 issue) [PMID: 32229306]

Azofeifa JG, Allen MA, Hendrix JR, Read T, Rubin JD, Dowell RD (2018). Enhancer RNA profiling predicts transcription factor activity. Genome Res 28: 334-344.

Rubin, J.D., & Taatjes, D. J. (2015). Molecular biology: Mediating transcription and RNA export. Nature, 526(7572), 199–200.

Farrar, M. J., Rubin, J. D., Diago, D. M., & Schaffer, C. B. (2015). Characterization of blood flow in the mouse dorsal spinal venous system before and after dorsal spinal vein occlusion. Journal of Cerebral Blood Flow & Metabolism, 35(4), 667–675.