Ph.D.: Organic Chemistry; Advisor: Dr. Tad Koch. University of Colorado at Boulder, 1994-1998
Postdoctoral Fellow: Molecular and Structural Biology; Advisor: Dr. Robert Tjian. University of California at Berkeley, 1999-2004
Structure and Mechanism of the human Transcription Machinery
The Taatjes lab investigates the molecular mechanisms by which the human transcription machinery functions and is regulated. Proper regulation of gene expression is fundamental to every major physiological process, and changes in gene expression patterns are hallmarks of human development and disease. Consequently, the questions that we address in the Taatjes lab are fundamental and of broad significance. At the moment, our research has direct implications for cardiac and neuronal development, inflammation, cancer, and aging.
The macromolecular assembly required to initiate gene expression consists of 8 protein complexes and is approximately 4.0 MDa in size. The human Mediator complex (26 subunits, 1.2 MDa) is a major sub-assembly within the transcription apparatus and represents the main focus of the lab. Although the mechanisms by which Mediator functions to control gene expression are poorly-defined, it is clear that Mediator is essential for expression of most protein-coding and non-coding RNA genes and regulates gene expression in myriad ways, including transcription initiation, elongation, RNA processing, and chromatin architecture. Mediator is generally targeted by DNA-binding transcription factors that control gene expression programs in response to developmental and environmental cues. Furthermore, the Mediator complex interacts directly with the RNA polymerase II (pol II) enzyme; thus, Mediator functions generally by communicating regulatory signals from DNA-binding transcription factors to the pol II enzyme. Mediator remains poorly understood in part because Mediator structure and even its composition can change, depending upon the context. For example, DNA-binding transcription factors alter Mediator structure upon binding the complex, and a four-subunit, 600 kDa “CDK8 module” can reversibly associate with Mediator and change its biological function.
In the Taatjes lab, we utilize an array of diverse experimental approaches and have the privilege of working with a talented group of collaborators. Techniques employed range from basic biochemistry (protein expression and purification, enzymatic assays, in vitro transcription), mass spectrometry (LC-MS/MS, linear ion-trap MS, SILAC, CXMS), structural biology (cryo-electron microscopy, X-ray crystallography and/or NMR), metabolomics, cellular assays, and genomics (ChIP, RT-qPCR, RNA-Seq, microarray, ChIP-Seq). We have biochemically purified each of the factors that, together with Mediator, comprise the fully functional, 4.0 MDa human transcription apparatus (which includes RNA polymerase II, TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIIH). This enables us to address specific mechanistic questions regarding Mediator’s role as a regulator of pol II transcription.
Poss, ZC; Ebmeier, CC; Taatjes, DJ. The Mediator complex and transcription regulation. Crit Rev Biochem Mol Biol. 2013, 48: 575 – 608.
Lin, SC; Karoly, ED; Taatjes, DJ. The human ΔNp53 isoform triggers metabolic and gene expression changes that activate mTOR and alter mitochondrial function. Aging Cell 2013, 12: 863 – 872.
He, Y; Fang, J; Taatjes, DJ; Nogales, E. Structural visualization of key steps in human transcription initiation. Nature 2013, 495: 481 – 486.
Bancerek, J; Poss, ZC; Steinparzer, I; Sedlyarov, V; Pfaffenwimmer, T; Mikulic, I; Dolken, L; Strobl, B; Muller, M; Taatjes, DJ; Kovarik, P. CDK8 Kinase Phosphorylates Transcription Factor STAT1 to Selectively Regulate the Interferon Response. Immunity 2013, 38: 250 – 262.
Bernecky, C; Grob, P; Ebmeier, CC; Nogales, E; Taatjes, DJ. Molecular architecture of the human Mediator–RNA Polymerase II–TFIIF assembly. PLoS Biol. 2011, 9: e1000603.
Kagey, MH; Newman, JJ; Bilodeau, S; Zhan, Y; Orlando, DA; van Berkum, NL; Ebmeier, CC; Goossens, J; Rahl, PB; Levine, SS; Taatjes, DJ; Dekker, J; Young, RA. Mediator and Cohesin connect gene expression and chromatin architecture. Nature. 2010, 467: 430-435.
Ebmeier, CC; Taatjes, DJ. Activator-Mediator binding regulates Mediator-cofactor interactions. Proc Natl Acad Sci. USA. 2010, 107: 11283-11288.
Meyer, KD; Lin, S; Bernecky, C; Gao, Y; Taatjes, DJ. p53 activates transcription by directing structural shifts in Mediator. Nat Struct Mol Biol. 2010, 17: 753-760.
Taatjes, DJ. The human Mediator complex: a versatile, genome-wide regulator of transcription. Trends Biochem Sci. 2010, 35: 315-322.
Donner, AJ; Ebmeier, CC; Taatjes, DJ; Espinosa JM. CDK8 is a positive regulator of transcriptional elongation within the serum response network. Nat Struct Mol Biol. 2010, 17: 194-201.
Knuesel, MT; Meyer, KD; Bernecky, C; Taatjes, DJ. The human CDK8 subcomplex is a molecular switch that controls Mediator co-activator function. Genes & Dev. 2009, 23: 439-451.
Knuesel, MT; Meyer, KD; Donner, AJ; Espinosa JM; Taatjes, DJ. The human CDK8 subcomplex is a histone kinase that requires Med12 for activity and can function independently of Mediator. Mol Cell Biol. 2009, 29: 650-661.
Meyer, KD; Donner, AJ; Knuesel, MT; York, AG; Espinosa, JM; Taatjes, DJ. Cooperative activity of CDK8 and GCN5L within Mediator directs tandem phosphoacetylation of histone H3. EMBO J 2008, 27: 1447-1457.