Dylan Taatjes

  • Professor
Address

Office: JSCBB B319
Lab: JSCBB B380
Lab Phone: 303-492-1089
Fax: 303-492-5894

Education

PhD: 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

Areas of Expertise

Biochemistry, Molecular Biology, Cancer Biology, Cell Signaling, Chromatin, Gene Expression and Regulation, Genetics and Chemical Biology, Molecular Biophysics, and Systems Biology.

Mechanisms of transcription regulation in human development and disease

The Taatjes lab seeks to discover molecular mechanisms that control human gene expression, and how transcription and signaling pathways are altered during development and disease.  We focus on sequence-specific, DNA-binding transcription factors (TFs) and the Pre-Initiation Complex (PIC), which consists of Mediator, RNA polymerase II (pol II), TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIIH.  The PIC controls the activity of the pol II enzyme, which transcribes all protein-coding genes and most non-coding RNAs in the human genome.  Within the PIC, the 1.4 MDa Mediator complex, the 1.3 MDa TFIID complex, and the 0.5 MDa TFIIH complex help regulate pol II activity in ways that remain poorly understood.  At a basic level, TFIIH regulates transcription initiation and post-initiation steps (e.g. RNA processing), whereas Mediator and TFIID function by converting biological inputs (communicated by TFs) to physiological responses (via changes in gene expression).  We utilize a variety of experimental techniques that include biochemical, biophysical, molecular and cell biology approaches, as well as metabolomics, proteomics, and transcriptomics.

See my NCBI bibliography for a full and up-to-date list

  • Palacio M; Taatjes DJ. Real-time visualization of reconstituted transcription reveals RNA polymerase II activation mechanisms at single promoters. bioRxiv 2025, 631569.
  • Luyties, O; Sanford, L; Rodino, J; Nagel, M; Jones, T; Rimel, JK; Ebmeier, CC; Palacio, M; Shelby, GS; Cozzolino, K; Brennan, F; Hartzog, A; Saucedo, MB; Watts, LP; Spencer, S; Kugel, JF; Dowell, RD; Taatjes DJ. Multi-omics and biochemical reconstitution reveal CDK7-dependent mechanisms controlling RNA polymerase II function at gene 5'- and 3'-ends. Cell Rep 2025, 44: 115904.
  • Jones, T; Feng, J; Luyties, O; Cozzolino, K; Sanford, L; Rimel, JK; Ebmeier, CC; Shelby, GS; Watts, LP; Rodino, J; Rajagopal, N; Hu, S; Brennan, F; Maas, ZL; Alnemy, S; Richter, WF; Koh, AF; Cronin, NB; Madduri, A; Das, J; Cooper, E; Hamman, KB; Chuaqui, C; Carulli, JP; Allen, MA; Spencer, S; Kotecha, A; Marineau, J; Greber, BJ; Dowell, RD; Taatjes DJ. TFIIH kinase CDK7 drives cell proliferation through a common core transcription factor network. Sci Adv 2025, 11: eadr9660.
  • Cozzolino, K; Sanford, L; Hunter, S; Molison, K; Erickson, B; Courvan, MCS; Jones, T; Ajit, D; Galbraith, MG; Espinosa, JM; Bentley, DL; Allen, MA; Dowell, RD; Taatjes, DJ. Mediator kinase inhibition suppresses hyperactive interferon signaling in Down syndrome. eLife 2025, 13: RP100197.
  • Nussbaum, DP; Martz, CA; Waters, AM; Barrera, A; Liu, A; Rutter, JC; Cerda-Smith CG; Stewart, AE; Wu, C; Cakir, M; Levandowski, CB; Kantrowitz, DE; McCall, SJ; Pierobon, M; Petricoin, EF; Smith, JJ; Reddy, TE; Der, C; Taatjes, DJ; Wood, KC. Mediator kinase inhibition impedes transcriptional plasticity and prevents resistance to ERK/MAPK-targeted therapy in KRAS-mutant cancers. NPJ Precision Oncology 2024, 8: 124.
  • Maia-Silva, D; Cunniff, PJ; Schier, AC; Skopelitis, D; Trousdell, MC; Moresco, P; Gao, Y; Kechejian, V; He, X; Sahin, Y; Wan, L; Alpsoy, A; Liverpool, J; Krainer, AR; Egeblad, M; Spector, DL; Fearon, DT; Dos Santos, CO; Taatjes, DJ; Vakoc, CR. Interaction between MED12 and DNp63 activates basal identity in pancreatic ductal adenocarcinoma. Nat Genet 2024, 56: 1377 - 1385.
  • Allen, BL; Quach, K; Jones, T; Levandowski, CB; Ebmeier, CC; Rubin, JD; Read, T; Dowell, RD; Schepartz, A; Taatjes, DJ.  Suppression of p53 response by targeting p53–Mediator binding with a stapled peptide. Cell Rep 2022, 39: 110630.
  • Levandowski, CB; Jones, T; Gruca, M; Ramamoorthy, S; Dowell, RD; Taatjes, DJ. The D40p53 isoform inhibits p53-dependent eRNA transcription and enables regulation by signal-specific transcription factors during p53 activation. PLoS Biol 2021, 19: e3001364.
  • Rimel, JK; Poss, ZC; Erickson, B; Maas, ZL; Ebmeier, CC; Johnson, JL; Decker, T-M; Yaron, TM; Bradley, MJ; Hamman, KB; Hu, S; Malojcic, G; Marineau, JJ; White, PW; Brault, M.; Tao, L.; DeRoy, P; Clavette, C; Nayak, S; Damon, LJ; Kaltheuner, IH; Bunch, H; Cantley, LC; Geyer, M; Iwasa, J; Dowell, RD; Bentley, DL; Old WM; Taatjes, DJ.  Selective inhibition of CDK7 reveals high-confidence targets and novel mechanisms for TFIIH function in transcription. Genes Dev 2020, 34: 1452 – 1473.
  • 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: 785 – 793.
  • Guo, YE; Manteiga, JC; Henninger, J; Sabari, BR; Dall'Agnese, A; Hannett, NM; Spille, J-H; Afeyan, LK; Zamudio, AV;  Shrinivas, K; Abraham, BJ; Boija, A; Decker, TM; Rimel, JK; Fant, CB; Lee, TI; Cisse, II; Sharp, PA; Taatjes, DJ; Young, RA. RNA polymerase II phosphorylation regulates a switch between transcriptional and splicing condensates. Nature 2019, 572: 543 – 548.
  • Steinparzer, I; Sedlyarov, V; Rubin, JD; Eislmayr, K; Galbraith MD; Levandowski, CB; Vcelkova, T; Sneezum, L; Wascher, F; Amman, F; Kleinova, R; Bender, H; Andrysik, Z; Espinosa, JM; Superti-Furga, G; Dowell, RD; Taatjes, DJ; Kovarik, P. Transcriptional responses to IFNg require Mediator kinase-dependent pause release and mechanistically distinct CDK8 and CDK19 functions. Mol Cell 2019, 76: 485 – 499.

  • Boija, A; Klein, IA; Sabari, BR; Dall'Agnese, A; Coffey, EL; Zamudio, AV; Li, CH; Shrinivas, K; Manteiga, J; Hannett, NM; Abraham, BJ; Schuijers, J; Afeyan, L; Guo, YE; Rimel, JK; Fant, CB; Lee, TI; Taatjes, DJ; Young, RA. Transcription factors activate genes through the phase separation capacity of their activation domains. Cell 2018, 175: 1842 – 1855.

     

Selected Review articles:

  • Nagel, M; Taatjes, DJ. Regulation of RNA polymerase II transcription through re-initiation and bursting. Mol Cell 2025, 85: 1907 - 1919.
  • Nayak, S; Taatjes DJ. SnapShot: Mediator Complex Structure. Cell 2022, 185: 3458.
  • Clopper, KC; Taatjes, DJ. Chemical inhibitors of transcription-associated kinases. Curr Opin Chem Biol 2022, 70: 102186.
  • Richter, WF; Nayak, S; Iwasa, J; Taatjes, DJ. The Mediator complex as a master regulator of transcription by RNA polymerase II. Nat Rev Mol Cell Biol 2022, 23: 732 - 749.
  • Luyties, O; Taatjes, DJ.  The Mediator kinase module: an interface between cell signaling and transcription. Trends Biochem Sci 2022, 47: 314 - 327.
  • Palacio, M; Taatjes DJ. Merging established mechanisms with new insights: Condensates, hubs, and the regulation of RNA polymerase II transcription. J Mol Biol 2022, 433: 167216.
  • Schier, AC; Taatjes, DJ. Structure and mechanism of the RNA polymerase II transcription machinery. Genes Dev 2020, 34: 465 – 488.