David T. Auble
Professor of Biochemistry & Molecular Genetics
Ph.D., Case Western University
Mechanisms of Transcription Initiation and DNA Repair

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Work in my laboratory is focused on understanding mechanisms of transcriptional regulation, the processes that control the synthesis of RNA. The complexity and abundance of RNA species made by a cell provide a signature defining cell identity and function, and defects in regulatory processes underlie many disease states including cancer. A wide variety of transcriptional regulators and co-regulators control the native state of chromatin as well as the assembly and activity of the transcription machinery on promoter DNA. Subsequent to the initiation of RNA synthesis, regulatory factors impinge on the elongating polymerase and control the elongation and termination processes. We employ biochemical, molecular, genetic, and genomic approaches to dissect regulatory phenomena using mainly budding yeast as a model system. For example, our work on an essential and conserved enzyme called Mot1 has provided unique and general insight into the transcription process. Mot1 is a remarkable enzyme that uses ATP hydrolysis to remove the TATA-binding protein (TBP) from DNA. TBP is at the heart of the promoter-bound transcription complex, and Mot1 therefore has fundamental and widespread effects on transcription in vivo. Mot1-mediated displacement of TBP can exert repressive effects on transcription, but surprisingly, Mot1 also positively affects the expression of thousands of genes. Our exploration of how and why Mot1 has such effects has led to new insights into how transcription complexes are regulated at active genes, and suggests that gene expression is far more dynamic than suggested by prior in vitro experiments. We are developing new approaches to capture the kinetics of transcription complex assembly and disassembly in vivo at specific promoters, and plan to integrate kinetic measurements of chromatin binding with knowledge of RNA synthesis rates and chromatin structure to develop models for how transcription occurs in living cells in real time. Such work will provide a foundation for detailed analyses of regulatory phenomena well beyond Mot1. Mot1 has also been a valuable focus of study because it is a member of a large and diverse family of enzymes, the Snf2/Swi2 family, whose members play roles in all aspects of chromatin metabolism. As such, an understanding of how Mot1 works on a biochemical and structural level continues to inform our general mechanistic understanding of enzymes in this family.

Selected References

Moyle-Heyrman G, Viswanathan R, Widom J, Auble DT. (2012) "Two-step mechanism for modifier of transcription 1 (Mot1) enzyme-catalyzed displacement of TATA-binding protein (TBP) from DNA." J Biol Chem. Mar 287(12):9002-12. doi: 10.1074/jbc.M111.333484. Epub 2012Feb 1. [PubMed]

Wollmann P, Cui S, Viswanathan R, Berninghausen O, Wells MN, Moldt M, Witte G,Butryn A, Wendler P, Beckmann R, Auble DT, Hopfner KP. (2011) "Structure and mechanism of the Swi2/Snf2 remodeller Mot1 in complex with its substrate TBP." Nature. Jul 475(7356):403-7. doi: 10.1038/nature10215. [PubMed]

Poorey K, Sprouse RO, Wells MN, Viswanathan R, Bekiranov S, Auble DT. (2010) "RNA synthesis precision is regulated by preinitiation complex turnover." Genome Res. 20(12):1679-88. doi: 10.1101/gr.109504.110. Epub 2010 Sep20. [PubMed]

Wade SL, Poorey K, Bekiranov S, Auble DT. (2009) "The Snf1 kinase and proteasome-associated Rad23 regulate UV-responsive gene expression." EMBO J. Oct 28(19):2919-31. doi: 10.1038/emboj.2009.229. Epub 2009 Aug 13. [PubMed]

Sprouse RO, Wells MN, Auble DT. (2009) "TATA-binding protein variants that bypass the requirement for Mot1 in vivo." J Biol Chem. Feb 284:4525-35. doi: 10.1074/jbc.M808951200. Epub 2008Dec 21. [PubMed]

Auble DT. (2009) "The dynamic personality of TATA-binding protein." Trends Biochem Sci. 34:49-52. doi: 10.1016/j.tibs.2008.10.008. Epub2008 Nov 27. [PubMed]

Sprouse RO, Karpova TS, Mueller F, Dasgupta A, McNally JG, Auble DT. (2008) "Regulation of TATA-binding protein dynamics in living yeast cells." Proc Natl Acad Sci U S A. Sep 105(36):13304-8. doi:10.1073/pnas.0801901105. Epub 2008 Sep 2. [PubMed]

Sprouse RO, Shcherbakova I, Cheng H, Jamison E, Brenowitz M, Auble DT. (2008) "Function and structural organization of Mot1 bound to a natural target promoter." J Biol Chem. Sep 283(36):24935-48. doi: 10.1074/jbc.M803749200. Epub 2008 Jul 7. [PubMed]