David Brow

Research Description:
We study two essential biological “nanomachines” of gene expression, the spliceosome and RNA polymerase II (Pol II), using brewer’s yeast as a model system. Our studies on the spliceosome focus on U6 RNA and the dynamic RNA-RNA and RNA-protein interactions required for its assembly into the active site. Using genetic suppression analysis and in vitro biochemistry, we have defined a complex network of interactions that involves 3 RNAs (U2, U4, and U6), two helicases (Prp28 and Brr2), an RNA-binding protein (Prp24), and the largest and most conserved spliceosomal protein (Prp8). In collaboration with Sam Butcher’s lab, we recently solved the crystal structure of the core U6 snRNP (Prp24 bound to U6 RNA) at 1.7 Å resolution (see Figure 1).

Figure 1. From EJ Montemayor et al. (2014) Nature Struct. Molec. Biol. 21: 544-551.

Our work on Pol II focuses on transcription termination as a strategy for gene regulation. We discovered and are characterizing a pathway that uses the helicase Sen1 and a collection of RNA-binding proteins, including Nrd1 and Nab3, to terminate synthesis of short transcripts by Pol II (see Figure 2). This pathway aids in the synthesis of non-coding RNAs, as well as the regulation of mRNA levels. Mutations in the human homolog of Sen1 result in neuro-degenerative disorders. We are exploring the function and targets of the Sen1 termination pathway by genetics, genomics, biochemistry, and structural biology.

Figure 2. From DA Brow (2011) Molec. Cell 42: 717-718.

Representative Publications:
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Brow, D.A. (2011). Sen-sing RNA terminators. Molec. Cell 42, 717-718.

Martin-Tumasz, S., Richie, A.C., Clos, L.J. II, Brow†, D.A., and Butcher†, S.E. (2011). A novel occluded RNA recognition motif in Prp24 unwinds the U6 RNA internal stem loop. Nucl. Acids Res. doi: 10.1093/nar/gkr455. †corresponding authors

Brow, D.A. Eye on RNA unwinding. (2009). Nature Struct. Molec. Biol. 16, 7-8.

Kuehner, J.N. and Brow, D.A. Regulation of a eukaryotic gene by GTP-dependent start site selection and transcription attenuation. (2008). Molec. Cell 31, 201-211. (Cover article)

McManus, C.J., Schwartz, M.L., Butcher, S.E. and Brow, D.A. (2007). A dynamic bulge in the U6 RNA internal stem-loop functions in spliceosome assembly and activation. RNA 13, 2252-2265.

Bae, E., N.J. Reiter, C.A. Bingman, S.S. Kwan, D. Lee, G.N. Phillips Jr., S.E. Butcher, and D.A. Brow. (2007). Structure and interactions of the first three RNA recognition motifs of splicing factor Prp24. J. Mol. Biol., 1447-1458.

Steinmetz, E.J., C.L. Warren, J.N. Kuehner, B. Panbehi, A.Z. Ansari, and D.A. Brow. (2006). Genome-wide distribution of yeast RNA polymerase II and its control by Sen1 helicase. Molec. Cell 24, 735-746. (Cover article)

Kuehner, J.N, and D.A. Brow. (2006). Quantitative analysis of in vivo initiator selection by yeast RNA polymerase II supports a scanning model. J. Biol. Chem. 281, 14119-14128.

Steinmetz, E.J., S.B.H. Ng, J.P. Cloute, and D.A. Brow. (2006). Cis- and trans-acting determinants of transcription termination by yeast RNA polymerase II. Molec. Cell. Biol. 26, 2688-2696.

Butcher, S. and Brow, D.A. (2005). Towards understanding the catalytic core structure of the spliceosome. Biochem. Soc. Transact. 33, 447-449.

Kwan, S.S. and D.A. Brow. (2005). The N- and C-terminal RNA recognition motifs of splicing factor Prp24 have distinct functions in U6 RNA binding. RNA 11, 808-820.

Kaiser, M.W., J. Chi and D.A. Brow. (2004). Position-dependent function of a B block promoter element implies a specialized chromatin structure on the S. cerevisiae U6 RNA gene, SNR6. Nucl. Acids Res. 32, 4297-4305.