Molecular Recognition in Biological Systems and Bioinformatics

Transcription regulation; ChIP-chip; Computational Biology; Saccharomyces cerevisiae; Genomics

The Buck Lab integrates both experimental and computational approaches to study transcription factor targeting in model organisms. The DNA sequences recognized by transcription factors are located all over the genome but a tiny faction is bound in living cells. Transcription factors are directed to their genomic targets by DNA sequence, epigenetic markers, and protein-protein interactions. Understanding how these modulators affect transcription factor binding remains a major unsolved biological problem.

We are currently: i) investigating transcription factor binding in response to environmental stress, ii) identifying and characterizing the mechanisms directing transcription factor target selection, iii) determining how developmental signals reshape the epigenetic landscape during development, and iv) developing bioinformatics tools to analyze and interpret ChIP-chip experiments.

SAS

Saccharomyces cerevisiae, Human

Rap1, Cbf1, Tup1, Mig1, p53

Cancer biology, cellular development

ChIP-chip, Microarrays, QPCR

CY-Dyes

Mieczkowski, P.A., Dominska, M., Buck, M.J., Lieb, J.D., and Petes, T.D. (2007). Loss of a histone deacetylase dramatically alters the genomic distribution of Spo11p-catalyzed DNA breaks in Saccharomyces cerevisiae. PNAS Mar 6;104(10):3955-60.

Xiao, T., Shibata, Y., Rao, B., Laribee, R.N., O%u2019Rourke, R., Buck, M.J., Greenblatt, J.F., Krogan, N.J., Lieb, J.D., Strahl, B.D. (2007). The RNA Pol II kinase Ctk1 regulates positioning of a 5' histone methylation boundary along genes. Molecular Cell Biology Jan; 27(2)721-31.

Buck, M.J., and Lieb, J.D. (2006). A chromatin-mediated mechanism for specification of conditional transcription factor targets. Nature Genetics Dec; 38(12): 1446-51. [PDF]

Mieczkowski, P.A., Dominska, M., Buck, M.J., Gerton, J.L., Lieb, J.D., Petes, T.D. (2006). A global analysis of the relationship between the binding of the Bas1p transcription factor and meiotic recombination activity in Saccharomyces cerevisiae. Molecular Cell Biology Feb; 26(3): 1014-27.

Buck, M.J., Nobel, A.B., and Lieb, J.D. (2005). ChIPOTle: A user-friendly tool for the analysis of ChIP-chip data. Genome Biology 6: R97. [PDF]

Buck, M.J., and Atchley, W.R. (2005). Networks of coevolving sites in structural and functional domains of serpin proteins. Molecular Biology and Evolution Jul; 22(7):1627-34.

Buck, M.J., and Lieb, J.D. (2004). ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics Mar; 83(3): 349-60. [PDF]

Buck, M.J., and Atchley, W.R. (2003). Phylogenetic analysis of plant basic Helix-Loop-Helix proteins. Journal of Molecular Evolution Jun; 56(6): 742-50.

Buck, M.J., Squire, T.L., and Andrews, M.T. (2002). Coordinate expression of the PDK4 gene: a means of regulating fuel selection in a hibernating mammal. Physiological Genomics Feb; 8(1): 5-13.