Department of Biochemistry
School of Medicine & Biomedical Sciences
Faculty
MICHAEL J. BUCK, Ph.D.
Assistant Professor
email: mjbuck@buffalo.edu
Link
to Dr. Buck's homepage
A Systems Biology Approach to Understanding Transcription Regulation
Transcription factors are directed to their genomic targets by DNA sequence, local chromatin structure, and protein-protein interactions. These modulators of transcription factor binding are not independent but function both cooperatively and competitively to regulate where transcription factors bind. Understanding how these modulators affect transcription factor binding in vivo remains a major unsolved biological problem.
My laboratory integrates both experimental and computational approaches to: i) investigate transcription factor binding in response to environmental stress, ii) identify and characterize the mechanisms directing transcription factor target selection, iii) determine how developmental signals reshape the epigenetic landscape during mouse development, and iv) develop bioinformatics tools to analyze and interpret ChIP-chip experiments.Selected Recent Publications
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’Rourke, 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.