Bethany A. Buck-Koehntop
Biological Chemistry Program Director
Associate Professor of Chemistry and Adjunct Associate Professor of Biochemistry
Associate Member HCI Cancer Center
Structural Biology, Biophysics, and Cancer Epigenetics
The primary focus of our research is to utilize a multidisciplinary approach incorporating structural biology, biophysics, biochemistry, molecular biology and cellular biology to explore structure-function relationships in protein/protein and protein/nucleic acid interactions. We are particularly interested in applying these methodologies to investigate specialized transcription factors termed methyl-CpG DNA binding proteins that specifically recognize methylated DNA sequences.
In mammals, DNA methylation is the primary mode of long-term transcriptional gene silencing in normal cells. Profound alterations in genomic DNA methylation patterns have also been associated with abnormal proliferation of cells preceding cancer development. These findings have prompted an interest in discerning the regulatory mechanisms of DNA methylation in gene transcription by investigating the factors that are involved in modification, recognition, and translation of the methylation signal. Methyl-CpG binding proteins directly interpret the methylation signal leading to chromatin remodeling and gene silencing. To date, we know very little about the complex mechanisms by which these events occur.
Active areas of research in our laboratory include: 1) Utilizing a parallel in vitro biophysical/structural and in cell genomic approach to delineate the molecular mechanisms by which these proteins recognize their cognate DNA targets and regulate transcription in the cancerous state; 2) structural characterization of these MBP:DNA interactions to ascertain modes of mCpG recognition for various MBPs; and 3) structural and biophysical characterizations of protein/protein interactions to begin evaluating how interpretation of the methylation signal triggers chromatin remodeling. Structure-function evaluation of MBPs with their interaction partners is critical for gaining mechanistic insight into the complex roles of these proteins in cancer epigenetics. It is anticipated that long-term this research will establish the basis for advancing therapeutic design directed toward key MBP regulatory networks/pathways.
Kumbhar, R., Sanchez, A., Perren, J., Gong, F., Corujo, D., Medina, F., Devanathan, S. K., Xhemalce, B., Matouschek, A., Buschbeck, M., Buck-Koehntop, B. A., Miller, K. M. Poly(ADP-ribose)-binding and macroH2A mediate recruitment and functions of KDM5A at DNA lesions, J. Cell. Biol., 2021, 220 (7), e202006149.
Hodges, A. J., Hudson, N. O., Buck-Koehntop, B. A.Cys2His2 zinc finger methyl-CpG binding proteins: Getting a handle on methylated DNA, J. Mol. Biol., 2020, 432, 1640-1660.
Hudson, N. O., Whitby, F. G., Buck-Koehntop, B. A. Structural insights into methylated DNA recognition by the C-terminal zinc fingers of the DNA reader protein ZBTB38, J. Biol. Chem., 2018, 293, 19835-19843.
Hudson, N. O., Buck-Koehntop, B. A. Zinc Finger Readers of Methylated DNA, Molecules, 2018, 23 (10), 2555.
Pozner, A., Hudson, N. O., Trewhella, J., Terooatea, T. W., Miller, S. A., Buck-Koehntop, B. A. The C-terminal Zinc Fingers of ZBTB38 are Novel Selective Readers of DNA Methylation, J. Mol. Biol., 2018, 430 (3), 258-271.
Pozner, A.; Terooatea, T. W.; Buck-Koehntop, B. A. Cell Specific Kaiso (ZBTB33) Regulation of Cell Cycle Through cyclin D1 and cyclin E1, J. Biol. Chem., 2016, 291 (47), 24538-24550.
Terooatea, T. W.; Pozner, A.; Buck-Koehntop, B. A. PAtCh-Cap: input strategy for improving analysis of ChIP-exo data sets and beyond.Nucleic Acids Res., 2016, 44 (21), e159.
Buck-Koehntop, B. A.; Defossez, P.-A. On how Mammalian Transcription Factors Recognize Methylated DNA. Epigenetics, 2013, 8, 131-137