Contact information
Department of Biochemistry and Molecular Biology
Michigan State University
East Lansing, MI 48824-1319
burtje@msu.edu

Education
Michigan Technological University
B.S. Biology, 1997

University of California, Berkeley
Ph.D. Molecular and Cellular Biology, 2003

Research Project

Since joining the Zacharewski lab, I have undertaken two major projects. The first project involved examining the gene expression changes elicited by ethynyl estradiol in estrogen-sensitive tissues and comparing and contrasting the changes. The second, and most recent, project I have been working on was developing a ChIP-chip assay for use in the lab and using the assay to investigate the genomic binding of the Aryl hydrocarbon receptor (AhR) upon treatment with TCDD in Hepa1c1c7 cells. In addition, being a large lab that uses toxicogenomics to examine traditional toxicological questions, much time has been spent aiding the lab’s parallel bioinformatics efforts by developing and beta testing computational tools, aiding various lab members with multi-person projects and training the many new members we have had join the lab.

To investigate systemic estrogenic effects, changes in gene expression in uterine, liver, kidney, femur and mammary tissue were examined in immature, ovariectomized C57BL/6 mice orally-gavaged with 17a-ethynyl estradiol (EE), a synthetic, orally active estrogen, at 2, 4, 8, 12, 18, 24, and 72 hours. cDNA microarrays containing 13361 clones (representing about 7500 unique genes) were used to compare the gene expression profiles of EE treated tissues to their time matched, vehicle control. With appropriate dye swaps and using three biological replicates, 42 microarrays were preformed per tissue leading to a total of 252 arrays. The data was normalized using a semiparametric approach (Eckel & Gennings et al., '05) and changes in expression were identified using an empirical Bayes screening method (Eckel & Gennings et al., '04) which generated initial lists of diferentially expressed genes per tissue. Gene function was assigned to changing genes using GO definitions and quantitative realtime PCR was used to verify gene expression changes. Finally, a parallel study was conducted in which histological and morphological changes were examined in an attempt to phenotypically anchor the gene expression changes observed with gross tissue level changes.

The following papers have used data generated from this study:

• A Cross-Species Analysis of the Rodent Uterotrophic Program: Elucidation of Conserved Responses and Mechanisms of Estrogen Signaling.
• Effects of culture conditions on estrogen-mediated hepatic in vitro gene expression and correlation to in vivo responses.

ChIP-chip is a newly developed, high-throughput method used to identify the genomic regions that show an interaction with a specific DNA binding protein that couples chromatin immunoprecipitation (ChIP) with microarray technology (chip). This emerging technology, when used in conjunction with gene expression arrays, proves to be useful in giving regulatory mechanistic insight into the changes observed in mRNA levels upon treatment of a toxicant. The project I have been working on, involves determining the regions of genomic binding of the AhR in Hepa1c1c7 cells upon treatment with 10nM TCDD for 2 hours. The arrays used are the Nimblegen Systems, Inc. ChIP-chip mouse promoter tiling array which consist of 15 unique probes tiled across the promoter region of about 30000 putative gene regions. The data generated was normalized, statistically screened, and genes were identified as having a putative AhR interaction if at least 6 out of the 15 probes passed the cut-offs. Genes identified included genes with known regulatory elements that bind to the AhR, genes that are known to be regulated by TCDD, as well as novel genes. Experiments are ongoing to verify these interections using site specific real time PCR as well as repeating the study to identify genomic regions that are bound by AhR’s binding partner, ARNT.