Regulation of Gene Expression
Dr. Cooper spent her graduate school days studying the mechanisms by which genes are regulated. She participated in the ENCODE pilot study, predicting and functionally testing promoter elements in 1% of the human genome (Cooper et al. 2006). She also contributed to early efforts to apply chromatin immunoprecipitation to identify transcription factor binding sites across the genome (Cooper et al. 2007, Trinklein et al. 2004). She maintains her interests in mechanisms of gene expression as well as the advances in technologies that facilitate these discoveries.
Transcriptional regulation is a critical driver of cell proliferation and contributes to prognosis in cancer. In two recent studies, Dr. Cooper and her group contributed to the characterization of the role for transcription factors in triple negative breast and liver cancers. In a study led by Dr. Joy McDaniel and in collaboration with Dr. Richard Myers, we used ChIP-Seq and RNA-seq to show that STAT3 plays a critical role in regulating metastasis in TNBC (McDaniel et al. 2017). With Drs. Savic and Myers, we used similar methods to demonstrate a role for PPARG and LXRs in cell proliferation in liver cancer (Savic et al. 2016).
Most recently, we applied the ChIP-seq platform to primary human liver allowing an analysis of similarities and differences between primary tissue and the large number of experiments done on immortalized cell lines. We combined this with phased whole genome sequencing data and RNA-sequencing to generate a resource that we have begun to use to understand in greater detail how genetic variants contribute to gene expression and ultimately human disease (Ramaker et al. 2017).