BME Lecture Series: Karmella Haynes, Arizona State University

McDonnell Douglas Engineering Auditorium (MDEA)
Karmella Haynes, Ph.D.

Assistant Professor of Biomedical Engineering

Abstract: Recombinant DNA technology has empowered scientists to control gene expression at will. Fusion transcription factors (TFs) are customizable proteins that can activate and repress virtually any target gene of interest. Typically, the mode of target site recognition is an interaction of the TF peptide (e.g., Gal4, TAL, ZF, etc.) or an RNA adapter (i.e., CRISPR) with DNA at promoters or enhancers near target genes. Our work represents a unique approach to TF targeting: the use of fusion proteins that bind epigenetic marks on histones rather than DNA sequences. In previous work, we developed and characterized the polycomb-based transcription factor (PcTF), a fusion protein that reads histone modifications through a protein-protein interaction between its N-terminal polycomb chromodomain (PCD) motif and trimethylated lysine 27 of histone H3 (H3K27me3). The C-terminal VP64 domain of PcTF recruits endogenous activators to silenced targets. We observed that dose-dependent, PcTF-mediated activation of target genes was accompanied by the loss of H3K27me3 and the accumulation of the activation-associated H3K4me3 mark over time. Expression of PcTF in triple negative breast cancer cells revealed that PcTF target genes include tumor suppressors. Therefore PcTF has significant implications for cancer treatment. We have implemented a cell-free to in-cell workflow to quickly identify more robust configurations of the modular PcTF fusion protein. Enzyme-linked immunosorbent assay (ELISA) and microspot array experiments showed that tandem PCD domains conferred enhanced and specific interaction with H3K27me3 in vitro. The double PCD fusion also showed enhanced target gene activation in a model cell line (HEK293). In conclusion, we have demonstrated a screening pipeline to support the design of functional histone-binding TFs. We believe that peptides that specifically interact with epigenetic marks are on the verge of becoming the next generation of synthetic transcriptional regulators.

Bio: Karmella Haynes is an assistant professor of biomedical engineering at Arizona State University. She earned her doctorate studying epigenetics and chromatin in Drosophila at Washington University, St. Louis. Postdoctoral fellowships at Davidson College and Harvard Medical School introduced her to synthetic biology. Today, her research aims to identify how the intrinsic properties of chromatin, the DNA-protein structure that packages eukaryotic genes, can be used to control cell development in tissues. Haynes received an NIH Young Faculty Award (K01) and an Arizona Biomedical Early Stage Investigator Award (AZ ESI). She is currently a councilor of the Engineering Biology Research Consortium (EBRC), a SynBioLEAP alum, and advisor and judge emeritus for the International Genetically Engineered Machines (iGEM) competition. She is a two-time featured guest on PRI’s Science Friday.