Synthetic Epigenetics

Many people are familiar with “genetics,” the inheritance of visible traits like eye and hair color. Traits are encoded by a molecular alphabet (A,T,C,G) in the well known double helix structure, DNA. Less well known, but quickly gaining attention, is the network of protein particles that interact with DNA to control the folding of chromosomes and the expression of inherited traits. This process is epi-genetics (epi, EH-pee = upon or above). Our research group uses gene and protein engineering to create new epigenetic machinery that regulates DNA at will. One day synthetic epigenetics may allow us to rationally design new biological systems with predictable, reliable behavior and replace “magic bullet medicine” with “smart medicine.”

We assemble interchangeable protein modules to build synthetic transcription factors that regulate gene activity in human cells. Unlike typical synthetic transcription factors that recognize specific DNA sequences, our Polycomb-based transcription factors (“PcTFs”) are engineered to read chromatin modifications. Thus, a single engineered TF could activate a group of silenced, therapeutic genes in cancer cells. Using strong gene activators could enhance cancer treatment and advance epigenetic medicine.

As synthetic biologists, our goal is to make the folded DNA-protein material, or chromatin (KRO-mah-tin = dark colored material in the nucleus of a fixed and stained cell), easier to design and engineer. Groups of genes often reside in the same compartments, and share the same DNA-protein packaging structures. Therefore, a small artificial change in one packaging protein can reprogram the expression of dozens, and even hundreds of genes. Is this outcome messy and useless, or is it a powerful mode of signal amplification that changes cells in useful ways? To answer this question, our group couples synthetic biology with bioinformatics by interrogating the expression of thousands of genes after we introduce artificial chromatin proteins into cells.

Current Projects

Synthetic Chromatin for Cancer Research

We are using the “PcTF” synthetic transcription activator described in Haynes & Silver 2011 to regulate genes in cancer cells. Powerful methods such as ChIP-seq and RNA-seq enable us to discover genes that are controlled by PcTF. We are also building and testing re-engineered versions of PcTF and using a model gene to understand epigenetic stochasticity of expression from tumor suppressors that have been silenced in cancer. Team: Daniel Vargas (Biological Design PhD), Stefan Tekel (Biological Design PhD). Collaborators: Dr. Melissa Wilson Sayres. Sponsor: NIH NCI

Synthetic Biologics for Breast Cancer Research

We are comparing the effect of PcTF on gene expression in normal cells and breast cancer-derived cells in two- and three-dimensional cell cultures. Team: Daniel Vargas (Biological Design PhD), David Nyer (past, Research Tech). Sponsor: Arizona Biomedical Research Commission (ABRC)

Opening Silenced Chromatin

We are using synthetic chromatin proteins to build a permanently re-opened state at epigenetically silenced genes. We aim to achieve unprecedented reliability for the expression of synthetic genes and improvement of CRISPR/Cas9-mediated gene editing in mammalian cells. Team: René Daer (past, Biological Design, PhD), Cassandra Barrett (Biological Design, PhD). Collaborators: Dr. Kaushal Rege (PI, ASU), Dr. Jacob Elmer (PI, Villanova). Sponsor: NSF CBET


Microbial Communication With Synthetic Quorum Sensing

Bacterial engineering is highly accessible to beginners in synthetic biology. Our ongoing ‘engineered quorum sensing’ project (founded by Rene Davis) helps new trainees to learn the connection between gene engineering and cell behavior, and provides a pathway towards advanced projects in human cell synthetic biology. The quorum sensing project characterizes cross-talk between decoupled cell-cell communication systems from bacteria. Team: Rotating graduate mentors and undergraduate trainees. Sponsors: Women and Philanthropy, ASU Fulton Undergraduate Research Initiative (FURI), Kern Entrepreneurial Engineering Network (KEEN)


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