Time-Course Expression Profiling Reveals Early and Late Responders to a Synthetic Chromatin Regulator
Synthetic Biology Engineering Evolution Design SEED
2021
2021 Synthetic Biology: Engineering, Evolution & Design (SEED)
Poster Session
Poster Presenters - Accepted
To fully elucidate the activation mechanism of PcTF we have developed stable MCF-7 cell lines that inducibly express full length PcTF or truncations of the full-length protein, to be utilized as controls. After induction, we harvested total mRNA at 10, 24, and 48 hours for RNA-seq. Bioinformatic analysis of the RNA-seq data stratified early and late-activated groups of target genes that specifically respond to full-length PcTF. This result shows that we can distinguish genes by their response to PcTF and establishes a foundation to investigate differences in the physical interaction of PcTF with specific promoters and enhancers, as well as differences in local chromatin structure. To this end, we are using CUT&RUN and a novel transposase mapping system (Calling Cards, R. Mitra lab) to track PcTF interactions and map chromatin features. Ultimately, our work will guide clinical use of synthetic reader-effectors to reprogram gene expression in cancer cells.