Karmella Haynes, Assistant Professor of Biomedical Engineering, Emory University

"Exploring Signal Processing within Chromatin with Protein Engineering"

Abstract:

Protein-protein interactions between transcriptional regulators, known as “reader-effectors” and their targets, post-translationally modified histones or methylated DNA, are a key step in the interpretation of chromatin marks that encode differential expression programs. Creative approaches such as synthetic biology can be used to push the boundaries of our understanding of reader-effector mechanisms by testing previously established models. Our lab has developed an approach called “epigenome actuation” where we use rational design to build synthetic reader-actuator (SRA) fusion proteins from functional domains found within natural reader-effector proteins.

This presentation will describe how the “design, build, test, learn” method of synthetic biology was used to develop the first SRA, “Polycomb-based transcription factor” (PcTF), which reads H3K27me3 via an N-terminal Polycomb chromodomain and activates transcription via a strong 4x-VP16 domain once it engages with target genes. At an artificially H3K27me3-enriched, transcriptionally-silenced luciferase reporter in HEK293 cells SRA-mediated reactivation of the reporter required the chromodomain. Tandem linked chromodomains enhanced transcriptional activation nearly 3-fold, revealing the critical role of chromodomain affinity in reader-effector activity.

We demonstrated a practical use of the SRA by using it to restore transcription in chemo-resistant triple negative breast cancer cells at tumor suppressor genes that had become hyper-repressed by H3K27me3 and polycomb complexes. SRA expression in BT-549 cells increased the expression of 122 genes, including cell-cycle arrest and apoptotic genes 2 to 20-fold, and completely blocked spheroid growth and Matrigel invasion in vitro. Finally, we investigated macro-scale, SRA-mediated regulation of chromatin domains in the extensively genomically-profiled cell line MCF7. Using a combination of cell engineering, transcriptomics, and chromatin mapping we have begun to elucidate the spatial organization of epigenetically plastic H3K27me3-enriched domains. We present exciting new evidence that these regions are compartmentalized within topologically-associated domains (TADs). Our results suggest that while histone PTM-targeted regulation is distributed across many loci, the effect may be restricted to specific TADs. These results have exciting implications for controlling transcription across genomic domains based on chromatin marks rather than specific DNA sequences.

Bio:

Karmella Haynes is an Assistant Professor of Biomedical Engineering at Emory University. She earned her Ph.D. 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. Her Davidson HHMI postdoc fellowship project on bacterial computers was recognized as “Publication of the Year” in 2008 by the Journal of Biological Engineering. Today, her research aims to apply the intrinsic properties of chromatin, the DNA-protein structure that packages eukaryotic genes, to engineer proteins and nucleic acids that control cell development.

After Dr. Haynes joined the faculty at the Emory School of Medicine in 2019, she received an NIH R21 grant (2019) to develop new protein engineering and computational tools for cancer epigenetics, and launched the annual NSF-funded AfroBiotech conference series (2019). She is a founder and instructor of the Cold Spring Harbor Summer Course on Synthetic Biology (2013 – present), a member of the national Engineering Biology Research Consortium (EBRC, 2014 – present), past advisor and current Judge Emeritus for the annual International Genetically Engineered Machines (iGEM) competition (2007 – present), and a member of the NIH National Scientific Advisory Board for Biosecurity (2021). She was named one of 1000 Inspiring Black Scientists by Cell Mentor (Cell Press 2020), was a featured guest on PBS NOVA (2020) and PRI’s Science Friday (2016), was profiled in Forbes magazine (2020), received Color Magazine’s Women of Color: Innovator in STEM award (2021), and was elected into the 2023 American Institute for Medical and Biological Engineering (AIMBE) College of Fellows.