EFRI CEE: Ascribing function to chromatin with coordinated live-cell epigenomic sensors and scalpels

North Carolina State University, Raleigh NC

Investigators

Abstract

This project will engineer new molecular tools to control how, when, and how strongly genes are expressed in cells, with direct impacts on our ability to understand and improve human and livestock health, crops, and bioproduction using microorganisms. Furthermore, the molecular tools developed will be broadly disseminated and applied to tackle the National Academy of Engineering's Grand Challenges of Reverse Engineering the Brain, Engineering Better Medicines, and Engineering Tools of Scientific Discovery as well as the National Science Foundation's goal of Understanding the Rules of Life. In addition, underrepresented student groups from local high school and undergraduate institutions will be directly integrated into research activities supporting the scientific aims of the project, with the ultimate goal of informing, inspiring, and mentoring students to pursue a sustained and successful career in engineering. The epigenome is the complex collection of proteins and RNAs layered on top of genomic DNA in eukaryotic cells. The epigenome, through its so-called chromatin organization, plays diverse integral roles in controlling gene expression; yet, currently our abilities to track and control changes in the epigenome are largely static, require large numbers of cells, and lack biochemical and spatial specificity. This limits the ability to directly demonstrate and harness the regulatory functions of the epigenome. To circumvent these barriers and enable direct, functional probes of epigenomic mechanisms, this project will engineer molecular and genetically-encoded tools that can track and perturb epigenome properties in living cells. This project will combine methods from epigenome editing, protein engineering, stem cell engineering, and live-cell super-resolution microscopy to address open questions regarding the structure function relationships of the three-dimensional shape of the epigenome and the biochemical specificity and biological relevance of histone modifications. The results are expected to provide new insights into key functional aspects of the epigenome, such as the heritability of topologically associating chromatin domains through DNA replication and cell division and the prevalence and roles of bivalent histone modifications. This award is co-funded by the Genetic Mechanisms Cluster in the Division of Molecular and Cellular Biosciences in the Biological Sciences Directorate, by the Physics of Living Systems Program in the Division of Physics in the Mathematical and Physical Sciences Directorate, and by the Emerging Frontiers in Research and Innovation Program in the Division of Emerging Frontiers and Multidisciplinary Activities in the Engineering Directorate. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.