IDBR: Type A: Whole-genome epigenetic profiling of single-cells

Non-Technical Description:

An award is made to North Carolina State University to develop a novel nanofluidic instrument for whole-genome epigenetic profiling of single cells. Epigenetic modification, and in particular cytosine methylation, is a modification of genetic material that enables control over gene activity which can be inherited through cell division and over multiple generations. Patterns of epigenetic modification can change as a response to the environment, during differentiation and development, or as part of disease onset, for example in cancer. In order to fully understand the dynamic character of cytosine modification patterns, in addition to identifying the the differences between individuals, and across tissue types within an individual, it is important to also identify the variability across cells within a tissue. To perform such mapping, an integrated device and associated hardware, will be developed and tested on sets of cultured cells that will have high and low epigenetic variability. The device will include a nanofluidic control system to conduct measurements. The project will train graduate students in bioinstrumentation, and will expose undergraduates to micro-and nanofluidic experiments. Additional educational activities involve a course for elementary school teachers.

Technical Description:

Current techniques for the determination of epigenetic patterns typically are based on methyl cytosine sensitive sequencing. It yields an overwhelming quantity of data for single-cells and whole genome for a tissue sample of 1000 cells. Differentially methylated regions are then found by coarse graining this large set of data. The instrument developed in this work will map methyl cytosine patterns with 250 bp-1000 bp resolution using a fluorescently labeled methylation-sensitive protein, and reading its binding location through a hybrid optic-electronic readout. All steps from single cell handling to detection are performed within one single device. Dissemination activities will include development of a webinar, provision of access to the finished device to the user community (a few devices will be fabricated and distributed to users), and training of undergraduate students in the basic principles of operation.