Research Program
Biomolecular Devices and Analysis

Objectives
Chromatin is the complex of DNA with five major histone proteins (H1, H2A, H2B, H3, and H4) found in the nucleus of eukaryotic cells.  Chemical modifications of the histones and methylation of cytosine nucleotides within the DNA of the chromatin can exert a potent influence on gene expression and are referred to as epigenetic modifications.  Though distinctly different from alterations in DNA sequence, these modifications have equally profound consequences, with fundamental impacts on normal development and mechanisms that lead to disease states.  Much effort is being devoted to identifying the genome placement of specific epigenetic marks in mammals and how they change during development and in diseases.  However, current methods require abundant sources of materials; report the average epigenetic state in a population and are limited to analysis of one epigenetic modification at a time.  We seek to develop methods that can query multiple epigenetic marks simultaneously on single molecules of chromatin. 

Methods
In the coming year, we will develop methods to label histones and methylated DNA in chromatin and analyze the fluorescence signals when chromatin is flowing through a nanoscale channel.  Specifically, we will optimize purification of chromatin and fluorescent probes for detecting epigenetic marks, and identify the buffer conditions and device designs that facilitate high throughput chromatin flow in nanoscale channels. These will enable us to then perform analysis of multiple epigenetic marks present on single chromatin fragments of mammalian cells.