Epigenetic modifications modulate the accessibility of genetic material for transcription, and are a method for persistent modulation of expression patterns. Epigenetic modifications do not change the DNA sequence but are inheritable, and cells can actively modify epigenetic marks in response to external stimuli or internal regulatory networks. Because of this highly dynamic nature, epigenetic modifications occur faster than sequence modifications, and they are a driving force behind human development and cancer progression. In order to understand the dynamic nature of histone modification, single-cell analysis of heterogeneous population appears necessary. We aim to provide key techniques in this field.
There are two main mechanisms for the epigenetic modification: methylation of cytosine bases, and modification of histone tails. We have demonstrated methylation mapping using a fluorescently labeled protein that binds to methylated copies of the essential CpG motif. We were able to demonstrate specificity, gene-relevant resolution, and profiling within single molecules.
Methylation mapping in nanochannels. DNA is green, and methylation markers are red.
We have divided the mapping of histone modification into the conceptual steps of chromatin stretching and labeling of histones. The stretching of chromatin was successful, and we found stretching consistent with a deGennes-like scaling. The fluorescent labeling of modifications is currently in process.
Detection of chromatin formation on lambda-DNA. (Left) Chromatin in nanochannels. (Right) DNA in nanochannels.
We are also investigating a method identifying epigenetic marks using label-free uv-resonant Raman scattering enhanced by near-field optics in nanochannels. This work is being perfomed in collaboration with Dr. Hallen at NC State's Physics departement.