- Using Mathematical Tools to Analyze Chromatin Structures
- Project Year:
2017
- REU Student (s):
Ondrej Maxian | Case Western Reserve University
- Student 1 Institution:
Case Western Reserve University
- Project Mentor:
Wilma Olson
- Project Mentor Area:
Chemistry and Chemical Biology
- Project Abstract:
The packing of DNA into nucleosome core particles (NCPs) is vital to the field of epigenetics and gene expression. Until now, the packing of NCPs has been studied physically via X-rays and cryogenic electron microscopy (cryo-EM), with few to little mathematical tools available. We here develop tools to quantitatively evaluate the amount of interaction between two nucleosomes on their faces and sides, as well as to give biological meaning to the regions of interaction. We apply our methods to X-ray crystal and cryo-EM structures, in the process confirming much of the existing observations while developing new insights into some atypical structures. We also deploy our algorithm to analyze configuration outputs from Markov Chain Monte Carlo (MCMC) simulations, which we found to closely resemble those from cryo-EM and X-ray.
