187. COMPUTATIONAL MODELING TO RECOVER HIGHER-ORDER CHROMATIN STRUCTURE FROM INTERACTION FREQUENCIES

Department: NanoEngineering
Faculty Advisor(s): Gaurav Arya

Primary Student
Name: Dario Meluzzi
Email: dmeluzzi@ucsd.edu
Phone: 858-534-2230
Grad Year: 2013

Abstract
In this project we investigate the higher-order three-dimensional structure of chromatin, the complex filamentous assembly of proteins and DNA present inside the nucleus of all eukaryotic cells. The spatial organization of chromatin is known to play important roles in regulating vital cellular processes like transcription, replication, recombination, and DNA repair. However, the specific arrangement of chromatin within the nucleus and the effects of such arrangement on the above processes are not well understood. Fortunately, a wealth of relevant information is provided by a recently developed class of experimental techniques, known as Chromosome Conformation Capture (3C), which measure the frequency of interaction between different parts of chromatin in vivo. Here we apply coarse-grained molecular simulations to observe the dynamic interactions between different parts of a chromatin model. We then apply adaptive filtering techniques to recover the three-dimensional structure of the chromatin model from the measured interaction frequencies. This method can be applied to deduce chromatin structures consistent with 3C experimental data. Our results indicate that coarse-grained molecular modeling methods can effectively complement experiments in the quest to understand chromatin structure and its implications to cell biology.

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