Investigating the role of molecular motors on chromatin organization

In eukaryotes, chromatin carrying most of the genetic material and information is densely packed within the cell nucleus. To facilitate the proper functioning of numerous life-essential biological processes, it possesses multiple levels of packaging. On one hand, nucleosomes, as the most fundamental packing unit, controls the accessibility of chromatin through their positioning along the DNA sequence, where ATP-driven remodelers, DNA-binding proteins are known to play essential roles. On the other hand, the spatial organization of the genome, folding into compartments to harbor the functional regions, is also impacted by these non-equilibrium motor activities. Therefore, we carried out theoretical and computational investigations to unveil the role of molecular motors on chromatin organization in both one-dimensional and three-dimensional levels. In one dimension, we showed that the effect of remodel- ing enzymes can be well approximated by effective equilibrium models with rescaled temperatures and interactions, when using a perturbation theory. We further constructed a unifying model to illustrate the construction of nucleosome positioning pattern during transcription. In three dimensions, we realized the conventional and inverted compartment distribution of chromatin with the interplay between active motors and passive interactions.

Name thesis:degree_name

Doctoral

Department dc:contributor.department

Massachusetts Institute of Technology. Department of Chemistry

Grantor dc:publisher

Massachusetts Institute of Technology

Year dc:date.issued

2022

Author dc:creator

• Jiang, Zhongling

Advisor dc:contributor.advisor

• Zhang, Bin

Statement dc:rights

• In Copyright - Educational Use Permitted
• Copyright MIT

Licence dc:rights.uri

• http://rightsstatements.org/page/InC-EDU/1.0/

Handle dc:identifier.uri

https://hdl.handle.net/1721.1/144507

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/144507