You are cordially invited to the M.S. Thesis Defense Presentation
“Exploring steric effects of lamina-associated domains by using polymer modeling”
Naz Bardakçı, M.S. Student in Materials Science and Nanotechnology Graduate Program
Abstract: 3D-genome organization within micron-scale cell nucleus is crucial for gene regulation, which can also vary between a healthy cell and a diseased one. Recent studies revealed the presence of lamina-associated domains (LADs) located in the nuclear periphery, which are 0.1-10 MB sized domains of chromatin fiber. LADs are considered large regions where transcription levels are low and genes are repressed, also biochemically exhibiting the characteristics of a gene repressing environment. Although there is a repressive environment in LADs, some genes can escape this repression although some key transcriptional proteins such as RNA Polymerase II are not present in LADs. These observations point out that LADs may control gene regulation and genome organization via their properties as an adsorbed polymer; however, the physical mechanisms behind their role and functionality remain mostly unknown. To address this, we used molecular dynamics simulations in which we modeled LADs as a diblock copolymer that consists of euchromatin and heterochromatin blocks. We investigate its non-specific interactions with the different sizes of protein particles inside of the cross section of the nucleus near the periphery. Our results showed that LADs sterically hinder spherical protein particles with sizes comparable to those of transcriptional factors to the proximity of the nuclear lamina according to their sizes. LADs behave as highly dense adsorbed polymer onto the static layer which is modeled as nuclear lamina. The control of the chromatin environment at nuclear periphery is possible by adjusting physical parameters such as chromatin self-affinity and chromatin-lamina affinity, which alters compaction and locality at LADs respectively. Interestingly, compaction and locality do not change with the presence of proteins in the system, and proteins partition according to their sizes in every chromatin environment. The total concentration of proteins does not change the hindrance effect. Overall, our results suggest that LADs have a role in regulating the presence of transcriptional machinery near the nuclear lamina. Our study provides a molecular perspective to genome organization via the modeling approach which is useful for future research of LADs biophysical roles at genome organization.
Keywords: polymer modeling, molecular dynamics, lamina associated domains, chromatin organization
Advisor: Assist. Prof. Aykut Erbaş
Date: Monday, June 15, 2026
Time: 11:00
Zoom
This is an online seminar. To request event details please send a message to department.