Abstract
The DEK oncoprotein is a ubiquitous nuclear factor that has been consistently associated with tumor progression: its expression level differs between normal and cancer cells, raising the possibility of using DEK as a tumor marker. Moreover, DEK is a non-histone architectural chromatin factor that may influence nucleosomal accessibility and therefore gene activity. The interest of this work is to investigate, using super-resolution microscopy approaches, the correlation between the organization of the DEK oncoprotein and the local chromatin structure depending on the degree of cell malignancy.
Highlights
Chromatin folding and interactions play essential roles in fundamental processes such as regulation of gene expression and cellular specialization
We introduce a polymer model to study the organization of the diploid human genome: it is data-driven as all parameters can be derived from high-throughput chromosome conformation capture (Hi-C) data; it is a mechanistic model since the energy function is explicitly written out based on a few biologically motivated hypotheses
While Hi-C measurements often detect numerous interactions (108), our previous results showed that only 2-9% of Hi-C interactions, which we call specific interactions, are required to generate ensembles of 3D single-cell chromatin conformations that collectively exhibit the observed Hi-C contact patterns
Summary
Chromatin folding and interactions play essential roles in fundamental processes such as regulation of gene expression and cellular specialization. We describe the self-attracting polymer chain as a liquid droplet and study the transitions between different types of chromatin organization at the mesoscale as a function of the droplet surface tension, the LAD fraction of the chromatin, and their interaction strength with the nuclear lamina. 1542-Pos Data-Driven Polymer Model for Mechanistic Exploration of Diploid Genome Organization Bin Zhang.
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