Public Library of Science
pcbi.1011142.g005.tif (2.91 MB)

Here, we present results from our block copolymer model, which simulates the chromosomes of the Drosophila genome.

Download (2.91 MB)
posted on 2023-05-25, 17:45 authored by Gaurav Bajpai, Samuel Safran

We represent the chromosomes as chains with two types of beads, each with different attraction strengths corresponding to euchromatic (relatively weak attraction) and heterochromatic (relatively strong attraction) regions. (a) The distribution of euchromatic and heterochromatic regions along each chromosome is based on experimental data from [93]. (b) A simulation snapshot of the chains mixing, where the euchromatic beads are transparent, allowing only the heterochromatic beads to be clearly visible. We observe that heterochromatic regions of different chains mix due to their large self-attraction. (c) The contact map calculated from the block copolymer model shows more than four regions along the diagonal (as in Fig 1) due to the separate intra-chain mixing of the euchromatic and heterochromatic blocks corresponding to the distribution shown in (a). To understand the role of the binding of chromatin to the lamina in chromosome mixing, we modeled the bonding of certain chromosome segments (LADs) to the nuclear lamina using our block copolymer model for Drosophila. (d) The distribution of LAD and non-LAD domains along each chromosome is based on experimental data from [94]. (e) A simulation snapshot for chromosome volume fraction ϕ = 0.1 is presented, showing that in the presence of lamin (green), the four chromosomes Chr2 (red), Chr3 (blue), Chr4 (orange), and ChrX (yellow) of the Drosophila chromosomes separate into distinct regions and do not mix. (f) The contact maps for case (e). Comparing this to the contact map for the same block copolymer model in the absence of binding to the lamina in Fig 5c, we observe a smaller probability of contact in the off-diagonal regions. From these results, it is clear that binding to the nuclear lamina decreases the mixing of chromosomes.