3D polymer simulations of genome organisation and transcription across different chromosomes and cell types

We employ the diffusing transcription factors model for numerical simulation of chromatin topology conformations and transcriptional processes of human chromatin. Simulations of a short chromatin filament reveal different possible pathways to regulate transcription: it is shown that the transcriptional activity profile can be regulated and controlled by either acting on the chain structural properties, or on external factors, such as the number of transcription factors. Additionally, comparisons between GROseq experimental data and large scale numerical simulation of entire chromosomes from the human umbilical vein endothelial cell and the B-lmphocyte GM12878 show that the model provides reliable and statistically significant predictions for transcription across different cell-lines.& COPY; 2023 Elsevier B.V. All rights reserved.