Our focus

Using Brownian dynamics simulations, we modelled chromosome structure in interphase nuclei of mammalian cells testing the possibility that transcription-induced supercoiling is involved in formation of TADs. In 2018, we proposed a new model of chromatin loop extrusion, in which cohesin rings are passively pushed by formation of chromatin plectonemes resulting from transcription-induced supercoiling. We also showed by numerical simulations that chromatin loop extrusion is capable of directing DNA knots for unknotting by DNA topoisomerases.

Main publications 2020

  • Goundaroulis D et al.
    Chromatin is frequently unknotted at the megabase scale
    Biophysical Journal, doi: 10.1016/j.bpj.2019.11.002
  • Barbensi A et al.
    Grid diagram approach to investigate knot spaces and topoisomerase-mediated simplification of DNA topology
    Science Advances, doi: 10.1126/sciadv.aay1458
  • Goundaroulis D et al.
    Knotoids and protein structure
    Contemporary Mathematics

Main publications 2019