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
- Dabrowski-Tumanski P et al.
KnotProt 2.0: A database of proteins with knots and other entangled structures
Nucleic Acids Res, https://doi.org/10.1093/nar/gky1140 - Racko D et al.
Are TADs supercoiled?
Nucleic Acids Res, doi: 10.1093/nar/gky1091 - Schvartzman J B et al.
Closing the DNA replication cycle: from simple circular molecules to supercoiled and knotted DNA catenanes
Nucleic Acids Res, https://doi.org/10.1093/nar/gkz586
