What we do
Using Brownian dynamics simulations, we model 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 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
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