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 2018

  • Racko D et al.
    Transcription-induced supercoiling as the driving force of chromatin loop extrusion during formation of TADs in interphase chromosomes.
    Nucleic Acids Res, doi: 10.1093/nar/gkx1123
  • Dorier J et al.
    Knoto-ID: a tool to study the entanglement of open protein chains using the concept of knotoids.
    Bioinformatics, doi: 10.1093/bioinformatics/bty365
  • Racko D et al.
    Are TADs supercoiled?
    Nucleic Acids Res, doi: 10.1093/nar/gky1091

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