What we do

Using the mathematical concept of knotoids, we were able to characterize the topology of protein structures without the necessity of imposing a closure of analysed protein chains. New simulation approaches permitted us to emulate the effect of torsional tension introduced during transcription into chromatin fibres, as well as the effects of torsional stress relaxation by DNA topoisomerases. Our modelling indicated that TAD-like self-interacting chromatin domains in chromosomes of S. pombe can simply arise as a result of torsional stress accumulated during diverging transcription.

Main publications 2017

  • Goundaroulis D et al. Studies of global and local entanglements of individual protein chains using the concept of knotoids. Sci Rep.2017; 7; 6309
  • Benedetti F et al. Transcription-induced supercoiling explains formation of self-interacting chromatin domains in S. pombe. Nucleic Acids Res. 2017; 45; 9850
  • Goundaroulis D et al. Topological models of open-knotted protein chains using the concepts of knotoids and bonded knotoids. Polymers 2017; 9; 444

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