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Free energy based high-resolution modeling of CTCF-mediated chromatin loops for human genome

Wayne Dawson, View ORCID ProfileDariusz Plewczynski
doi: https://doi.org/10.1101/105676
Wayne Dawson
1Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Banacha 2c, Warsaw 02–089, Poland,
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Dariusz Plewczynski
1Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Banacha 2c, Warsaw 02–089, Poland,
2Faculty of Pharmacy, Medical University of Warsaw, Banacha 1, 00-001 Warsaw, Poland
3Centre for Innovative Research, Medical University of Bialystok, Białystok, Poland
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  • ORCID record for Dariusz Plewczynski
  • For correspondence: w.dawson@cent.uw.edu.pl d.plewczynski@cent.uw.edu.pl
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Abstract

A thermodynamic method for computing the stability and dynamics of chromatin loops is proposed. The CTCF-mediated interactions as observed in ChIA-PET experiments for human B-lymphoblastoid cells are evaluated in terms of a polymer model for chain folding physical properties and the experimentally observed frequency of contacts within the chromatin regions. To estimate the optimal free energy and a Boltzmann distribution of suboptimal structures, the approach uses dynamic programming with methods to handle degeneracy and heuristics to compute parallel and antiparallel chain stems and pseudoknots. Moreover, multiple loops mediated by CTCF proteins connected together and forming multimeric islands are simulated using the same model. Based on the thermodynamic properties of those topological three-dimensional structures, we predict the correlation between the relative activity of chromatin loop and the Boltzmann probability, or the minimum free energy, depending also on its genomic length. Segments of chromatin where the structures show a more stable minimum free energy (for a given genomic distance) tend to be inactive, whereas structures that have lower stability in the minimum free energy (with the same genomic distance) tend to be active.

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Posted February 03, 2017.
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Free energy based high-resolution modeling of CTCF-mediated chromatin loops for human genome
Wayne Dawson, Dariusz Plewczynski
bioRxiv 105676; doi: https://doi.org/10.1101/105676
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Free energy based high-resolution modeling of CTCF-mediated chromatin loops for human genome
Wayne Dawson, Dariusz Plewczynski
bioRxiv 105676; doi: https://doi.org/10.1101/105676

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