Transcription-induced supercoiling explains formation of self-interacting chromatin domains in S. pombe
| Autor: | Dušan Račko, Fabrizio Benedetti, Yannis Burnier, Andrzej Stasiak, Julien Dorier |
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| Rok vydání: | 2017 |
| Předmět: |
0301 basic medicine
Rotation Transcription Genetic Biology Molecular Dynamics Simulation 03 medical and health sciences 0302 clinical medicine Gene Expression Regulation Fungal Schizosaccharomyces Genetics Molecular motor Scaffold/matrix attachment region DNA Fungal DNA clamp DNA Superhelical Circular bacterial chromosome Computational Biology DNA-Directed RNA Polymerases Chromatin ChIP-sequencing Biomechanical Phenomena 030104 developmental biology Eukaryotic chromosome fine structure Biophysics DNA supercoil Chromatin/chemistry Chromatin/metabolism Chromosomes Fungal/chemistry Chromosomes Fungal/metabolism DNA Topoisomerases/chemistry DNA Topoisomerases/genetics DNA Topoisomerases/metabolism DNA Fungal/chemistry DNA Fungal/genetics DNA Fungal/metabolism DNA Superhelical/chemistry DNA Superhelical/genetics DNA Superhelical/metabolism DNA-Directed RNA Polymerases/chemistry DNA-Directed RNA Polymerases/genetics DNA-Directed RNA Polymerases/metabolism Schizosaccharomyces/genetics Schizosaccharomyces/metabolism Chromosomes Fungal 030217 neurology & neurosurgery DNA Topoisomerases |
| Zdroj: | Nucleic Acids Research Nucleic Acids Research, vol. 45, no. 17, pp. 9850-9859 |
| ISSN: | 1362-4962 |
| Popis: | The question of how self-interacting chromatin domains in interphase chromosomes are structured and generated dominates current discussions on eukaryotic chromosomes. Numerical simulations using standard polymer models have been helpful in testing the validity of various models of chromosome organization. Experimental contact maps can be compared with simulated contact maps and thus verify how good is the model. With increasing resolution of experimental contact maps, it became apparent though that active processes need to be introduced into models to recapitulate the experimental data. Since transcribing RNA polymerases are very strong molecular motors that induce axial rotation of transcribed DNA, we present here models that include such rotational motors. We also include into our models swivels and sites for intersegmental passages that account for action of DNA topoisomerases releasing torsional stress. Using these elements in our models, we show that transcription-induced supercoiling generated in the regions with divergent-transcription and supercoiling relaxation occurring between these regions are sufficient to explain formation of self-interacting chromatin domains in chromosomes of fission yeast (S. pombe). |
| Databáze: | OpenAIRE |
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