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DNA knots occur in intracellular chromatin
In vivo DNA molecules are narrowly folded within chromatin fibers and self-interacting chromatin domains. Therefore, intra-molecular DNA entanglements (knots) might occur via DNA strand passage activity of topoisomerase II. Here, we assessed the presence of such DNA knots in a variety of yeast circu...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5778459/ https://www.ncbi.nlm.nih.gov/pubmed/29149297 http://dx.doi.org/10.1093/nar/gkx1137 |
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author | Valdés, Antonio Segura, Joana Dyson, Sílvia Martínez-García, Belén Roca, Joaquim |
author_facet | Valdés, Antonio Segura, Joana Dyson, Sílvia Martínez-García, Belén Roca, Joaquim |
author_sort | Valdés, Antonio |
collection | PubMed |
description | In vivo DNA molecules are narrowly folded within chromatin fibers and self-interacting chromatin domains. Therefore, intra-molecular DNA entanglements (knots) might occur via DNA strand passage activity of topoisomerase II. Here, we assessed the presence of such DNA knots in a variety of yeast circular minichromosomes. We found that small steady state fractions of DNA knots are common in intracellular chromatin. These knots occur irrespective of DNA replication and cell proliferation, though their abundance is reduced during DNA transcription. We found also that in vivo DNA knotting probability does not scale proportionately with chromatin length: it reaches a value of ∼0.025 in domains of ∼20 nucleosomes but tends to level off in longer chromatin fibers. These figures suggest that, while high flexibility of nucleosomal fibers and clustering of nearby nucleosomes facilitate DNA knotting locally, some mechanism minimizes the scaling of DNA knot formation throughout intracellular chromatin. We postulate that regulation of topoisomerase II activity and the fractal architecture of chromatin might be crucial to prevent a potentially massive and harmful self-entanglement of DNA molecules in vivo. |
format | Online Article Text |
id | pubmed-5778459 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-57784592018-01-30 DNA knots occur in intracellular chromatin Valdés, Antonio Segura, Joana Dyson, Sílvia Martínez-García, Belén Roca, Joaquim Nucleic Acids Res Gene regulation, Chromatin and Epigenetics In vivo DNA molecules are narrowly folded within chromatin fibers and self-interacting chromatin domains. Therefore, intra-molecular DNA entanglements (knots) might occur via DNA strand passage activity of topoisomerase II. Here, we assessed the presence of such DNA knots in a variety of yeast circular minichromosomes. We found that small steady state fractions of DNA knots are common in intracellular chromatin. These knots occur irrespective of DNA replication and cell proliferation, though their abundance is reduced during DNA transcription. We found also that in vivo DNA knotting probability does not scale proportionately with chromatin length: it reaches a value of ∼0.025 in domains of ∼20 nucleosomes but tends to level off in longer chromatin fibers. These figures suggest that, while high flexibility of nucleosomal fibers and clustering of nearby nucleosomes facilitate DNA knotting locally, some mechanism minimizes the scaling of DNA knot formation throughout intracellular chromatin. We postulate that regulation of topoisomerase II activity and the fractal architecture of chromatin might be crucial to prevent a potentially massive and harmful self-entanglement of DNA molecules in vivo. Oxford University Press 2018-01-25 2017-11-15 /pmc/articles/PMC5778459/ /pubmed/29149297 http://dx.doi.org/10.1093/nar/gkx1137 Text en © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Gene regulation, Chromatin and Epigenetics Valdés, Antonio Segura, Joana Dyson, Sílvia Martínez-García, Belén Roca, Joaquim DNA knots occur in intracellular chromatin |
title | DNA knots occur in intracellular chromatin |
title_full | DNA knots occur in intracellular chromatin |
title_fullStr | DNA knots occur in intracellular chromatin |
title_full_unstemmed | DNA knots occur in intracellular chromatin |
title_short | DNA knots occur in intracellular chromatin |
title_sort | dna knots occur in intracellular chromatin |
topic | Gene regulation, Chromatin and Epigenetics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5778459/ https://www.ncbi.nlm.nih.gov/pubmed/29149297 http://dx.doi.org/10.1093/nar/gkx1137 |
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