ArticleNucleic acids research2015
Topological constraints strongly affect chromatin reconstitution in silico.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Loops are geometric catalysts for DNA integration.Nucleic acids research · 2024Article
- Bridging condensins mediate compaction of mitotic chromosomes.The Journal of cell biology · 2024Article
- Mechanistic modeling of chromatin folding to understand function.Nature methods · 2020Review
- Nucleosome positions alone can be used to predict domains in yeast chromosomes.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Crosstalk between chromatin structure, cohesin activity and transcription.Epigenetics & chromatin · 2019Article
- Physical principles of retroviral integration in the human genome.Nature communications · 2019Article
- Chromatin organization by an interplay of loop extrusion and compartmental segregation.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Epigenetic Transitions and Knotted Solitons in Stretched Chromatin.Scientific reports · 2017Article
- Identification of multiple roles for histone acetyltransferase 1 in replication-coupled chromatin assembly.Nucleic acids research · 2017Article
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4 authors.
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Abstract
The fundamental building block of chromatin, and of chromosomes, is the nucleosome, a composite material made up from DNA wrapped around a histone octamer. In this study we provide the first computer simulations of chromatin self-assembly, starting from DNA and histone proteins, and use these to understand the constraints which are imposed by the topology of DNA molecules on the creation of a polynucleosome chain. We take inspiration from the in vitro chromatin reconstitution protocols which are used in many experimental studies. Our simulations indicate that during self-assembly, nucleosomes can fall into a number of topological traps (or local folding defects), and this may eventually lead to the formation of disordered structures, characterised by nucleosome clustering. Remarkably though, by introducing the action of topological enzymes such as type I and II topoisomerase, most of these defects can be avoided and the result is an ordered 10-nm chromatin fibre. These findings provide new insight into the biophysics of chromatin formation, both in the context of reconstitution in vitro and in terms of the topological constraints which must be overcome during de novo nucleosome formation in vivo, e.g. following DNA replication or repair.
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