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Intracellular nucleosomes constrain a DNA linking number difference of −1.26 that reconciles the Lk paradox

AuthorsSegura, Joana ; Joshi, Ricky S. ; Díaz-Ingelmo, Ofelia ; Valdés, Antonio ; Dyson, Sílvia ; Martínez-García, Belén ; Roca, Joaquim
Issue Date28-Sep-2018
PublisherNature Publishing Group
CitationNature Communications 9: 3989 (2018)
AbstractThe interplay between chromatin structure and DNA topology is a fundamental, yet elusive, regulator of genome activities. A paradigmatic case is the “linking number paradox” of nucleosomal DNA, which refers to the incongruence between the near two left-handed superhelical turns of DNA around the histone octamer and the DNA linking number difference (∆Lk) stabilized by individual nucleosomes, which has been experimentally estimated to be about −1.0. Here, we analyze the DNA topology of a library of mononucleosomes inserted into small circular minichromosomes to determine the average ∆Lk restrained by individual nucleosomes in vivo. Our results indicate that most nucleosomes stabilize about −1.26 units of ∆Lk. This value balances the twist (∆Tw  ≈ + 0.2) and writhe (∆Wr ≈ −1.5) deformations of nucleosomal DNA in terms of the equation ∆Lk = ∆Tw + ∆Wr. Our finding reconciles the existing discrepancy between theoretical and observed measurement of the ΔLk constrained by nucleosomes.
Publisher version (URL)http://dx.doi.org/10.1038/s41467-018-06547-w
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