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

Joana Segura, Ricky S. Joshi, Ofelia Díaz-Ingelmo, Antonio Valdés, Silvia Dyson, Belén Martínez-García and Joaquim Roca ()
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Joana Segura: Spanish National Research Council (CSIC)
Ricky S. Joshi: Spanish National Research Council (CSIC)
Ofelia Díaz-Ingelmo: Spanish National Research Council (CSIC)
Antonio Valdés: Spanish National Research Council (CSIC)
Silvia Dyson: Spanish National Research Council (CSIC)
Belén Martínez-García: Spanish National Research Council (CSIC)
Joaquim Roca: Spanish National Research Council (CSIC)

Nature Communications, 2018, vol. 9, issue 1, 1-9

Abstract: Abstract The 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.

Date: 2018
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DOI: 10.1038/s41467-018-06547-w

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