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.
Highlights
The interplay between chromatin structure and DNA topology is a fundamental, yet elusive, regulator of genome activities
According to the general equation ΔLk = ΔTw + ΔWr14, it was expected that a nucleosome should stabilize a ΔLk value close to −2, considering that DNA describes near two left-handed superhelical turns (ΔWr ≈ −2) and assuming no significant changes in the double helical DNA twist (ΔTw ≈ 0)
The first hypothesis put forward to explain the linking number (Lk) paradox was that core DNA was notably overtwisted (ΔTw ≈ + 0.7)[9,23], which meant that the helical periodicity (h) of DNA was smaller in the nucleosome than in free DNA in the solution (h ≈ 10.5 bp/turn)[24]
Summary
The interplay between chromatin structure and DNA topology is a fundamental, yet elusive, regulator of genome activities. The nucleosomal STw was calculated from a derivation for a straight solenoidal helix to be −0.1934,35 These figures indicated that the overall ΔTw of the core DNA is about + 0.2, a value that was later corroborated by its direct measurement on the nucleosome structure at atomic resolution[1]. Another proposal involving the topology of DNA outside the core region was based on the study of single nucleosomes reconstituted on small DNA circles[39] and on the torsional resilience of nucleosomal fibers in vitro[40] These studies suggested that nucleosomes fluctuate between three conformations: one in which incoming and outgoing linker segments form a negative crossing, one with uncrossed linkers, and one in which the linker segments cross positively. Since these fluctuations depend on external constraints and forces, their plausible relevance to explain the Lk paradox is uncertain
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