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

Author

Listed:
  • 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))

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.

Suggested Citation

  • Joana Segura & Ricky S. Joshi & Ofelia Díaz-Ingelmo & Antonio Valdés & Silvia Dyson & Belén Martínez-García & Joaquim Roca, 2018. "Intracellular nucleosomes constrain a DNA linking number difference of −1.26 that reconciles the Lk paradox," Nature Communications, Nature, vol. 9(1), pages 1-9, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-06547-w
    DOI: 10.1038/s41467-018-06547-w
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