DNA topology in chromatin is defined by nucleosome spacing

Abstract

In eukaryotic chromatin, DNA makes about 1.7 left superhelical turns around an octamer of core histones implying that formation of nucleosomes would alter the overall topology of DNA by a comparable difference of the DNA linking number (dLk) per nucleosome. However, earlier experiments have documented a significantly (about 50%) lower absolute value |dLk| than expected from the nucleosome geometry. Recently, using computer modeling, we have predicted two families of energetically stable conformations of the arrays with precisely positioned nucleosomes, one with an integer number of DNA turns in the linker DNA {L = 10n} and the other with extra five base pairs in the linker {L = 10n + 5}, to be topologically different. Here, using arrays of precisely positioned clone 601 nucleosomes, topological electrophoretic assays, and electron microscopy we experimentally tested these predictions. First, for small 12-mer nucleosome circular arrays we observed that dLk per nucleosome changes from -1.4 to -0.9 for the linkers {L = 10n} and {L = 10n + 5}, respectively. Second, for larger hybrid arrays containing a mixture of positioned and non positioned nucleosomes we found that changing the DNA linker length within the positioned arrays was sufficient to significantly alter the overall DNA topology fully consistent with our prediction. The observed topological polymorphism of the circular nucleosome arrays provides a simple explanation for the DNA topology in native chromatin with variable DNA linker length. Furthermore, our results may reflect a more general tendency of chromosomal domains containing active or repressed genes to acquire different nucleosome spacing to retain topologically distinct higher-order structures.