DNA Topology and Global Architecture of Point Centromeres

DNA is wrapped in a left-handed fashion around histone octasomes containing the centromeric histone H3 variant CENP-A. However, DNA topology studies have suggested that DNA is wrapped in a right-handed manner around the CENP-A nucleosome that occupies the yeast point centromere. Here, we determine the DNA linking number difference (ΔLk) stabilized by the yeast centromere and the contribution of the centromere determining elements (CDEI, CDEII, and CDEIII). We show that the intrinsic architecture of the yeast centromere stabilizes +0.6 units of ΔLk. This topology depends on the integrity of CDEII and CDEIII, but it is independent of cbf1 binding to CDEI and of the variable length of CDEII. These findings suggest that the interaction of the CBF3 complex with CDEIII and a distal CDEII segment configures a right-handed DNA loop that excludes CDEI. This loop is then occupied by a CENP-A histone complex, which does not have to be inherently right-handed. [Display omitted] •Point centromeres increase the ΔLk of DNA by +0.6 units in yeast minichromosomes•This ΔLk change is constrained by the topology of CDEs within the point centromere•Centromere DNA topology is independent of CDEII length and of cbf1 binding to CDEI•Constraining of ΔLk +0.6 is established by the integrity of CDEII and CDEIII Díaz-Ingelmo et al. show that the point centromere of budding yeast constrains a positive DNA supercoil, which requires the centromere DNA elements CDEII and CDEIII, but not CDEI. This positive supercoil suffices to accommodate a sub-octameric histone complex, which does not have to be inherently right-handed.