Right-Handed Nucleosome: Myth or Reality?

In their recent paper in Cell, Furuyama and Henikoff (2009) report that nucleosomes in centromeres may be right-handed, that is, they wrap DNA in a right-handed manner and induce positive supercoils. This raises intriguing new questions, such as how centromeric histone variants may be assembled into right-handed particles, and why chromatin would retain negative supercoiling in chromosome arms but positive supercoiling in centromeres. We wish to comment on these new findings in the context of topological insights that we have gained from recent in vitro experiments with centromeric nucleosomes and single chromatin fibers submitted to tor-sional constraints and from 3D modeling of chromatin dynamics. We will also discuss alternative compositions of centro-meric nucleosome particles and suggest potential mechanisms by which local positive supercoiling may be established. Henikoff and coworkers previously identified half-nucleosomes—containing only one copy each of H2A, H2B, and H4 his-tones and the CenH3 histone variant—in the centromeres of Drosophila interphase nuclei (Dalal et al., 2007). In their new work, Furuyama and Henikoff (2009) propose that these tetrameric particles, now called hemisomes (Lavelle and Prunell, 2007), wrap DNA in a right-handed manner compared to " canonical " nucleosomes that wrap DNA in a left-handed manner. To reach that conclusion, these authors analyzed centromeric particles obtained from the in vitro reconstitution of purified components of Drosophila cells and from direct assembly in budding yeast in vivo. Because the histone composition of these particles was not determined, the question remains as to whether they are truly composed of right-handed hemisomes (H2A/H2B-CenH3/H4), or whether they are composed of right-handed tetrasomes [(CenH3/H4) 2 ], hexasomes [H2A/H2B-(CenH3/H4) 2 ], or even nucleosomes [H2A/ H2B-(CenH3/H4) 2-H2A/H2B]. Based on topological assays of nucleosomes reconstituted on DNA minicircles, Prunell and colleagues provided the first in vitro evidence for the existence of right-handed (H3-H4) 2 tetrasomes (Hamiche et al., 1996; Alilat et al., 1999). We later showed that nucleosome arrays subjected to a large positive torsional stress transiently trap approximately one positive turn of DNA supercoiling per particle. We suggested that this may reflect the chiral transition of nucleosomes, resulting in the formation of metastable octameric particles built on the right-handed tetrasome (so-called rever-somes for reverse nucleosomes) (Bancaud et al., 2007). We were able to model the transition steps and to propose an atomic structure for the reversome (Figure S1 and Movie S1 available online). The absence of docking domains between the H2A/H2B dimers and the (H3-H4) 2 …