Crystal structure of the overlapping dinucleosome composed of hexasome and octasome

Abstract

Nucleosomes are dynamic entities that are repositioned along DNA by chromatin remodeling processes. A nucleosome repositioned by the switch-sucrose nonfermentable (SWI/SNF) remodeler collides with a neighbor and forms the intermediate "overlapping dinucleosome." Here, we report the crystal structure of the overlapping dinucleosome, in which two nucleosomes are associated, at 3.14-angstrom resolution. In the overlapping dinucleosome structure, the unusual "hexasome" nucleosome, composed of the histone hexamer lacking one H2A-H2B dimer from the conventional histone octamer, contacts the canonical "octasome" nucleosome, and they intimately associate. Consequently, about 250 base pairs of DNA are left-handedly wrapped in three turns, without a linker DNA segment between the hexasome and octasome moieties. The overlapping dinucleosome structure may provide important information to understand how nucleosome repositioning occurs during the chromatin remodeling process.

Structure of histone-based chromatin in Archaea

“…Notably, the interactions within the archaeal superhelix do not resemble any of the nucleosome-nucleosome stacking interactions reported so far (reviewed in (15), and refs. (16, 17)).…”

Direct Observation of H3–H4 Octasome by High‐Speed AFM

“…Here, it is demonstrated that ah istone H3-H4 octasome could be constructedw ithoutt he involvement of histoneH 2A-H2B under in vitro reconstitution conditions. [7] However,t he occurrenceo fs ub-nucleosomal and non-nucleosomals tructures like the hexasome, [8] and overlapping dinucleosome [9] formed by the dynamic environmenta re also known.Frequently occurring post-translational modification in H3 and H4 can affect histone-DNA interactions, which in turn destabilizet he nucleosome and facilitate histonee xchange. The octasome also displayed ao ne-step histone-dissociation pattern under heat treatment, distinct micrococcal nuclease and peplomycin accessibility,w hich suggests ad ifferent wrapping pattern to that in nucleosomes.…”

“…[1] The nucleosome comprises an octamero ff our core histone proteins (H3, H4, H2A, and H2B) and a1 45 to 147-base pair (bp) segment of DNA, [2][3][4] Histone H3 and H4 proteins act as the precursor in nucleosome reconstitution and orientatet he DNA sequencet of orm at etrasome, the intermediate stage in the nucleosome formation. [7] However,t he occurrenceo fs ub-nucleosomal and non-nucleosomals tructures like the hexasome, [8] and overlapping dinucleosome [9] formed by the dynamic environmenta re also known. [7] However,t he occurrenceo fs ub-nucleosomal and non-nucleosomals tructures like the hexasome, [8] and overlapping dinucleosome [9] formed by the dynamic environmenta re also known.…”

Single‐molecule nucleosome remodeling by INO80 and effects of histone tails

“…A). A possible conformation that can explain the observed reduced mobility is that of an overlapping dinucleosome . At intermediate concentrations, nucleosomes are packed completely and no additional side products are observed (e.g., 1.7 : 1 molar ratio in Fig.…”