A highly basic histone H4 domain bound to the sharply bent region of nucleosomal DNA

Abstract

A nucleosomal core particle is composed of two each of histones H2A, H2B, H3 and H4 located inside the particle with ∼147 base pairs (bp) of DNA wrapped around the octamer in about 1.8 turns of a left-handed superhelix^1,2. The path of the superhelix is not smooth; the DNA is sharply bent, or kinked, at positions symmetrically disposed at a distance of about one and four double-helical turns in both directions from the nucleosomal dyad axis (designated as sites ±1 and ±4 respectively³). This non-uniform bending is considered archetypal to other DNA-protein complexes, but its mechanism is not clear (reviewed in ref. 4). DNA-histone chemical cross-linking within the core particle has revealed strong binding of each of the two histone H4 molecules to DNA at a distance of 1.5 helical turns either side of the nucleosomal dyad axis (sites ±1.5)^5,6. In each of these sites, a single flexible domain of H4 was previously shown to contact three points⁷, at about nucleotides 55 and 65 on one strand and nucleotide 88 on the complementary strand, numbering from the 5′ terminus of each 147-base strand; these three locations are closely juxtaposed across the highly compressed¹ minor and major grooves (Fig. 1). Here we report that the amino-acid residue of histone H4 cross-linked at the 1.5 site is histidine-18, embedded in a highly basic cluster Lys-Arg-His-Arg-Lys-Val-Leu-Arg which is probably involved in the sharp bending of the DNA double helix at the ±1 sites.