Alteration of the nucleosomal DNA path in the crystal structure of a human nucleosome core particle

Abstract

Gene expression in eukaryotes depends upon positioning, mobility and packaging of nucleosomes; thus, we need the detailed information of the human nucleosome core particle (NCP) structure, which could clarify chromatin properties. Here, we report the 2.5 Å crystal structure of a human NCP. The overall structure is similar to those of other NCPs reported previously. However, the DNA path of human NCP is remarkably different from that taken within other NCPs with an identical DNA sequence. A comparison of the structural parameters between human and Xenopus laevis DNA reveals that the DNA path of human NCP consecutively shifts by 1 bp in the regions of superhelix axis location −5.0 to −2.0 and 5.0 to 7.0. This alteration of the human DNA path is caused predominantly by tight DNA–DNA contacts within the crystal. It is also likely that the conformational change in the human H2B tail induces the local alteration of the DNA path. In human NCP, the region with the altered DNA path lacks Mn2+ ions and the B-factors of the DNA phosphate groups are substantially high. Therefore, in contrast to the histone octamer, the nucleosomal DNA is sufficiently flexible and mobile and can undergo drastic conformational changes, depending upon the environment.

Structural basis of instability of the nucleosome containing a testis-specific histone variant, human H3T

“…The structures of the H3T and H3.1 nucleosomes were initially solved to 2.7 and 2.5 Å resolutions, respectively, by the molecular replacement method, using the MOLREP program (29) and the human nucleosome structure (Protein Data Bank ID code 2CV5) as a guide (13). For H3T nucleosome, the Ramachandran plot of the final structure showed 93.3% of the residues in the most favorable regions and no residues in the disallowed region.…”

Electrostatic interactions in biological DNA-related systems

“…331 In NCP crystals of other species, Mn 2+ might hardly be involved in histone-histone contacts, such as NCP crystals of frog 5 or human. 357 The NCP crystals for all these 3 species however contain 5-10 Mn 2+ per NCP that are associated with the DNA, see the green spheres in Fig. 16d.…”

Structure of human nucleosome containing the testis-specific histone variant TSH2B

“…After the sample was dialyzed against 10 mM Tris-HCl buffer (pH 7.5) containing 1 mM EDTA, 2 M KCl, 1 mM DTT, and the KCl concentration was gradually decreased to 0.25 M during dialysis. The 146 base-pair DNA was derived from a palindromic human -satellite DNA fragment (Luger et al, 1997), which was previously used for structural studies of human nucleosomes containing canonical histone H2B (Tsunaka et al, 2005;Tachiwana et al, 2010Tachiwana et al, , 2011. To remove the nonspecific histone-DNA aggregates, the samples were incubated at 328 K for 2 h. The TSH2B nucleosome was further purified by nondenaturing polyacrylamide gel electrophoresis using a Prep Cell apparatus (Bio-Rad) (Figs.…”