Cryo–electron microscopy structure of the H3-H4 octasome: A nucleosome-like particle without histones H2A and H2B

Abstract

The canonical nucleosome, which represents the major packaging unit of eukaryotic chromatin, has an octameric core composed of two histone H2A-H2B and H3-H4 dimers with ∼147 base pairs (bp) of DNA wrapped around it. Non-nucleosomal particles with alternative histone stoichiometries and DNA wrapping configurations have been found, and they could profoundly influence genome architecture and function. Using cryo–electron microscopy, we solved the structure of the H3-H4 octasome, a nucleosome-like particle with a di-tetrameric core consisting exclusively of the H3 and H4 histones. The core is wrapped by ∼120 bp of DNA in 1.5 negative superhelical turns, forming two stacked disks that are connected by a H4-H4’ four-helix bundle. Three conformations corresponding to alternative interdisk angles were observed, indicating the flexibility of the H3-H4 octasome structure. In vivo crosslinking experiments detected histone–histone interactions consistent with the H3-H4 octasome model, suggesting that H3-H4 octasomes or related structural features exist in cells.

Structural insights into histone binding and nucleosome assembly by chromatin assembly factor-1

“…S10 and table S2). The left-handed ditetrasome structure is nearly identical to the recently reported H3-H4 octasome structure ( 53 ); hence, we will not discuss it further here. We then repeated the cryo-EM procedures using the full-length CAF-1 complex and obtained similar results (fig.…”

“…Using the 147-bp Widom 601 DNA, we observed two different forms of ditetrasomes—a left-handed one and a CAF-1–bound right-handed one—from our in vitro assembly with H3-H4, DNA, and CAF-1. Considering that the left-handed ditetrasome was also obtained from the assembly of H3-H4 and DNA without CAF-1 ( 53 ), it most likely resulted from excessive H3-H4 added in our sample preparation. Handedness aside, the first critical question is whether ditetrasomes do occur during nucleosome assembly.…”

Beyond the Usual Suspects: Examining the Role of Understudied Histone Variants in Breast Cancer

“…H4 D67H/N and R93T mutations are also found in cancer patients [ 148 ]. These residues form a hydrogen bond with H2B to stabilize the nucleosome structure [ 184 ], so altering these residues may result in nucleosome instability.…”

Structural Transition of the Nucleosome during Transcription Elongation

“…Recently, the structure of the H3-H4 octasome, consisting of two molecules of the H3-H4 tetramer, was reported [121,122]. The H3-H4 octasome wraps approximately 120 base pairs of DNA, forming a nucleosome-like structure, and lacks the acidic patch on its surface due to the absence of the H2A-H2B dimer.…”