Catch me if you can: how the histone chaperone FACT capitalizes on nucleosome breathing

Abstract

Nucleosomes confer a barrier to processes that require access to the eukaryotic genome such as transcription, DNA replication and repair. A variety of ATP-dependent nucleosome remodeling machines and ATP-independent histone chaperones facilitate nucleosome dynamics by depositing or evicting histones and unwrapping the DNA. It is clear that remodeling machines can use the energy from ATP to actively destabilize, translocate or disassemble nucleosomes. But how do ATP-independent histone chaperones, which "merely" bind histones, contribute to this process? Using our recent structural analysis of the conserved and essential eukaryotic histone chaperone FACT in complex with histones H2A-H2B as an example, we suggest that FACT capitalizes on transiently exposed surfaces of the nucleosome. By binding these surfaces, FACT stabilizes thermodynamically unfavorable intermediates of the intrinsically dynamic nucleosome particle. This makes the nucleosome permissive to DNA and RNA polymerases, providing temporary access, passage, and read-out.

Keywords: chromatin; histone chaperone; nucleosome (reorganization); structure / crystallography; thermodynamics / kinetic of nucleosome (un)folding; transcription through chromatin.

Figure 1. Crystal structure of the Spt16M- H2A-H2B complex and overview of three surfaces of the histone octamer recognizes by Spt16M. (A) The 2.35 Å crystal structure of the trimeric complex between Ch. thermophilum Spt16M and the globular cores (g) of histone H2A and histone H2B reveals the interaction is mediated by Spt16’s U-turn motif (red) and the α1 helix of H2B (dark blue). Spt16M PHL-1 (light orange), Spt16M PHL-2 (dark orange); H2A (light green), N-termini (N), C-termini (C). (B) Close-up view of the histone octamer surfaces recognized by Spt16M (sphere representation of the amino acid side chains): The H2B N-terminal tail (light pink) extrudes between the gyres of DNA and might serve as an initial, solvent-accessible point of attachment for Spt16 to the nucleosome. The αN helix of H3 (blue) and the α1 helix of H2B (dark pink) are DNA-covered in the structure of the canonical nucleosome but become accessible upon DNA breathing.

Figure 2. The FACT chaperone domain may compete with DNA for binding to histones H2A-H2B. The structure of the Spt16M–H2A-H2B complex (Spt16M in light green, U-turn in blue, H2A in yellow, H2B in red) was superimposed onto the structure of the nucleosome core particle (histones in gray, DNA in orange, dyad marked with ϕ) by aligning histones H2A-H2B. Intrinsic dynamics of the nucleosome, DNA “breathing” (A) and nucleosome “gaping” (B), are indicated by arrows. The path of the DNA putatively displaced during breathing is sketched in dotted lines (A).

Figure 3. Alignment of selected Spt16M PHL-1 residues of different species. Secondary structure elements are marked above the sequence. Fungal Pob3 does not contain a HMG box, but the SSRP1 protein of higher eukaryotes does; the order of sequences is the same as for the PHL-1 sequence alignment.