The histone shuffle: histone chaperones in an energetic dance

Abstract

Our genetic information is tightly packaged into a rather ingenious nucleoprotein complex called chromatin in a manner that enables it to be rapidly accessed during genomic processes. Formation of the nucleosome, which is the fundamental unit of chromatin, occurs via a stepwise process that is reversed to enable the disassembly of nucleosomes. Histone chaperone proteins have prominent roles in facilitating these processes as well as in replacing old histones with new canonical histones or histone variants during the process of histone exchange. Recent structural, biophysical and biochemical studies have begun to shed light on the molecular mechanisms whereby histone chaperones promote chromatin assembly, disassembly and histone exchange to facilitate DNA replication, repair and transcription.

Figure 1. Stepwise assembly and disassembly of nucleosomes mediated by histone chaperones

DNA is wrapped around two H3–H4 dimers and two H2A–H2B dimers to form the nucleosome core particle. The stepwise assembly, along with the different possible intermediates including the tetrasome and hexasome, are represented here. Histone chaperones mediate each step of the assembly/disassembly process. Histone H2A is depicted in yellow, H2B in red, H3 in blue, and H4 in green.

Figure 2. Structural classification of histone chaperones

(a) β-sandwich structures aligned. The Asf1 N-terminal domain (PDBID: 1ROC) and Yaf9 YEATS domain (PDBID: 3FK3) are represented as ribbons colored blue to red from the N- to the C-terminus of each domain. Structures of Asf1 bound to H3–H4 (PDBID: 2HUE) and ASF1A bound to the B domain of HIRA (PDBID: 2I32) are shown with the histone chaperone colored in magenta, H3 in blue, H4 in green, and the B-domain peptide colored and highlighted in orange. Note that the binding sites for H3–H4 and HIRA are located on the opposite sides of ASF1A. (b) α/β-earmuff histone chaperones. Aligned structures of NAP1 (PDBID: 2AYU) and Vps75 (PDBID: 3DM7) are colored according to secondary structure elements (helix in cyan, beta-strands in magenta and turns in gold). The second view is rotated by 90° about the horizontal axis of the page. The corresponding electrostatic surface diagrams (blue, red and white colors correspond to the electro-positive, electro-negative and neutral charge) highlight the histone binding surfaces with grey ovals indicating the likely positions of H2A–H2B or H3–H4. (c) β-propeller chaperones. The structures of nucleoplasmin (Np, PDBID: 1K5J) and the RbAp46–H4 complex (PDBID: 3CFS) along with electrostatic surface potential diagram (colored as in panel (b)) are illustrated. Nucleoplasmin is a pentamer (subunits colored differently), whereas RbAp46 (magenta) is composed of 7WD repeats. The alpha helical H4 peptide is shown in green. (d) β-barrel and half barrel chaperones. Domains from Pob3 (a FACT subunit) (PDBID: 2GCL) and Rtt106 (PDBID: 3GYP) are represented. The blue oval indicates a likely binding site for H3–H4. The structure of the N terminus of Spt16 (a FACT subunit) (PDBID: 3CB5) has a unique fold. (e) Irregular – Chz1. The structure of H2AZ–H2B bound to Chz1 (PDBID: 2JSS) shows the exposed surface of the H2AZ–H2B dimer in the context of the nucleosome. The view on the right is rotated by 180° about the vertical axis of the page to show the surface of H2AZ–H2B that would be in contact with H3–H4 in the nucleosome. Chz1 is shown in cyan, H2AZ in yellow and H2B in red.

Figure 3. Model for the histone chaperone-mediated hand-off during chromatin assembly

Histone chaperones relay histones to their nucleosomal destination. Some histone chaperones, such as nucleoplasmin, act as a cytosolic histone storage platform. Question marks indicate uncertainty about the exact components of specific protein complexes, or the steps that are likely or suggested from the literature but have not definitively been proven to occur. The red rings around the newly synthesized DNA represent PCNA. The model shown is compiled from experimental evidence derived from yeast and / or higher eukaryotic systems, depending on the available information. In particular, the role of H3 K56Ac in chromatin assembly that is depicted is implied from the findings of studies only in the yeast system to date.

Figure 4. Histone chaperone mediated “nucleosome assembly funnel”

Analogous to the protein-folding funnel, the stages of nucleosome assembly are represented here with a funnel. DNA and H2A–H2B and H3–H4 dimers, the more dynamic entities in a higher free energy state, exist at the top of the funnel. Histone chaperones facilitate the assembly of histones and DNA into more stable intermediates (such as the tetrasome) and finally into the fully assembled nucleosome core particle, which is depicted as thermodynamically the most stable state and hence at the bottom of the funnel. Histone chaperones ensure an ordered nucleosomal assembly pathway and prevent histones from getting trapped in local minima during the process. The red star denotes H3 K56Ac. The purple oval and orange arc represent single subunit chaperones, the cyan objects represent chaperones that have multimeric or multi-subunit interactions with histones, and the grey pentamer represents the pentameric or decameric histone chaperones.

Box 1, Figure I. Chemical nature of histones

(a) The primary structure of histones H2A (yellow), H2B (red), H3 (blue), and H4 (green). Colored boxes enclose the regions of the histones that are folded in the context of the nucleosome. (b) The three dimensional structures of the H2A–H2B dimer (yellow and red) and H3–H4 dimer (blue and green) are illustrated in two views. The α-helices in H3 and H4 that are referred to in this review are labeled. (c) The distribution of basic and acidic regions of the histones is illustrated in surface renderings of the same views shown in (b). The basic regions are colored in blue, the red regions indicate acidic patches and the white regions indicate neutral and hydrophobic sites.