Towards a mechanism for histone chaperones

Abstract

Histone chaperones can be broadly defined as histone-binding proteins that influence chromatin dynamics in an ATP-independent manner. Their existence reflects the importance of chromatin homeostasis and the unique and unusual biochemistry of the histone proteins. Histone supply and demand at chromatin is regulated by a network of structurally and functionally diverse histone chaperones. At the core of this network is a mechanistic variability that is only beginning to be appreciated. In this review, we highlight the challenges in determining histone chaperone mechanism and discuss possible mechanisms in the context of nucleosome thermodynamics. We discuss how histone chaperones prevent promiscuous histone interactions, and consider if this activity represents the full extent of histone chaperone function in governing chromatin dynamics. This article is part of a Special Issue entitled: Histone chaperones and Chromatin assembly.

Fig. 1

Structure of the major-type nucleosome (A), (H3-H4)₂ tetramer (B) and H2A-H2B dimer (C). Cartoons were made using PDB 1KX5. DNA is white, H3 is blue, H4 is green, H2A is yellow and H2B is red. Missing residues at the N-terminus of H2B are shown by a dotted line. In B and C, an N indicates the proteins N-terminus, and the representation on the right shows only the core histone fold. The four α-helix bundle that mediates H3-H4 tetramer formation and the second α-helix of H3 are indicated.

Fig. 2

Model of sequential nucleosome assembly. The (H3-H4)₂ tetramer (or two H3-H4 dimers) bind to DNA to form the tetrasome. This is followed by the addition of two H2A-H2B dimers. The intermediate, a tetrasome plus a single H2A-H2B dimer, is described as a hexasome. This process is reversible in salt gradient experiments as indicated. A similar sequence of events has been delineated for Nap1 nucleosome assembly in vitro.

Fig. 3

Prerequisites of nucleosome formation and contexts of histone chaperone activity. Histone chaperones may facilitate nucleosome formation by being involved in some or all of the processes I-VI indicated. Histones may be transferred between chaperones to complete all these processes in a regulated manner.

Fig. 4

Nature of histone-DNA (A) and histone-histone chaperone (B, C) interactions. A shows a vacuum electrostatic surface charge of (H3-H4)₂ with 72 base pairs of DNA from PDB 1KX5. Basic surfaces occur along the path of DNA. The opposite surface is involved in inter-histone interactions and is more hydrophobic. The four α-helix bundle of the (H3-H4)₂ tetramer is buried in A. B shows Asf1 (cartoon) preventing (H3-H4)₂ tetramer formation by interfering with four α-helix bundle formation (PDB 2HUE). C shows HJURP (cartoon) binding along α2 of cenH3, disrupting (cenH3-H4)₂ tetramer formation. HJURP also blocks DNA binding through a C-terminal β-sheet domain (PDB 3R45). In B and C, the H3-H4 dimers are shown as surface in an identical orientation to A.

Fig 5

Models of histone chaperone function illustrated as free-energy reaction diagrams. The change in free-energy is plotted along the reaction coordinate as the substrate (DNA and histones, middle) becomes the product (precipitate, left, or tetrasome, right). Analogous to a standard chemical reaction, substrates are postulated to go through a ‘transition state’ of highest free-energy (‡) before forming the product. The transition state represents a kinetic barrier for the reaction. A shows that in the absence of histone chaperones, non-specific interactions of histones (here H3-H4) with DNA are favored (left) over the tetrasome formation (right). Tetrasome formation requires histones and DNA to encounter in a non-random orientation. B shows that a Nap1-type chaperone binds histones with a free-energy similar to the final tetrasome product. In the chaperone-bound state, non-specific interaction with DNA (left) is costly, and thus the tetrasome formation (right) is favored. C shows an alternative mode of chaperone action. The chaperone binds to form a ‘transition state’ that is competent to directly deposit histones onto DNA. This state might represent a chaperone-histone-DNA trimeric complex, or a conformationally activated histone moiety that is primed to form nucleosomal DNA contacts (right).

Fig. 6

Important questions relevant to histone chaperone mechanism.