The role of the nucleosome acidic patch in modulating higher order chromatin structure

Abstract

Higher order folding of chromatin fibre is mediated by interactions of the histone H4 N-terminal tail domains with neighbouring nucleosomes. Mechanistically, the H4 tails of one nucleosome bind to the acidic patch region on the surface of adjacent nucleosomes, causing fibre compaction. The functionality of the chromatin fibre can be modified by proteins that interact with the nucleosome. The co-structures of five different proteins with the nucleosome (LANA, IL-33, RCC1, Sir3 and HMGN2) recently have been examined by experimental and computational studies. Interestingly, each of these proteins displays steric, ionic and hydrogen bond complementarity with the acidic patch, and therefore will compete with each other for binding to the nucleosome. We first review the molecular details of each interface, focusing on the key non-covalent interactions that stabilize the protein-acidic patch interactions. We then propose a model in which binding of proteins to the nucleosome disrupts interaction of the H4 tail domains with the acidic patch, preventing the intrinsic chromatin folding pathway and leading to assembly of alternative higher order chromatin structures with unique biological functions.

Figure 1.

The nucleosome and its acidic patch. (a) Electrostatic potential view of the nucleosome surface. The electrostatic rendering was performed using APBS tools in PyMOL (http://www.poissonboltzmann.org/apbs/examples/visualization/apbs-electrostatics-in-pymol#TOC-Generating-the-PQR). A pqr file was generated from the 1KX5 histone octamer (no DNA), using pdb2pqr software. APBS was then run through PyMOL. The electrostatic potential displayed is between −25 (red) and +25 (blue) kT e^–1. (b) Close-up view of the acidic patch. Histone H2A is shown in yellow and H2B in red. The α1- and αC-helices of H2B, α2- and αC-helices of H2A and the eight residues that make up the acidic patch are labelled. PDB 1KX5.

Figure 2.

H4 tail domain–acidic patch interactions. (a) Close-up view of the H4 tail–acidic patch interaction observed in the crystal structure [1]. The H4 tail is shown in lime green. Histones are in grey, with acidic patch residues shaded pink. PDB 1A01. (b) Close-up view of the modelled H4 peptide–acidic patch interaction taken from [22]. The H4 peptide is shown in green. Histones are in grey, with acidic patch residues shaded pink. PDB provided courtesy of Dr G. Arya.

Figure 3.

Nucleosome-binding protein co-structures. (a) Close-up view of the LANA peptide–acidic patch interaction. The LANA peptide is shown in dark green. Histones are in grey, with acidic patch residues shaded pink. PDB 1ZLA. (b) RCC1–acidic patch interaction. RCC1 is shaded in cyan. Histones are in grey, with acidic patch residues shaded pink. PDB 3MVD. (c) Sir3–acidic patch interaction. Sir3 BAH domain is shaded in magenta. Histones are in grey, with acidic patch residues shaded pink. PDB 3TU4. (d) Modelled HMGN2–acidic patch interaction. HMGN2 is shown in black, with key residues labelled in red. Histones are in grey, with acidic patch residues shaded pink. PDB provided courtesy of Dr Y. Bai.

Figure 4.

Nucleosome-binding proteins display overlapping complementarity with the acidic patch. The regions of LANA (green), RCC1 (yellow), Sir3 (cyan) and HMGN2 (black) that interact with the acidic patch are overlaid together. Peptides are shown in backbone view in which the α-carbons are connected by straight tubes. The nucleosome is shown in surface mode. The acidic patch region is shaded red.

Figure 5.

A model for the mechanism of remodelling of chromatin higher order structure by nucleosome-binding proteins. K_GS is the equilibrium constant for the ground state H4 tail–acidic patch interaction. K₁ is the equilibrium constant for the interaction of nucleosome-binding protein 1 with the acidic patch. K₂ is the equilibrium constant for the interaction of nucleosome-binding protein 2 with the acidic patch. The specific chromatin structure induced by a particular nucleosome-binding protein can range from completely decondensed to hypercondensed. See text for details.