Beyond the mono-nucleosome

Abstract

Nucleosomes, the building block of chromatin, are responsible for regulating access to the DNA sequence. This control is critical for essential cellular processes, including transcription and DNA replication and repair. Studying chromatin can be challenging both in vitro and in vivo, leading many to use a mono-nucleosome system to answer fundamental questions relating to chromatin regulators and binding partners. However, the mono-nucleosome fails to capture essential features of the chromatin structure, such as higher-order chromatin folding, local nucleosome-nucleosome interactions, and linker DNA trajectory and flexibility. We briefly review significant discoveries enabled by the mono-nucleosome and emphasize the need to go beyond this model system in vitro. Di-, tri-, and tetra-nucleosome arrays can answer important questions about chromatin folding, function, and dynamics. These multi-nucleosome arrays have highlighted the effects of varying linker DNA lengths, binding partners, and histone post-translational modifications in a more chromatin-like environment. We identify various chromatin regulatory mechanisms yet to be explored with multi-nucleosome arrays. Combined with in-solution biophysical techniques, studies of minimal multi-nucleosome chromatin models are feasible.

Keywords: chromatin; chromatin remodeler; multi-nucleosome array; nucleosome.

Figure 1. Chromatin qualities visualized by minimal array systems.

(A) Mono-nucleosome systems show alterations in histone–histone contacts within the octamer and histone–DNA interfaces within a nucleosome. (B) Di-nucleosomes additionally show DNA trajectory between NCPs and effects on adjacent nucleosome upon modifications (white star) such as PTMs and variant incorpoaration. (C) Tri-nucleosomes have the added benefit of demonstrating nucleosome–nucleosome stacking and effects on non-sequential nucleosomes.

Figure 2. NCP1 of minimal nucleosome arrays compared to the mono-nucleosome each with linker histone H1.

(A) Solved structure of a 197 bp nucleosome in complex with linker histone H1.4 (PDB:7K5Y). (B) NCP1 of a 338 bp di-nucleosome bound to linker histone H1.X (PDB:6L9Z). (C) NCP1 of the 4×177 bp nucleosome array containing H1.4 (PDB:7PET). (D) The superposition of structures A–C, with respect to (H3-H4) ₂, highlights the DNA orientation difference at the entry and exit points of DNA.