Nucleosome Structure and Function

When fully extended, one copy of the three billion base pair human genome reaches a length of over two meters. Yet, it must be packaged into the nucleus of a cell with an average diameter of less than 10 μm. Within this context, specific segments of the genome must be transcriptionally active or repressed in a coordinated fashion to allow a cell to react to its ever-changing environment. This is akin to arranging 30 miles of thread inside a basketball such that at moment’s notice key segments can be accessed. To establish such compaction while maintaining coordinated accessibility, organisms ranging from yeast to man organize their genomes in a polymeric complex called chromatin. The fundamental unit of the chromatin polymer is the nucleosome, which repeats every 160 to 240 bp across the genome.1 Each nucleosome contains a nucleosome core, composed of an octameric complex of the core histone proteins, which forms a spool to wrap 145 to 147 bp of DNA. The nucleosome core is connected to the adjacent nucleosome core through a segment of linker DNA, which often associates with the linker histone protein (H1 or H5). The nucleosome core with ∼165 bp of DNA together with the linker histone is called the chromatosome.2 The chromatosome and the additional linker DNA constitutes a nucleosome.2 Despite these technical definitions, the nucleosome core particle is often colloquially referred to as the nucleosome. The nucleosome serves three primary functions. First, it brings about the first level of genomic compaction, organizing ∼200 bp of DNA. Second, the nucleosome acts as a signaling hub for chromatin-templated processes by providing a scaffold for the binding of chromatin enzymes and displaying a combinatorial array of post-translational modifications (PTMs). This array of PTMs further regulates the recruitment of chromatin enzymes3 and tunes both nucleosome stability4 and the higher-order compaction of chromatin.5−7 Third, the nucleosome can self-assemble into higher-order chromatin structures, allowing for further compaction of the genome. The first level of higher-order compaction is the 30 nm chromatin fiber for which several models have been created based on experimental data using cryogenic-electron microscopy (cryo-EM) and X-ray crystallography.8 This review focuses on recent advances in our understanding of the structure and function of the nucleosome and is divided into four parts. First, we present a primer covering the fundamentals of the nucleosome core particle structure determined at atomic scale by X-ray crystallography in 1997.9 Next we discuss recent insights into the role of DNA sequence in the structure of nucleosomal DNA based on structure–function studies of nucleosome core particles containing derivatives of the Widom 601 nucleosome positioning sequence.10 We then introduce patterns of nucleosome recognition by chromatin factors using recent crystal structures and NMR and cryo-EM models of peptide and protein macromolecular chromatin factors bound to the nucleosome core particle. Finally, we will compare a recent cryo-EM model for the 30 nm chromatin fiber11 to two previous models based on crystallographic and cryo-EM data.12,13