Nucleosomes are the DNA-histone complex, where the DNA strand is wound around the histone core. The histone core is an octamer containing two copies of H2A, H2B, H3, and H4 histone proteins.

The paradox

Nucleosomes, paradoxically, perform two opposite functions simultaneously. On the one hand, their main responsibility is to protect the delicate DNA strands from physical damage and help achieve a higher compaction ratio. While on the other hand, they must allow polymerase enzymes to access DNA bound to the histones for replication and transcription. The mechanism by which nucleosomes solve these two problems is via partial unfolding of the DNA from the nucleosomes or histone protein modifications.

Core structure

The histone core proteins share a common structurally conserved motif called the “histone fold” and have a mobile extended tail region. The histone fold is made up of alpha-helices and loops. During the histone dimerization, loops of two histone proteins align together, forming a histone dimer.

Each histone binds to the three consecutive minor grooves of DNA. The alpha-helix and the N-terminal tail of each histone protein play a crucial role in binding to the DNA. Hence, any chemical modifications to the histone tail can modify the chromatin assembly and function. Some of the most common histone modifications include acetylation, methylation, and phosphorylation.

Histone variants

Histone proteins have various isoforms or variants like H2A.1, H2A.2, H2A.X, H3.3, or CENP-A. These variants differ in their amino acid sequences and perform distinct functions. The nucleosomes with histone variants are significantly more mobile than ordinary nucleosomes. For example, incorporation of H2A.Z into the nucleosome is shown to activate the transcription.