The Structure of Chromatin

Abstract

Chromatin is the physical representative of the epigenome. Histones are the main protein component of chromatin and form octamer cores, around which genomic DNA is wrapped. These nucleosomes are the regularly repeating units of chromatin, but they can vary from one genomic region to the other by (i) different post-translational modifications of amino acid residues of the histone proteins and (ii) the introduction of histone variants. These genomic site-specific modifications are reversible and an important component of the epigenomic memory affecting transcription factor binding and differential gene expression in every cell type. Moreover, the spatial organization of chromatin not only allows dense packaging of otherwise “long” genomic DNA into a small nucleus, but is also an important level of distinction of open chromatin (euchromatin) and closed chromatin (heterochromatin). Chromatin architecture is formed in a hierarchical manner and engages dynamic chromatin loops. The formation of these loops is mediated by architectural proteins, such as CTCF and cohesin, and other regulatory components, such as transcription factors, PcG proteins and heterochromatin. This gives rise to structural landmarks, such as TADs and chromosome territories.

In this chapter, we will introduce the different levels of chromatin structure and their functional impact. We will discuss histone proteins, their post-translational modifications and their variants. Moreover, we will present the different regulatory layers of chromatin ranging from single nucleosomes, looping of genomic regions as well as large-scale folding of whole chromosomes into territories within the nucleus.