DNA-histone interactions in nucleosomes

Abstract

We have utilized micrococcal nuclease digestion and thermal denaturation studies to investigate the binding of DNA to the histone core of the nucleosome. We conclude that a total of approximately 168 base pairs (bp) of DNA can interact with the histone core under appropriate solution conditions, even in the absence of lysine-rich histones. The interactions in this total length of DNA can be divided into three classes: (a) approximately 22 bp at the ends is bound only at moderate ionic strength. It is easily displaced, and its removal yields the 146 bp core particle. (b) approximately 46 bp near the ends of the core DNA are quite weakly bound to the core, and are displaced at quite moderate temperatures. (c) The remaining central 100 bp are strongly bound, and interact with all of the sites on the histones which strongly protect DNA against DNAse I digestion. A theoretical analysis of the cleavage of nucleosomal DNA by DNAse I has been used to develop evidence that the pattern of protection offered by the histone core is very similar in nuclei to that in isolated core particles.

Dissection of the unusual structural and functional properties of the variant H2A.Bbd nucleosome

“…The digestion pattern of the conventional particle showed discrete kinetics intermediates at about 208, 160, 146 and 128 bp, whereas the kinetics intermediates of the H2A.Bbd particle were observed mainly at about 146, 128, 118 and 110 bp. The band at 160 bp, generated upon digestion of the conventional nucleosome, was attributed to the interaction of the N‐terminal histone tails with nucleosomal DNA (van Holde, 1980), the 146 bp band represents the core particle, whereas the 128 bp band reflects a subnucleosomal digestion (van Holde, 1980). The origin of the 208 bp band is unknown, but it might be associated with the presence of histones on DNA, as upon digestion of naked 601 DNA, no such band was observed (data not shown).…”

Molecular and Epigenetic Mechanisms of MLL in Human Leukemogenesis

“…The basic subunit of chromatin is the nucleosome and each nucleosome is composed of an H3/H4 tetramer and two H2A/H2B dimers [17,18]. Post-translational modifications of histone proteins are considered to be one of the epigenetic mechanisms that multicellular organisms use in order to guarantee tight spatial and temporal expression of key genes during development and differentiation [19,20,21].…”

The diverse functions of Dot1 and H3K79 methylation

“…Eukaryotic DNA is wrapped around a histone octamer (H3/H4 heterotetramer and two H2A/H2B dimers) to form the nucleosome, the fundamental building block of chromatin (Van Holde et al 1980;Luger et al 1997;Kornberg and Lorch 1999;Zhang and Dent 2005). Histone proteins are subject to reversible post-translational modifications, which play an important role in the establishment and maintenance of gene expression patterns within any given cell type of an organism.…”