Intra- and inter-nucleosomal protein-DNA interactions of the core histone tail domains in a model dinucleosome and oligonucleosome arrays

The core histone tail domains are key regulators of eukaryotic chromatin structure and function. They are likely involved in complex intra- and inter-nucleosomal histone-DNA interactions, yet little is known about either the structures or interactions of these domains. In this thesis I introduce a method for examining inter-nucleosomal interactions of the tail domains in dinucleosomes and oligonucleosome arrays. A nucleosome containing a single site specifically modified with a photo inducible cross-linker in the histone tail domain was reconstituted and ligated with another nucleosome or a 12-mer oligonucleosome array. After ligation, cross-linking was induced by brief UV irradiation under various solution conditions. The two DNA templates were then separated so that cross-linking representing inter-nucleosomal histone-DNA interactions could be unambiguously distinguished from intra-nucleosomal cross-links by examining radio-labeled DNA in the dinucleosome or radio-labeled histories in the oligonucleosome array. In the dinucleosome system, I found evidence for internucleosomal histone-DNA interactions made by the N-terminal tails of H2A and H2B, but not by H3 and H4. The relative extent of intra- to inter-nucleosomal interactions was not strongly dependent on ionic strength. Additionally, I found that binding of a linker histone to the dinucleosome increased the association of the H3 and H4 tails with the linker DNA region. Using the oligonucleosome array, I find the H3 tail makes both intra- and inter-nucleosomal histone-DNA interactions along the tail region with the latter observed only in maximally folded states of the array.