Hybrid Trypsinized Nucleosomal Arrays: Identification of Multiple Functional Roles of the H2A/H2B and H3/H4 N-Termini in Chromatin Fiber Compaction

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Abstract
A defined 12-mer nucleosomal array in solution exists in a complex equilibrium between an unfolded 29S conformation, a 40S folding intermediate, an extensively folded 55S conformation, and soluble oligomeric states formed from cooperative intermolecular association of individual 12-mer arrays. Proteolytic removal of all of the core histone N-terminal tail domains previously has been shown to abolish both salt-dependent nucleosomal array folding and oligomerization. To elucidate the individual contributions of the H2A/H2B and H3/H4 tail domains to nucleosomal array condensation, “hybrid” trypsinized nucleosomal arrays have been assembled from tandemly repeated 5S rDNA and either trypsinized H3/H4 tetramers and intact H2A/H2B dimers or trypsinized H2A/H2B dimers and intact H3/H4 tetramers. Neither of the hybrid trypsinized arrays formed either the 40S or the 55S folded conformations in 2 mM MgCl2. In ≥4 mM MgCl2, however, both fully trypsinized arrays and each hybrid trypsinized array formed the 40S folding intermediate, but not the 55S conformation. In contrast to folding, each hybrid trypsinized nucleosomal array oligomerized completely in MgCl2. These studies have identified three mechanistically distinct functions performed by the core histone N-termini during salt-dependent condensation of nucleosomal arrays. The complexity of tail domain function in chromatin is discussed in the context of a competitive interaction model in which the core histone N-termini provide direct mechanistic links between the structure and function of the chromatin fiber.