Intra- and inter-nucleosomal protein-DNA interactions of the core histone tail domains in a model system.
The core histone tail domains are key regulators of eukaryotic chromatin structure and function and alterations in the tail-directed folding of chromatin fibers and higher order structures are the probable outcome of much of the post-translational modifications occurring in these domains. The functions of the tail domains are likely to involve complex intra- and inter-nucleosomal histone-DNA interactions, yet little is known about either the structures or interactions of these domains. Here we introduce a method for examining inter-nucleosome interactions of the tail domains in a model dinucleosome and determine the propensity of each of the four N-terminal tail domains to mediate such interactions in this system. Using a strong nucleosome "positioning" sequence, we reconstituted a nucleosome containing a single histone site specifically modified with a photoinducible cross-linker within the histone tail domain, and a second nucleosome containing a radiolabeled DNA template. These two nucleosomes were then ligated together and cross-linking induced by brief UV irradiation under various solution conditions. After cross-linking, the two templates were again separated so that cross-linking representing inter-nucleosomal histone-DNA interactions could be unambiguously distinguished from intra-nucleosomal cross-links. Our results show that the N-terminal tails of H2A and H2B, but not of H3 and H4, make internucleosomal histone-DNA interactions within the dinucleosome. The relative extent of intra- to inter-nucleosome interactions was not strongly dependent on ionic strength. Additionally, we find that binding of a linker histone to the dinucleosome increased the association of the H3 and H4 tails with the linker DNA region.
Zheng
Chunyang
C
Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA.
Hayes
Jeffrey J
JJ
D000818:Animals; D001665:Binding Sites; D004247:DNA / Q000378:metabolism*; D006657:Histones / Q000737:chemistry* / Q000378:metabolism*; D008956:Models, Chemical; D009707:Nucleosomes / Q000737:chemistry* / Q000378:metabolism; D009994:Osmolar Concentration; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D014981:Xenopus
D006657:Histones; D009707:Nucleosomes; D004247:DNA