NF-Y associates with H3-H4 tetramers and octamers by multiple mechanisms

NF-Y is a CCAAT-binding trimer with two histonic subunits, NP-YB and NF-YC, resembling H2A-H2B. We previously showed that the short conserved domains of NF-Y efficiently bind to the major histocompatibility complex class II E a Y box in DNA nucleosomized with purified chicken histones. Using wild-typ e NF-Y and recombinant histones, we find that NF-Y associates with H3-H4 ea rly during nucleosome assembly, under conditions in which binding to naked DNA is not observed. In such assays, the NF-YB-NF-YC dimer forms complexes with H3-H4, for whose formation the CCAAT box is not required. We investiga ted whether they represent octamer-like structures, using DNase I, micrococ cal nuclease, and exonuclease III, and found a highly positioned nucleosome on Ea, whose boundaries were mapped; addition of NF-YB-NF-YC does not lead to the formation of octameric structures, but changes in the digestion pat terns are observed. NF-YA can bind to such preformed DNA complexes in a CCA AT-dependent way. In the absence of DNA, NF-YB-NF-YC subunits bind to H3-H4 , but not to H2A-H2B, through the NF-YB histone fold. These results indicat e that (i) the NF-Y histone fold dimer can efficiently associate DNA during nucleosome formation; (ii) it has an intrinsic affinity for H3-H4 but does not form octamers; and (iii) the interactions between NF-YA, NF-YB-NF-YC, and H3-H4 or nucleosomes are not mutually exclusive. Thus, NF-Y can interve ne at different steps during nucleosome formation, and this scenario might be paradigmatic for other histone fold proteins invovled in gene regulation .