Eukaryotic genome is organized into the nucleus through several compaction steps. Core histones form a "beads-on-a-string" structure of nucleosomes together with DNA. Linker histones are also found in eukaryotes, and contribute to establish thicker 30-40 nm chromatin fibers. Interestingly, however, the linker histones do not always play a role in the genome packaging in some eukaryotes.
To investigate an effect of the differences in genome organization, chromatin unfolding processes were comparatively analyzed using Schizosaccaromyces pombe, Saccharomyces cerevisiae, and chicken erythrocyte. S. pombe has a smaller genome size (1.4 x 107 bp), which is packed into the chromatin without linker histone, and a series of the nucleosomes align every 156 bp of DNA. S. cerevisiae also has a small genome (1.2 x 107 bp) with 165 bp of the nucleosome repeat length. In the chicken chromatin, 1.1 x 109 bp of genome DNA is organized by means of nucleosomes repeated in every ~210 bp together with linker histones. AFM imaging of salt-induced structural changes of the chromatins clarified effects of the nucleosome repeat length and the linker histone on the structure. 400-1000 mM NaCl facilitated beads with ~115 nm in diameter in S. pombe chromatin. A similar transition was also observed in S. cerevisiae chromatin. This process did not involve core histone dissociation from the chromatin, and the persistence length after the transition was ~26 nm for S. pombe and ~28 nm for S. cerevisiae, indicating a salt-induced unfolding to "beads-on-a-string" fibers. Reduced salt concentration recovered the original structure, suggesting that electrostatic interaction would regulate this discrete folding-unfolding process. On the other hand, the linker histone was extracted from chicken chromatin at 400 mM NaCl, and AFM observed the "beads-on-a-string" fibers around a nucleus. Unlike yeast chromatin, therefore, this unfolding was irreversible due to linker histone dissociation. These results indicate that the chromatin unfolding and refolding depend on the presence and absence of the linker histone, and the length of the linker DNA.
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