Effects of plasmid length and positioned nucleosomes on chromatin assembly in vitro

Histone H5 induces extensive nucleosome alignment in vitro, with a 210 +/- 5 base pair (bp) average unit repeat, on some of the constructs derived from plasmid pBR327. Plasmid pBR327 itself aligns nucleosomes poorly, even though it possesses a chromatin organizing region which nucleates the alignment reaction [Jeong et al. (1991) J. Mol. Biol. 222, 1131-1147]. Examination of various regions of pBR327 chromatin by Southern hybridization revealed no substantial regional differences, suggesting an essentially all-or-none alignment mechanism. Twenty-four pBR327 deletion constructs, with the chromatin organizing region intact, were analyzed for nucleosome alignment in vitro, in addition to the six previously described. Although nucleosome alignment on plasmids of size greater than 5 kb was not affected by small length changes, circular plasmids with total lengths between 2400 and 3600 bp generally permitted alignment only when their lengths were close to integer multiples of 210 +/- 3 bp. The measured repeat lengths for the large plasmids and the smaller ones that aligned nucleosomes were all 210 bp, within experimental precision. The failure of two approximately 3.2-kb plasmids to align nucleosomes, even though their lengths were close to 15 x 210 bp, could be attributed to the effects of four strongly positioned nucleosomes that form on pBR327 sequences. Evidence is provided that nucleosome arrays can be quasicrystalline and are capable of transmitting information over a distance of more than 2 kb.