Characterization of rat liver oligonucleosomes enriched in transcriptionally active genes: evidence for altered base composition and a shortened nucleosome repeat

A transcriptionally active chromatin fraction of oligonucleosome size has been separated and isolated by a modified micrococcal nuclease fractionation procedure. After mild enzymatic digestion, rat liver nuclei were lysed, and the chromatin was separated by centrifugation on linear sucrose gradients. Fractions from four regions of the gradient were pooled and labeled, from the top to the bottom, A, B, C, and D, respectively. Fraction A, which contained 20% or less of the total DNA, was determined to have a mean size of a hexanucleosome. By hybridization with [3H]cDNA transcribed from total cytoplasmic poly(A) mRNA, DNA from fraction A was shown to be 10-15-fold enriched in transcribing genes when compared with total DNA. This fraction also has a somewhat higher concentration of AT base sequences. Significant differences were observed in nucleosome phasing. Fraction A has the shortest repeat length, fractions B and C are intermediate, and fraction D, which is depleted in transcribing DNA sequences, has the longest. Thus, we have isolated a chromatin fraction of oligonucleosome size enriched in transcribing genes and organized with reduced nucleosome spacing.