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

Abstract

A transcriptionally active chromatin fraction of oligonucleosome size was 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 4 regions of the gradient were pooled and labeled, from the top to the bottom, A, B, C and D, respectively. Fraction A, which contained .ltoreq. 20% of the total DNA, was determined to have a mean size of a hexanucleosome. By hybridization with [3H]c[complementary]DNA transcribed from total cytoplasmic poly(A) mRNA, DNA from fraction A was shown to be 10- to 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. A chromatin fraction of oligonucleosome size enriched in transcribing genes and organized with reduced nucleosome spacing was isolated.