Fractionation of chromatin in a two-phase aqueous polymer system

Characterisation of a chromatin fraction bearing pulse-labelled RNA. 1. Nascent RNA, RNA polymerase B and transcribed DNA sequence content

We have further characterised a fraction of polynucleosomal chromatin from mouse cells which is enriched in transcribing regions, after separation by multistep partition in a dextran /poly(ethylene glycol) two-phase mixture [Faber, A. J. (1972) Methods Cell Biol. 16, 447--457]. This fraction contains an average of 16% of the total DNA and 63% of the 3-min pulse-labelled RNA in chromatin which, by a number of criteria, represents nascent RNA transcripts. Of the total transcribing RNA polymerase B molecules in chromatin, 52% are found in this fraction by titration with radioactive alpha-amanitin. About 28% of the single-copy DNA sequences in this fraction hybridise to nuclear polyadenylated RNA, compared with only 1.5% of the single-copy sequences in the remaining (nontranscribing) chromatin fraction.

Characterisation of a chromatin fraction bearing pulse-labelled RNA. 2. Quantification of histones and high-mobility-group proteins

The histone variants and high-mobility-group (HMG) proteins of a transcribing fraction of chromatin, described in the preceding paper of this journal, have been analysed qualitatively and quantitatively by a combination of one-dimensional and two-dimensional gel electrophoresis. The stoichiometry of the four core histones (all variants included) in this fraction is equimolar and is not detectably different from that in the nontranscribing fraction or in total chromatin. The molar ratio of histone H1 to the core histones is markedly lower, by approximately 72%, than that in the nontranscribing fraction. A minor histone variant identified as M1 (an H2A variant) is detected only in the transcribing fraction, while variant H3.1 is found only in the non-transcribing fraction. Proteins A24, HMG1 and HMG2 are essentially absent from the transcribing fraction; HMG14 is found uniquely in this fraction, while HMG17 occurs at a relatively lower level.