Location of endogenous RNA polymerase B in a sub-fraction of rat liver chromatin

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.

Separation of transcriptively active and inactive chromatin. Agarose gel chromatography

Sheared chromatin fractionated by currently accepted methods of agarose gel exclusion chromatography, undergoes a limited and non-specific aggregation resulting from the high ionic strength and divalent cation concentration of the column elution buffer. Such aggregation causes the artifactual appearance of radioactively labeled, newly synthesized RNA within the column exclusion volume, erroneously suggesting an enrichment for actively transcribed chromatin. Claims for the efficacy of agarose gel exclusion as a method for separating template-active and -inactive chromatin are based largely on assays for active chromatin which rely on localization of specific molecular complexes of chromatin and nascent RNA. Under the conditions employed, the present studies invalidate this assay and thus cast considerable doubt on the agarose gel exclusion method itself.