Nuclease Digestion of RNA in Chromatin

This chapter describes the methods for the nuclease digestion of RNA in chromatin. The RNA/DNA ratio is highest in chromatin isolated from tissues active in RNA synthesis. The presence of RNA as ribonucleoprotein associated with regions of chromatin active in transcription is well known. The chapter describes a procedure for investigation of the chromatin-associated RNA by digestion with staphylococcal nuclease. The procedure includes the preparation of chromatin, nuclease digestion, and the isolation of a structure containing the protected RNA fragment. The distinct advantage by use of the nuclease is that all of the protected chromatin DNA and chromatin protein precipitates from the limit digest, and they can then be easily removed by low-speed centrifugation leaving the protected RNA–protein complex as the only macromolecular material in the supernate.