Isolation, fractionation and reconstitution of a nuclear extract capable of transcribing ribosomal DNA

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Abstract
A procedure for preparing a nuclear extract that efficiently transcribes rat rDNA in vitro has been developed. This procedure, which is based on the protocol described by Dignam et al. (Nucl Acids Res 11:1475, 1983), allows the preparation of extract from large or small amounts of material and requires neither ultracentrifugation nor column chromatography. These extracts were found to be more efficient than other transcription systems. Extract prepared as described routinely synthesize 1–2 transcripts per linear template, and could synthesize upto 6 transcripts per linear template at an elongation rate of 2.1 nucleotides per second. 0.3 M NaCl extracts of nuclei contained RNA polymerase I, but did not transcribe rat rDNA in vitro, whereas extract prepared with 0.42 M NaCl did. The 0.42 M NaCl extract of nuclei was fractionated by chromatography on DEAE-Sephadex and heparin-Sepharose. Two activities were identified that were required for accurate in vitro transcription by endogenous RNA polymerase I. One of these activities was required for accurate initiation, and the second inhibited non-specific transcription. The fraction required for accurate initiation by the endogenous RNA polymerase I is that factor which directs species specific transcription, as it also directed the transcription of rat rDNA by nuclear extracts of HeLa cells. Combining that same chromatographic fraction of the 0.42 M NaCl extract with the 0.3 M NaCl extract resulted in specific transcription. These results suggest that a fraction of the RNA polymerase I molecules may exist in a complex with some, or all, of the factors required for transcription.