Transcription of fractionated calf thymus chromatin by RNA polymerase of calf thymus and Escherichia coli.

Calf thymus chromatin has been sheared and fractionated on sucrose gradients. Approximately 5-10% of the chromatin is resolved from the bulk of the imput chromatin as a slowly sedimenting fraction. The protein/DNA ratio of the slowly sedimenting fraction is not greatly different from the protein/DNA ratio of the more rapidly sedimenting chromatin fraction. Analysis of DNA of the chromatin fractions by CsC1 equilibrium density gradient centrifugation indicates that DNA of the slowly sedimenting fraction is depleted in the satellite DNA banding at 1.716 g/cm3. The template properties of the chromatin fractions have been examined with Escherichia coli RNA polymerase and form II and form III RNA polymerases of calf thymus. At rate-limiting concentrations, the slowly sedimenting fraction is twofold more active than the rapidly sedimenting fraction as a template for E. coli RNA polymerase. Homologous form II and form III RNA polymerases are respectively 30-fold and 16-fold more active with the slowly sedimenting fraction than the rapidly sedimenting fraction. The activity of form II RNA polymerase in transcribing the slowly sedimenting fraction exceeds its activity in transcribing an equal concentration of native DNA. Kinetic studies, in which RNA polymerase activity is assayed at various concentrations of chromatin, indicate that the greater activity of E. coli RNA polymerase with the slowly sedimenting fraction is due to an increased rate of transcription at saturating concentrations of template (Vmax), and is not due to a lower concentration required for half-maximal rate of transcription (Km). In contrast, the increased rates of transcription of the slowly sedimenting chromatin faction by the homologous polymerases are due to a decrease in concentration required for half-maximal rate of transcription rather than an increased rate of transscription at saturation concentrations of template. The relative degrease of satellite DNA in the slowly sedimenting fraction of chromatin and the enhanced template activity of the slowly sedimenting fraction suggest that this fraction is equivalent to nuclear euchromatin while the more rapidly sedimenting chromatin is equivalent to nuclear heterochromatin.