Figure 5.

In vivo DNase I digestion of the S.coelicolor genome results in fractionation according to transcriptional activity. (A) HCHO-crosslinked DNA–protein complexes from S.coelicolor collected at T1 (shown as an example with the triangle representing increasing amounts of DNase I) and T3 were digested in vivo with increasing amounts of DNase I, and the nucleoprotein complexes separated by 0.7% agarose gel electrophoresis. DNA was extracted from the soluble fraction, defined as that resolved by the gel and indicated by a box, and used as a probe in the subsequent slot-blot experiment. (B) DNA and RNA samples were labeled with DIG-dUTP and used as probes in slot-blot hybridizations with 12 ∼500 bp PCR products corresponding to the panel of genes used in the experiment. At each time point, the RNA and DNA probes detect the same targets, demonstrating that in vivo DNase I treatment had fractionated the genome based on transcriptional activity. Different targets were detected by samples from time points T1 and T3, consistent with the transcriptional programme changing as S.coelicolor enters stationary phase.