Multiple Pol I initiation sequences in rDNA spacers of Drosophila melanogaster

Sequence analysis of the rDNA nontranscribed spacer (NTS) of D.melanogaster shows that it contains many regions that are perfectly homologous with the Pol I transcription initiation site. Each initiation site homology is contained within a 240 base pair repeated sequence which are organised in a tandem array terminating 140 bases pairs upstream from the transcription initiation site. We discuss the significance of these regions and the maintenance of multiple homologies against the observed high rate of spacer divergence between related Drosophila species. In addition there are two other regions of repetition in the NTS: a 90 base pair periodicity commencing 16 bases downstream from the 3' end of the 28S gene and a number of 340 base pair repeats. A similar complex of different periodicities has been described in Xenopus and may be a general feature of NTS sequences.