Preferential DNase I sensitivity of insert-free ribosomal RNA repeats of Drosophila melanogaster

The five predominant types of rDNA repeats in D. melanogaster were analyzed with respect to their DNase I sensitivity. Only the insert-free repeats showed a generalized DNase I sensitivity pattern whereas the major type I, both minor type I and type II repeats were not as extensively degraded by the nuclease. For XX and XY embryonic nuclei, where there is rapid cell division, the majority of the In^- repeats were DNase I sensitive. This indicated that these In^- repeats have the potential to be transcribed during this developmental stage. When compared to the In^- repeats, the chromatin configuration of the In⁺ repeats is indicative of a higher order of chromatin folding. The paucity of In⁺ primary gene transcripts observed in vivo could result from In⁺ repeats being packaged into a more condensed form of chromatin.