The rare transcripts of interrupted rRNA genes in Drosophila melanogaster are processed or degraded during synthesis

About 50% of the ribosomal transcription units in females of the bobbed 8 mutant of Drosophila melanogaster contain an intervening sequence of 5 kb in the 28S region of the gene. We analysed the transcription of ribosomal genes in this mutant using electron microscopy and found that the majority of the active ribosomal transcription units in larval fat bodies and guts are not long enough to contain the 5-kb intervening sequence; only approximately 1% of active transcription units have a length consistent with the presence of the 5-kb intervening sequence. Transcription units of this length show an interrupted gradient of nascent RNA fibril lengths indicative of processing or degradation during transcription. The position of the discontinuity in RNA length coincides with the position of the intervening sequence. This observation suggests that even though RNA polymerase may infrequently transcribe an entire interrupted gene, the process does not result in a full-length RNA.