Role of Udd protein and heterochromatin in transcriptional selection of individual rRNA genes in the Drosophila germline

Eukaryotic genomes contain hundreds of nearly identical rRNA genes, many of which are transcriptionally silent. However, the mechanisms of selective regulation of individual rDNA units remain poorly understood. In Drosophila melanogaster, rDNA repeats containing insertions of R1/R2 retrotransposons within the 28S rRNA sequence undergo inactivation. Here we found that rRNA genes with insertions are specifically enriched with H3K9me3 and HP1a repressive marks, but disruption of heterochromatin components only slightly affects their silencing. Intriguingly, the loss of Udd (Under-developed) protein interacting with Pol I transcription initiation complex, causes an upregulation of R2-inserted rDNA copies in germ cells by two orders of magnitude that is accompanied by the reduction of heterochromatin marks. Thus, for the first time we revealed a factor required for distinguishing between active and silent rDNA units to such a large extent. To clarify a relationship between the rDNA transcriptional status and heterochromatin establishment, we showed that inhibition of transcription by actinomycin D increases the level of H3K9me3 mark erasing the epigenetic differences between inserted and uninserted rRNA genes. Altogether, we suggest that Udd coupled with Pol I transcription initiation machinery defines activation or silencing of individual rDNA units, whereas their transcription level consequently dictates their chromatin state.