SRP233367 PRJNA591917 GSE141068 Repression of damaged and intact rDNA by the SUMO pathway Ribosomal RNAs (rRNAs) are essential components of the ribosome and are among the most abundant macromolecules in the cell. To ensure high rRNA level, eukaryotic genomes contain dozens to hundreds of rDNA genes, however, only a fraction of the rRNA genes seems to be active, while others are transcriptionally silent. In Drosophila rDNA units damaged by insertions of retrotransposons are repressed by an unknown mechanism. Here, we established a new model to study regulation of rDNA expression using molecularly marked rDNA transgenes. Using this model, we show that insertion of any heterologous sequence into rDNA leads to transcriptional repression. We found that SUMO (Small Ubiquitin-like Modifier) is required for efficient repression of damaged rDNA units. Surprisingly, SUMO also controls expression of intact rDNA, demonstrating that a single pathway is responsible for both selective repression of damaged units and silencing of surplus rDNA. Overall design: Transposons profiling by high throughput sequencing GSE141068 pubmed 33164748