Ribosomal DNA (rDNA) is essential but inherently unstable due to its repetitive structure, requiring mechanisms like rDNA magnification to restore lost copies, particularly in proliferative germ cells. In Drosophila, this recovery occurs via unequal sister chromatid exchange (USCE). A new publication from the lab identifies the zinc-finger protein Indra as a key negative regulator of rDNA magnification. Indra suppresses RNA polymerase II (Pol II)-dependent transcription of rDNA, preventing unnecessary DNA double-strand breaks (DSBs). Under low rDNA copy number, Indra levels decrease, allowing Pol II activity, activation of the R2 retrotransposon, and initiation of DSBs to trigger magnification. These findings suggest that selective Pol II activation underpins a finely tuned mechanism to expand rDNA CN only when needed, balancing genome stability and copy number recovery.