RNA exosome-dependent transcriptional adaptation masks gene essentiality

CRISPR-based gene knockouts assume that phenotypes directly reflect gene function. Here, we show that RNA exosome-dependent buffering frequently masks knockout phenotypes. Using combinatorial CRISPR screens, we identify RNA exosome-dependent genes whose loss-of-function phenotypes are revealed only when RNA surveillance is impaired. We find that the RNA exosome is required for both the initiation and maintenance of transcriptional adaptation, in which disruption of a trigger gene induces the compensatory upregulation of a buffering gene. Mechanistically, intronic Alu elements provide sequence homology between trigger-buffer gene pairs and regulate the formation of circular RNAs that suppress compensatory transcription. Disrupting splicing, deleting intronic Alu elements, or targeting the resulting circular RNAs reduces circular RNA abundance and enables transcriptional adaptation. Our results uncover a sequence-encoded mechanism in which intronic Alu-derived circular RNAs gate RNA exosome-dependent transcriptional adaptation to mask gene phenotypes, and suggest that gene essentiality is actively regulated by RNA exosome-mediated buffering, with broad implications for the interpretation of context-specific gene dependencies.