Ribosome biogenesis is an essential yet highly energy-demanding process. Both up- and down-regulation of ribosome biogenesis displays risks of cancer transformation, underlining the necessity for proper maintenance of ribosome metabolism. Proper coordination of its hundreds of factors requires monitoring mechanisms to assess the rate and quality of ribosome synthesis. An increasing body of evidence shows that ribosomal proteins possess regulatory functions outside the ribosome. Those extra-ribosomal functions have been linked in many occasions to the regulation of proliferative and stress pathways in response to perturbation of ribosome biogenesis. As such, they may act both as sensors and regulators of ribosome homeostasis.
We discovered that Drosophila Ribosomal Protein L12 (RpL12/uL11) may possess such an extra-ribosomal function. Indeed, we demonstrated that RpL12 can be trimethylated on lysine 3, and that this modification is specifically recognized by the chromodomain of the epigenetic cofactor Corto. As a member of the Enhancer of Trithorax and Polycomb family of cofactors, Corto is involved both in up and down regulation of target genes, through its interaction with Trithorax and Polycomb complexes. Further analysis showed that RpL12 and Corto bind the same loci on polytene chromosomes and regulate the same genes, mainly genes involved in ribosome biogenesis (Coléno-Costes et al., 2012, PLoS Genet 8, e1003006).
To determine the biological meaning of this interaction, we have created an RpL12 variant whose lysine 3 is mutated to an alanine (RpL12K3A), preventing its interaction with Corto. To confirm whether it retains the ability to participate in translation, we analyzed its distribution in polysomal fractions. We found that RpL12K3A was associated to actively translating ribosomes, showing that RpL12 methylation is not required for translation. RpL12K3A expression rescues the cell lethality induced by RNAi-mediated depletion of RpL12 in wing imaginal discs but not in adult wings, suggesting that it retains but a part of endogenous RpL12 functions. To test whether RpL12 methylation underlies a role in regulation of transcription, we overexpressed RpL12, RpL12K3A or the Corto chromodomain (CortoCD) in wing imaginal discs and sequenced their transcriptome. We found that ribosome biogenesis genes were repressed by RpL12 and CortoCD, yet insensitive to RpL12K3A overexpression, showing that they are specifically targeted by methylated RpL12. Altogether, these data suggest a role for RpL12 methylation in transcriptional regulation of ribosome biogenesis, possibly involving the epigenetic complexes associated with Corto.