Ribosome biogenesis demands lots of energy, and rDNA transcription falls during glucose starvation to keep cells from dying. Histone methylation, a modification associated with silencing, has been reported at rDNA. But whether this was the silencing mechanism during glucose starvation—and if so, which factors might be responsible—was unknown.
To find rDNA silencers, the authors purified proteins from nucleoli that bind to histone H3 deacetylated at Lys9—the target substrate for the silencing modification previously reported at rDNA. They identified a known nucleolar peptide and named it nucleomethylin (NML). Transfection with NML increased the number of methylated histones at rDNA and decreased rDNA transcription. Knockdown of NML had the opposite effect.
The histone deacetylase SIRT1 coimmunoprecipitated with NML, and disabling SIRT1's deacetylase activity prevented NML from silencing rDNA. Despite some structural features suggesting that NML might be the methylator, it turned out that that role was played by SUV39H1, a third coprecipitant and known methyltransferase. NML was required for binding, but its other potential functions are unclear.
The authors then showed that calorie restriction increased the binding of the entire complex to rDNA and reduced pre-rRNA transcript production. The authors thus named the complex eNoSC, or energy-dependent nucleolar silencing complex. “We found that without eNoSC, cells cannot adapt to glucose starvation, and die more quickly,” Yanagisawa says. SIRT1 is likely the energy-sensing component, since it is known to be regulated by the NAD+/NADH ratio—a readout of cells' metabolic activity. The authors also suggest that the multiple functions of the complex may explain how silencing spreads along repeated rRNA genes: with NML bound to a deacetylated, dimethylated lysine, SUV39H1 and SIRT1 can modify adjacent lysines, which in turn become binding sites for other eNoSC complexes.