Amus and Bin3 methylases functionally replace mammalian MePCE for capping and the stabilization of U6 and 7SK snRNAs.

U6 and 7SK snRNAs have a 5' cap, believed to be essential for their stability and maintained by mammalian MePCE or Bin3 enzymes. Although both proteins are required for 7SK stability, loss of neither destabilizes U6, casting doubts on the function of capping U6. Here, we show that the Amus protein, homologous to both proteins, is essential for U6 but not 7SK stability. The loss of U6 is rescued by the expression of an Amus-MePCE hybrid protein harboring the methyltransferase domain from MePCE, highlighting the conserved function of the two proteins as the U6 capping enzyme. Our investigations in human cells establish a dependence of both U6 and 7SK stability on MePCE, resolving a long-standing uncertainty. While uncovering a division of labor of Bin3/MePCE/Amus proteins, we found a "Bin3-Box" domain present only in enzymes associated with 7SK regulation. Targeted mutagenesis confirms its importance for Bin3 function, revealing a possible conserved element in 7SK but not U6 biology.