Termination of pre-mRNA splicing requires that the ATPase and RNA unwindase Prp43 acts on the catalytic snRNA U6

The termination of pre-mRNA splicing functions to discard suboptimal substrates, thereby enhancing fidelity, and to release excised introns in a manner coupled to spliceosome disassembly, thereby allowing recycling. The mechanism of termination, including the RNA target of the DEAH-box ATPase Prp43, remains ambiguous. We discovered a critical role for nucleotides at the 3-end of the catalytic U6 small nuclear RNA in splicing termination. Though conserved sequence at the 3-end is not required, 2 hydroxyls are, paralleling requirements for Prp43 biochemical activities. While the 3-end of U6 is not required for recruiting Prp43 to the spliceosome, the 3 end crosslinks directly to Prp43 in an RNA-dependent manner. Our data indicate a mechanism of splicing termination in which Prp43 translocates along U6 from the 3 end to disassemble the spliceosome and thereby release suboptimal substrates or excised introns. This mechanism reveals that the spliceosome becomes primed for termination at the same stage it becomes activated for catalysis, implying a requirement for stringent control of spliceosome activity within the cell.