RNA modifications and Prp24 coordinate Lsm2-8 binding dynamics during S. cerevisiae U6 snRNP assembly

In eukaryotes, the process of intron removal from nuclear pre-mRNA is performed by the spliceosome, a dynamic molecular machine composed of small nuclear ribonucleoproteins (snRNPs; U1, U2, U4, U5, and U6) and dozens of other protein splicing factors. The U6 snRNP contains the U6 small nuclear RNA (snRNA) and the proteins Prp24 and Lsm2-8 heteroheptamer. A key feature of the snRNP is a modified U6 snRNA 3' end, which in Saccharomyces cerevisiae (yeast) contains a 3' phosphate. U6 plays an essential role in splicing, and the U6 snRNP must be completely disassembled for splicing to occur. Once splicing is finished, the snRNP must then be reassembled to participate in a subsequent splicing reaction. While splicing efficiency depends on rapid U6 snRNP assembly, this process has not yet been kinetically characterized. Here, we use colocalization single-molecule spectroscopy to dissect the kinetic pathways of yeast U6 snRNA association with the Lsm2-8 complex and their dependence on the Prp24 protein and post-transcriptional snRNA modification. In the absence of 3'-end processing, Lsm2-8 association with the RNA is highly dependent on Prp24. However, processed RNAs can rapidly recruit Lsm2-8 in the absence of Prp24. Post-transcriptional processing facilitates Lsm2-8 association, whereas the presence of Prp24 promotes both recruitment and retention of the complex. This suggests that efficient U6 snRNP assembly could depend on kinetic selection of Lsm2-8 binding to 3'-end modified or Prp24-bound U6 snRNAs in order to discriminate against association with other RNAs.