LUC7 proteins define two major classes of 5' splice sites in animals and plants

Abstract

Mutation or deletion of the U1 snRNP-associated factor LUC7L2 is associated with myeloid neoplasms, and knockout of LUC7L2 alters cellular metabolism. Here, we uncover that members of the LUC7 protein family differentially regulate two major classes of 5 splice sites (5SS) and broadly regulate mRNA splicing in both human cell lines and leukemias with LUC7L2 copy number variation. We describe distinctive 5SS features of exons impacted by the three human LUC7 paralogs: LUC7L2 and LUC7L enhance splicing of "right-handed" 5SS with stronger consensus matching on the intron side of the near-invariant /GU, while LUC7L3 enhances splicing of "left-handed" 5SS with stronger consensus matching upstream of the /GU. We validated our model of sequence-specific 5SS regulation both by mutating splice sites and swapping domains between human LUC7 proteins. Evolutionary analysis indicates that the LUC7L2/LUC7L3 subfamilies diverged before the divergence of animals and plants. Analysis of Arabidopsis thaliana mutants confirmed that plant LUC7 orthologs possess specificity similar to their human counterparts, indicating that 5SS regulation by LUC7 proteins is deeply conserved.