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

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