A GFP splicing reporter in a coilin mutant background reveals links between alternative splicing, siRNAs and coilin function in Arabidopsis thaliana

Coilin is a scaffold protein essential for the structure of Cajal bodies, which are nucleolar-associated, nonmembranous organelles that coordinate the assembly of nuclear ribonucleoproteins (RNPs) including spliceosomal snRNPs. To learn more about coilin functions and pathways in plants, we conducted a genetic suppressor screen using a coilin (coi1) mutant in Arabidopsis thaliana and performed an immunoprecipitation-mass spectrometry analysis on coilin protein. The coi1 mutations modify alternative splicing of a GFP reporter gene, resulting in a ‘hyper-GFP’ phenotype in young coi1 seedlings relative to the intermediate wild-type level. As shown here, this hyper-GFP phenotype is extinguished in older coi1 seedlings by posttranscriptional gene silencing triggered by siRNAs derived from aberrant splice variants of GFP pre-mRNA. In the coi1 suppressor screen, we identified suppressor mutations in WRAP53, a putative coilin-interacting protein; SMU2, a predicted splicing factor; and ZC3HC1, an incompletely characterized zinc finger protein. These suppressor mutations return the hyper-GFP fluorescence of young coi1 seedlings to the intermediate wild-type level. Additionally, zc3hc1 coi1 mutants display more extensive GFP silencing and elevated levels of GFP siRNAs, suggesting the involvement of wild-type ZC3HC1 in siRNA biogenesis or stability. The immunoprecipitation-mass spectrometry analysis reinforced coilin’s roles in pre-mRNA splicing, nucleolar chromatin structure, and rRNA processing. Coilin’s participation in these processes, at least some of which incorporate small RNAs, supports the hypothesis that coilin acts as a chaperone for small noncoding RNAs. Our study demonstrates the usefulness of the GFP splicing reporter for investigating alternative splicing, ribosome biogenesis, and siRNA-mediated silencing in the context of coilin function.