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Survival motor neuron (SMN) functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs) that catalyze pre-mRNA splicing. Here, we used disruptions in Smnand two additional snRNP biogenesis genes, Phaxand Ars2, to classify RNA processing differences as snRNP-dependent or gene-specific in Drosophila. Phaxand Smnmutants exhibited comparable reductions in snRNAs, and comparison of their transcriptomes uncovered shared sets of RNA processing changes. In contrast, Ars2mutants displayed only small decreases in snRNA levels, and RNA processing changes in these mutants were generally distinct from those identified in Phaxand Smnanimals. Instead, RNA processing changes in Ars2mutants support the known interaction of Ars2 protein with the cap-binding complex, as splicing changes showed a clear bias toward the first intron. Bypassing disruptions in snRNP biogenesis, direct knockdown of spliceosomal proteins caused similar changes in the splicing of snRNP-dependent events. However, these snRNP-dependent events were largely unaltered in three Smnmutants expressing missense mutations that were originally identified in human spinal muscular atrophy (SMA) patients. Hence, findings here clarify the contributions of Phax, Smn, and Ars2 to snRNP biogenesis in Drosophila, and loss-of-function mutants for these proteins reveal differences that help disentangle cause and effect in SMA model flies.

Reduced expression of the survival motor neuron (SMN) protein causes spinal muscular atrophy (SMA) in humans and animal models of severe SMA display defects in pre-mRNA splicing late in the disease course. Using RNA deep-sequencing (RNA-seq) of wild-type and survival motor neuron (Smn) null mutant larvae, we identified a developmental arrest in the mutants that precedes the onset of widespread disruptions in splicing. Comparison of genome-wide mRNA expression profiles of Smn mutants revealed only small changes in levels of minor intron-containing mRNAs; in contrast, we observed a prominent increase in levels of stress-signaling transcripts that may be a conserved feature of SMA.