Transcriptomic comparison of Drosophila snRNP biogenesis mutants: implications for Spinal Muscular Atrophy

Abstract

Spinal Muscular Atrophy (SMA) is caused by deletion or mutation of the Survival Motor Neuron 1 gene (SMN1), but the mechanism whereby reduced levels of SMN protein lead to disease is unknown. SMN functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs) and potential splicing defects have been uncovered in various animal models of SMA. We used disruptions in Smn and two additional snRNP biogenesis genes, Phax and Ars2, to classify RNA processing differences as snRNP-dependent or Smn gene specific. Although more numerous, the processing changes in Ars2 mutants were mostly distinct from those identified in Phax and Smn animals. Phax and Smn null mutants exhibited comparable reductions in steady-state snRNA levels, and direct comparison of their transcriptomic profiles uncovered a shared set of alternative splicing changes. However, these RNA processing differences were largely absent in three different models of intermediate SMA. Instead, the three hypomorphic Smn point mutants displayed an activation of stress responsive transcripts that correlated with phenotypic severity. In summary, genome-wide analyses showed that mRNA expression and alternative splicing defects are not conserved between hypomorphic and complete loss-of-function Smn mutants. Because disease phenotypes are unlikely to result from global changes in RNA processing, additional hypotheses for the etiology of SMA should be considered.