EIF4A3 associated splicing and nonsense mediated decay defined by a systems analysis with novel small molecule inhibitors. Homo sapiens

Here we map the associationof eIF4A3 with transcript expression, NMD and alternative splicing using a set of selectivenovel small molecule allosteric helicase inhibitors whose synthesis and chemical properties we haverecently described. We show through analysis of dose monotonic transcriptional responses to increasinginhibition that both full length and NMD prone transcripts link eIF4A3 to normal functioning ofcell division including chromosome segregation and cell cycle checkpoints, pointing to a conservedrole of splicing and transcript quality processing in cell cycle functions. Cell cycle analysis andmicroscopy of inhibitor treated cells demonstrates chromosome mis-segregation and spindle defects,associated with a G2/M arrest, validating this observation. Through analysis of conserved alternativesplicing patterns exhibiting monotonic responses, we find that eIF4A3 dependent alternativesplicing involves exons that are longer and introns that are shorter than transcripts not modulatedby eIF4A3. Moreover we observe conservation of over/under representation of RBP binding motifdensity over introns and exons implicated eIF4A3 modulated skipped exon and retained introns.The distribution of motif densities over 5’ and branch intron sites and 5’ exons is consistent withfunction of the exon-junction complex. Taken together we have defined a fraction of the transcriptomedependent on eIF4A3 functions and revealed a link between eIF4A3 and cell cycle regulation.The systems approach described here suggests additional avenues for therapeutic exploitation ofeIF4A3 functions in cancer and related diseases.2