Ultraconserved elements are associated with control of splicing regulators by alt splicing and nonsense mediated decay. Mus musculus

We blocked nonsense-mediated mRNA decay (NMD) pathway and used a custom alternative transcript sensitive Affymetrix microarray to seek alternatively spliced RNAs whose levels increased compared to controls. Keywords: Nonsense Mediated Decay (NMD) Overall design: We used two difference methods of NMD inhibition. In one method, we transfected N2A cells with Upf1 siRNA. In the second method, we treated N2A with emetine. Three individual total RNA samples from Upf1 siRNA transfected cells and control siRNA transfected cells, and two individual total RNA samples from each of emetine treated cells and control cells, were applied on custom Affymetrix microarrays with probes specific to different alternative splicing events, including splice junction probes. Perfect match probes only.