Figure 5

AS-NMD within the NAPA gene. A. Histogram representing QPCR validation results for NAPA. Bars represent mean fold change in mRNA levels in response to either UPF1 knockdown (left panel, N = 8) or cycloheximide treatment (right panel, N = 8) ± SEM. p-value summary (Student's t test, one tail): * p < 0.05, ** p < 0.01, *** p < 0.001. QPCR primers were located upstream of the schematic shown in B, in a region expected to be unaffected by alternative splicing. B. Schematic of the AS-NMD event within 3' UTR of NAPA produced using the UCSC genome browser [114]. Boxes represent exons while lines with chevrons represent introns. The upper blue cartoon indicates the Refseq annotated 3' UTR structure, the thinning of the box indicating the end of the protein coding sequence. The underlying cartoons are Genbank mRNAs illustrating the AS isoforms predicted by our analysis, the red mRNA represents the NMD sensitive isoform - a retained intron is spliced to make the normal stop codon appear premature. The lower blue histogram represents conservation across 17 vertebrate species as calculated by [115]. C. Histogram representing QPCR validation results of the predicted AS-NMD. Bars represent mean fold change in of the detailed exon junction in response to either UPF1 knockdown (± SEM, N = 3). p-value summary (Student's t test, one tail): * p < 0.05, ** p < 0.01, *** p < 0.001.