Comparison of mRNA populations between mutants with and without active HIF-1, and with and without functional nonsense-mediated decay.

Given the role of HIF-1 as a transcription factor, and the role of NMD in degrading mRNA, we hypothesized that changes in both of these pathways would impact mRNA levels. To identify specific mRNAs that might be regulated by HIF-1 and/or NMD, we performed whole animal RNA-sequencing of samples of nine different genotypes, which had active or inactive HIF-1, and functional or nonfunctional NMD.

Specifically, for HIF-1 activation samples were: wildtype [HIF-1 inactive], egl-9(-) [HIF-1 perpetually active] or egl-9(-) hif-1(-) [HIF-1 inactive]; and for NMD functionality samples were: wild type [functional NMD], smg-1(-) [NMD deficient] or smg-2(-) [NMD deficient]. Comparisons between genotypes can be used to identify HIF-1-dependent and NMD-dependent target mRNA.