Gene expression under short-term moderate hypoxia and in the HIF-1 negative regulator mutants in Caenorhabditis elegans

Hypoxia inducible transcription factor HIF is the master regulator of hypoxia response in metazoans. The stability and activity of HIF are tightly regulated. In the model organism C. elegans, the homolog of HIF is HIF-1. The stability and activity of HIF-1 are negatively regulated by vhl-1, egl-9, rhy-1 and swan-1 when HIF-1 is stabilized by vhl-1 mutation. Here, we are using Affymetrix microarray to measure the immediate gene expression changes under short-term hypoxia treatment (2 hours of 0.5% oxygen treatment). We also want to understand whether the HIF-1 acvitity negative regulators function in common pathway(s) to regulate HIF-1 activity or not. We find that gene expression patterns in these HIF-1 activity negative regulator mutants are extraordinarily similar, which supports the model that they function in common pathway(s) to regulate HIF-1 activity. Randomized complete block design was followed for the microarray experiments, with three biological replicates treated as three blocks. Each block included eight treatments: N2 wild type, N2 wild type with hypoxia treatment, hif-1(ia04) loss-of-function mutants, hif-1(ia04) loss-of-function mutants with hypoxia treatment, vhl-1(ok161) loss-of-function mutants, rhy-1(ok1402) loss-of-function mutants, egl-9(sa307) loss-of-function mutants, and swan-1(ok267);vhl-1(ok161) loss-of-function double mutants.