Under prolonged hypoxic conditions cells adapt to the lowered available energy by inhibition of global mRNA translation. Interestingly, a subset of mRNAs can still be effectively translated under such circumstances. At present, the mechanism behind the selection of mRNAs for ongoing translation is not clear. We are currently investigating whether active protein synthesis occurs at sites other than at cytoplasmic or "free" polysomes. The isolation of an endoplasmic reticulum (ER) fraction from hypoxic HT1080 cells (human fibrosarcoma cell line, 0.5% oxygen for 36 h) compared to cells grown at control conditions (21% oxygen for 36 h) and subsequent micro-array analysis indicate that mRNAs of genes that belong to the gene ontology "hypoxia response" or "glycolysis" are indeed increasingly present in the ER fraction. Interestingly, only 190 out of 615 total up-regulated genes were found to be elevated at the ER. In contrast, a group of 296 non-hypoxia inducible genes was found to be enriched at the ER during prolonged hypoxia, suggesting that mRNA localization might dictate the selection of mRNAs for active protein synthesis under conditions of global suppression. In addition, we identified trans-acting factors by mass spectrometry, including RNA-binding proteins HSPA5, HSPA8, Annexin A2 and ribosomal proteins RPL3, RPS3, RPS4X that might be involved in active, ER associated, translation during hypoxia. Our data suggest that during hypoxia, protein synthesis is regulated, at least in part, by localized mRNA translation. We hypothesize that this mechanism is crucial for a cell type specific hypoxia response.