Transcriptome partitioning for mRNA translation in hypoxia

Protein synthesis belongs to the most energy consuming processes in the cell. Lowering oxygen tension below normal (hypoxia) causes a rapid inhibition of global mRNA translation due to the decreased availability of energy. Interestingly, subsets of mRNAs pursue active translation under such circumstances. In human fibrosarcoma cells (HT1080) exposed to prolonged hypoxia (36 h, 1% oxygen) we observed that transcripts are either increasingly or decreasingly associated with ribosomes localized at the endoplasmic reticulum (ER). In a global setting it turned out that only 31% of transcripts showing elevated total-RNA levels were also increasingly present at the ER in hypoxia. These genes, regulated by its expression as well as its ER-localization, belong to the gene ontology’s “hypoxia response”, “glycolysis” and “HIF-1 transcription factor network” supporting the view of active mRNA translation at the ER during hypoxia. Interestingly, a large group of RNAs was found to be unchanged at the expression level, but translocate to the ER in hypoxia. Among these are transcripts encoding translation factors and >180 ncRNAs. In summary, we provide evidence that protein synthesis is favoured at the ER and, thus, partitioning of the transcriptome between cytoplasmic and ER associated ribosomes mediates adaptation of gene expression in hypoxia. Human fibrosarcoma HT1080 cells were cultured for 36 h under control/atmospheric (21% O2, 5% CO2, 37 °C) or hypoxic (1% O2, 5% CO2, 37°C) conditions. Total RNA (representing expression level) and ER (endoplasmatic reticulum)-RNA (representing transcript localization at ER) was isolated for both conditions. Pooled RNA samples from 5 independent biological experiments were used for microarray analysis.