siRNA silencing and hypoxia challenge indicate that the function of common carp (Cyprinus carpio) hif-1αb genes are tightly linked to hif-1αa and hif-3α genes.

Background: Fishes are susceptible to hypoxia stress, while the common carp is known for its high tolerance to hypoxia. The hypoxia-inducible factor (HIF) pathway directly regulates the cell's response to hypoxia. Still, it is currently unknown which members of the hif-α genes are present in common carp and their specific functions.

Results: In this study, we found that the hif-1α, hif-2α, and hif-3α genes of common carp all contained twice the number of copies of their orthologs in zebrafish. Common carp has four copies of the hif-1α gene, of which the two hif-1αa genes were expressed at low levels in the vast majority of tissues, while the two hif-1αb genes were expressed at high levels in multiple tissues. We silenced the two hif-1αb genes using chitosan nanoparticles (CSNPs) carrying siRNA and subjected two groups to hypoxic stress. Transcriptome sequencing results show that whether under normoxia or hypoxia, the number of differentially expressed genes (DEGs) caused by silencing the hif-1αb genes in the heart exceeds 1,000, far more than the number of DEGs in the gills or brain. GO enrichment and KEGG enrichment showed that DEGs in the heart were mainly related to immune function and myocardial contraction. DEGs in the gills and brain also enriched many immune-related terms, and some DEGs in the gills were related to iron metabolism and erythropoiesis. Among the paralogs, the two hif-1αa genes were most obviously up-regulated under normoxia, while the hif-3α genes were most obviously up-regulated under hypoxia. We did not find any downstream genes of the HIF pathway that were specifically regulated by the hif-1αb genes.

Conclusions: The main effect site of the common carp hif-1αb genes is the heart, and their main functions are to regulate immune response and myocardial contraction. Their functions are partially redundant with the hif-1αa genes and hif-3α genes. When their expressions are inhibited, the expression of hif-1αa genes or hif-3α genes would be up-regulated in specific contexts, thereby compensating for their loss of function. The downstream genes of the HIF pathway in common carp may be generally regulated by multiple hif-α genes.