Comparative Transcriptome Analysis of Organ-Specific Adaptive Responses to Hypoxia Provides Insights to Human Diseases.

The common carp is a hypoxia-tolerant fish, and the understanding of its ability to live in low-oxygen environments has been applied to human health issues such as cancer and neuron degeneration. Here, we investigated differential gene expression changes during hypoxia in five common carp organs including the brain, the gill, the head kidney, the liver, and the intestine. Based on RNA sequencing, gene expression changes under hypoxic conditions were detected in over 1800 genes in common carp. The analysis of these genes further revealed that all five organs had high expression-specific properties. According to the results of the GO and KEGG, the pathways involved in the adaptation to hypoxia provided information on responses specific to each organ in low oxygen, such as glucose metabolism and energy usage, cholesterol synthesis, cell cycle, circadian rhythm, and dopamine activation. DisGeNET analysis showed that some human diseases such as cancer, diabetes, epilepsy, metabolism diseases, and social ability disorders were related to hypoxia-regulated genes. Our results suggested that common carp undergo various gene regulations in different organs under hypoxic conditions, and integrative bioinformatics may provide some potential targets for advancing disease research.

Meis1, Hi1α, and GATA1 are integrated into a hierarchical regulatory network to mediate primitive erythropoiesis.

During development, erythroid cells are generated by two waves of hematopoiesis. In zebrafish, primitive erythropoiesis takes place in the intermediate cell mass region, and definitive erythropoiesis arises from the aorta-gonad mesonephros. TALE-homeoproteins Meis1 and Pbx1 function upstream of GATA1 to specify the erythroid lineage. Embryos lacking Meis1 or Pbx1 have weak gata1 expression and fail to produce primitive erythrocytes. Nevertheless, the underlying mechanism of how Meis1 and Pbx1 mediate gata1 transcription in erythrocytes remains unclear. Here we show that Hif1α acts downstream of Meis1 to mediate gata1 expression in zebrafish embryos. Inhibition of Meis1 expression resulted in suppression of hif1a expression and abrogated primitive erythropoiesis, while injection with in vitro-synthesized hif1α mRNA rescued gata1 transcription in Meis1 morphants and recovered their erythropoiesis. Ablation of Hif1α expression either by morpholino knockdown or Crispr-Cas9 knockout suppressed gata1 transcription and abrogated primitive erythropoiesis. Results of chromatin immunoprecipitation assays showed that Hif1α associates with hypoxia-response elements located in the 3'-flanking region of gata1 during development, suggesting that Hif1α regulates gata1 expression in vivo. Together, our results indicate that Meis1, Hif1α, and GATA1 indeed comprise a hierarchical regulatory network in which Hif1α acts downstream of Meis1 to activate gata1 transcription through direct interactions with its cis-acting elements in primitive erythrocytes.

Cloning of zebrafish (Danio rerio) heat shock factor 2 (HSF2) and similar patterns of HSF2 and HSF1 mRNA expression in brain tissues.

The transcriptional activation of heat shock protein (HSP) genes is initiated by the binding of heat shock factors (HSFs) to heat shock elements (HSEs) located at the promotor regions. Multiple HSFs exist in larger eukaryotic organisms in order to sense various types of stress signals. Here we report the cloning of zebrafish (Danio rerio) HSF2 (zHSF2) cDNA (GenBank accession number AF412833 ) that has an open reading frame of 1470 nucleotides, encoding a polypeptide of 489 amino acids. Domain architecture analysis of the deduced zHSF2 sequence revealed the presence of a DNA-binding domain at the N-terminal end, an adjacent oligomerization domain and a vertebrate heat shock transcription factor domain. Amino acid alignment showed a 70% sequence identity between zHSF2 and human or mouse HSF2, while only a 45% identity was found between zHSF1a and zHSF2. Recombinant zHSF2 bound with a very high specificity to HSEs arranged as inverted arrays of 5'-nGAAn-3', as replacing one GAA with GTA almost abolished the formation of HSE-binding complex. Similar patterns of zHSF1a and zHSF2 mRNA expression in the brain regions of developing zebrafish were detected by whole mount in situ hybridization and paraffin sectioning, suggesting that most of the two HSF gene activities were controlled by a common mechanism during the embryonic development of zebrafish. The levels of both zHSF1a and zHSF2 mRNA in zebrafish tissues were moderately increased after heat stress.