Abstract
Cyprinus carpio is world’s most widely distributed freshwater species highly used in aquaculture. It is a hypoxia-tolerant species as it lives in oxygen-deficient environment for a long period. The tolerance potential of an animal against hypoxia relates it to induced gene expression, where a hypoxia-inducible factor (HIF) binds to a transcriptionally active site, hypoxia response element (HRE), a 5-base short motif that lies within the promoter/enhancer region of a certain gene, for inducing gene expression and preventing/minimizing hypoxia effects. HRE is functionally active when it contains another motif, the hypoxia ancillary sequence (HAS), which is typically adjacent to downstream of HRE within 7- to 15-nt space. Here, an attempt was made for mining HRE and identifying functional HIF binding sites (HBS) in a genome-wide analysis of C. carpio. For this, gene information along with the 5,000-nt upstream (−4,900 to +100) sequences of 31,466 protein coding genes was downloaded from “Gene” and “RefSeq” databases. Analysis was performed after filtration of the impracticable genes. A total of 116,148 HRE consensus sequences were mined from 29,545 genes in different promoter regions. HRE with HAS consensus motifs were found in the promoter region of 9,589 genes. Further, the already reported genes for hypoxia response in humans and zebrafish were reanalyzed for detecting HRE sites in their promoters and used for comparative analysis with gene promoters of C. carpio for providing support to identify functional HBS in the gene promoter of C. carpio. An interactive user interface HREExplorer was developed for presenting the results on the World Wide Web and visualizing possible HBS in protein coding genes in C. carpio and displaying the comparative results along with the reported hypoxia-responsive genes of zebrafish and reported hypoxia-inducible genes in humans. In this study, a set of Perl program was written for the compilation and analysis of information that might be used for a similar study in other species. This novel work may provide a workbench for analyzing the promoter regions of hypoxia-responsive genes.
Highlights
Cyprinus carpio, commonly known as common carp, is a worldwide distributed freshwater carp fish of Family Cyprinidae, having vulnerable conservation status, and is a widely cultivated aquaculture species contributing about 10% to the total freshwater aquaculture production
The localization of possible HIF binding sites (HBS) in different core, proximal and distal promoter regions was explored in the comparative analysis
The results of analysis are available on the web server that can be seen using HREExplorer for each chromosome
Summary
Commonly known as common carp, is a worldwide distributed freshwater carp fish of Family Cyprinidae, having vulnerable conservation status, and is a widely cultivated aquaculture species contributing about 10% to the total freshwater aquaculture production. It is a hypoxiatolerant species that lives for a prolonged period in oxygendepleted environment and reported for different physiologic and metabolic adaptations under hypoxia, including renal (Kakuta et al, 1992), cardiorespiratory (Stecyk and Farrell, 2002), and cellular and molecular (Tasaki et al, 2017) responses. Fishes encounter hypoxia more frequently than the air-breathing animal and can adopt tolerability potential through natural selection to preserve oxygen contents and cellular energy for hypoxia survival. Their adaptation is associated with behavioral responses, inducing higher hematocrit and altering/ reducing metabolic activity to preserve more oxygen for survival during hypoxia and maintenance of oxygen homeostasis (Perry et al, 2009; Vornanen et al, 2009; Richards, 2011). Hypoxia-sensitive fish attempt to meet high metabolic demands with insufficient ATP during hypoxia without any further change in the behavioral and physiologic responses that can lead to even mortality
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