Warm Hearts for White Sharks
Geneticists often refer to the “genome” of a species, the DNA sequences that specify the development and physiology of an animal. In reality though, the genome is only a set of instructions for creating that individual, it is the RNAs and proteins within each cell that carry out the DNA’s instructions. Under the “Central Dogma” of molecular biology, the DNA sequence of an active gene directs the production of RNA molecules, mobile pieces of nucleic acid that reflect the subset of genes turned on in each different cell type. The RNA molecules in turn direct the production of proteins, the true workhorses of a cell. The DNA complement of each cell in an animal is identical, yet the cells making up that animal are widely varied in form and function. It is the way the DNA is handled in each cell that confers their uniqueness - which genes are activated, and to what level, and which genes remain silent. The RNAs produced in a cell, and therefore the proteins they direct, specify the identity of a liver cell or a brain cell or a heart cell. Among the genomic resources that have become available within the last few decades is the ability to identify the entire complement of RNAs made within any given cell or tissue type in the body. Such a collection of sequences is called the “transcriptome” of that organ or tissue. While this was previously a slow and laborious process, the development of high-throughput sequencing technologies over the past 10 years has allowed the generation of transcriptomes for many tissues of humans, mice and other research organisms. Less common, at least so far, are the transcriptomes of elasmobranchs -- not surprising perhaps, as genomic resources in general have been slow to be applied to the study of sharks and rays.
A recent report by Richards et al has now produced one of the first transcriptome collections for elasmobranchs of any species, and the first for white sharks. Specifically, they have identified the entire collection of RNA sequences - representing all the genes that are active - in the heart tissue of a juvenile white shark. Obtaining a full transcriptome sequence is only the beginning of such an experiment, more complicated is to sort and study the 20,000 individual RNA sequences that were generated. To make sense of such large data sets, researchers often use Gene Ontology (GO) terms, categories of biological function to which various RNAs are assigned. Richards et al sorted the white shark heart transcriptome by GO terms, and then compared it with the transcriptome of humans, and with the widely used model fish species Danio rerio, the zebrafish.
While their results are preliminary, and suffer from certain limitations - the human and zebrafish transcriptomes used for comparison were not limited to the heart, for example - interesting data can be gleaned from these comparisons. The percentage of white shark RNAs that are involved in metabolic processes, for example, is more similar to that of endothermic (warm-blooded) humans than of exothermic (cold-blooded) zebrafish. It has been proposed that certain pelagic fishes - swordfish, tuna, and lamnid sharks such as white and mako sharks - possess some characteristics of endothermy, including elevated muscle and stomach temperatures. These modifications may allow for long-distance swimming and/or the active pursuit of prey. The greater similarity of the white shark heart transcriptome to that of mammals, in comparison to the zebrafish, may identify genes involved in controlling shark endothermy. Further investigation of these metabolic transcripts will lead to a better understanding of shark physiology.
The article is: Richards, VP, Suzuki, H, Stanhope, MJ and Shivji, MS. (2013) Characterization of the heart transcriptome of the white shark (Carcharodon carcharias). BMC Genomics 14:697.
It is open access and can be found here: www.biomedcentral.com/1471-2164/14/697