Naming 'junk': Human non-protein coding RNA (ncRNA) gene nomenclature

At the beginning of this century, many geneticists were predicting that the human genome contained around 100,000 protein-coding genes, partly based on the assumption that more complex organisms would have a greater number of genes. Ten years later, with far more genomic data from a wide variety of organisms and a much better-quality, well-annotated human genome, this original expectation has been downsized to around 20,000 protein-coding genes. This means that highly complex organisms like the human have about the same number of protein-coding genes as much simpler life forms such as the roundworm, Caenorhabditis elegans. If we look to the human's closest living relative, the chimpanzee, we see that the equivalent proteins in human and chimpanzee typically differ by only two amino acids, and approximately 29 per cent of all the orthologous proteins encoded in human and chimpanzee are identical [1]. Why, then, when the protein-coding components of our genomes are so similar, are humans and chimpanzees so strikingly different? Since protein-coding genes comprise only two per cent of the human genome, the answer may lie in the large swathes of the genome previously regarded as 'junk DNA'. Indeed, the ENCyclopedia Of DNA Elements (ENCODE) Consortium,[2] which is aiming to identify all the functional elements in the human genome, suggests that the vast majority of the genome is transcribed as non-protein-coding RNA (ncRNA). These RNAs could be responsible for some of the complex differences between humans and other primates, especially since the expression of many genes is now thought to be regulated by ncRNAs. They are also known to be involved in many other diverse and vital roles within our bodies, including protein biosynthesis and the splicing of messenger RNAs (mRNAs), and have been implicated in many diseases, such as Prader-Willi syndrome and various cancers (for review, see Taft et al.[3]). It is not surprising, then, that interest in ncRNAs has accelerated eve