Exactly what the total gene count i

Exactly what the total gene count is for the human genome will probably remain vague for some time to come, but it seems likely that the number will move upwards as the sequence is refined and annotation improves. Numbers are firmer for the C. elegans genome, and have not changed much over the past two years. About half of all C. elegans genes are currently enigmatic in terms of sequence similarity and function, however, and their existence was initially based only on GeneFinder predictions [2]. According to some analyses, many could be pseudogenes [3].

The question of how many of these predicted worm genes are real has recently been tackled by Reboul et al. [4], using an OST (open-reading-frame sequence tag) approach. They chose 1,222 predicted genes for which no EST (expressed sequence tag) had yet been obtained, and attempted to amplify a predicted product from cDNA. At least 70% of the genes were thereby verified, indicating that they are real, although the predicted intron/exon structure was not always correct. Their study resulted in a minimum, and therefore conservative, estimate for the C. elegans gene number of 17,387. This can be compared with the most recent genome-sequence-based number of 19,404 protein-coding genes [5], which is not too dissimilar. Both approaches are likely to have missed a substantial number of small genes, such as those encoding neuropeptides, antimicrobial peptides, cuticle components and small regulatory proteins such as egl-1 [6]. The high total gene count therefore does not seem to be an artifact of the prediction programs, nor to be explained by the presence of numerous pseudogenes.

Moreover, the numbers above apply only to protein-coding genes, and there are a substantial number of RNA-encoding genes which have to be added to the gene tally. These RNA-encoding genes are often difficult to recognize on the basis of sequence, so they are usually even harder to count than the protein-coding genes. Some of the classes, such as ribosomal RNA genes, are easy to enumerate. Worms have one cluster of 55 large ribosomal genes, encoding the 18S, 5.8S and 28S rRNAs, and another cluster of 110 genes for 5S rRNA. Transfer RNA genes are for the most part also fairly easy to recognize, and have been extensively annotated in the worm genome. About 900 tRNA genes can be recognized; 200 of these are probably pseudogenes, but the majority look real. This is consistent with the one family that has been examined in detail (the twelve Trp tRNA genes), in which eight are demonstrably functional, and two look like pseudogenes [7]. The relative number of tRNA genes is high compared to the number in the human genome, in one of the many small mysteries of comparative genomics.

Other RNA genes include snRNAs (small nuclear RNAs), snoRNAs (small nucleolar RNAs), scRNAs (small cytoplasmic RNAs), telomere RNAs, splice leaders and small regulatory RNAs. Some of these, such as the snoRNAs, are hard to recognize in raw sequence [8], and consequently their exact number is unknown. Others, such as the developmental timing regulators lin-4 and let-7, are known to perform important biological functions, but their discovery has depended entirely on genetic methods [9]. It is an open question how many other non-coding regulatory RNAs like these remain to be found in eukaryotic genomes. The two known examples of regulatory RNAs in C. elegans represent fewer than 0.5% of the genes defined by mutation and subsequently cloned, which implies that regulatory RNAs cannot be all that numerous, but that still leaves room for many more genes in this category. In summary, the number of known RNA genes is already well over 1,000. These can be added to the 18,000-19,000 predicted protein-coding genes, to give a total of something like 20,000 as a nice round number - hence the title of this article.

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