RNA polymerase II dependent genes that do not code for protein

In recent years more and more examples of RNA polymerase II dependent non-coding transcripts have been described. Although these have frequently been ignored as "selfish DNA elements", it is becoming increasingly clear that many, if not all, of them have very important biological roles. Examples of such "genes" from Drosophila, mammals, other vertebrates, yeast etc. are considered. Although the specific mechanisms through which these non-coding transcripts function in the cell are not clear, comparisons reveal certain common themes, particularly the importance of secondary structures, rather than the primary base sequence of these transcripts. While some of these transcripts may function as ribozymes or as anti-sense regulators, most others may function more directly through their specific protein-binding properties. Since RNA is believed to be the first "living" molecule, it is very likely that some genes even today function only through this class of molecules. It is expected that instead of being ignored as examples of "selfish DNA", a more positive search for their functions will help unravel the significance of this novel class of genes.