Identifying Noncoding RNAs in Genome Sequences
Sean R. Eddy: "According to the RNA world hypothesis, RNA catalysts and replicators preceded modern protein/DNA machines. This hypothesis arose from the discovery of catalytic RNAs and also from the fact that functional RNAs are used instead of protein enzymes in some ancient, highly conserved roles in modern organisms. Some proponents of the RNA world hypothesis view extant functional RNAs as 'molecular fossils' of the RNA world.
Because noncoding RNA (ncRNA) genes tend to be small and are inherently immune to frameshift or nonsense mutations, they are hard to find by classical mutational genetic screens. They are also difficult to recognize in genomes because they do not have open reading frames and thus cannot be discovered by gene-finding programs. Their sequences also tend to evolve rapidly, conserving their structure more than their primary sequence, making them difficult to discover by standard database searches.
Our results, and results from several other labs, seem to indicate that ncRNA genes are more prevalent than even we thought. For those new genes where we have some indication of their function, most appear to be functioning as highly adapted regulatory molecules, which is not consistent with the idea that they are ancient molecular fossils of the RNA world. It is beginning to appear that ncRNAs could be a large class of genes that have been overlooked because it is so difficult to identify them."
Because noncoding RNA (ncRNA) genes tend to be small and are inherently immune to frameshift or nonsense mutations, they are hard to find by classical mutational genetic screens. They are also difficult to recognize in genomes because they do not have open reading frames and thus cannot be discovered by gene-finding programs. Their sequences also tend to evolve rapidly, conserving their structure more than their primary sequence, making them difficult to discover by standard database searches.
Our results, and results from several other labs, seem to indicate that ncRNA genes are more prevalent than even we thought. For those new genes where we have some indication of their function, most appear to be functioning as highly adapted regulatory molecules, which is not consistent with the idea that they are ancient molecular fossils of the RNA world. It is beginning to appear that ncRNAs could be a large class of genes that have been overlooked because it is so difficult to identify them."