In my research, I look at a lot of gene predictions / annotations. Frequently, I see loci where multiple gene models overlap. I haven't taken a systematic approach to analyzing these cases, but I do remember seeing quite a bit of variation in the direction of the overlapping genes (same vs different directions), the amount of overlap, and even the number of overlapping genes.
I know enough about gene prediction to take any computational predictions with a grain of salt--even those supported by transcript and peptide alignments. However, these cases have me thinking--does overlap of genetic information *really* occur in eukaryotes? I seem to remember learning (or hearing anecdotally) that it can happen in prokaryotes, and that seems to be understandable given the compactness of prokaryotic genomes. But can this happen in eukaryotes? Has this been studied, and are there cases that have been confirmed experimentally?
Yes, a single gene can serve many roles. This is the basis of splicing events and differential expression. There is also tertiary structure and epigenetic modification of DNA that can cause a set of genes to produce a completely different phenotype.
