Abstract
BackgroundIncreasing evidence suggests that overlapping genes are much more common in eukaryotic genomes than previously thought. In this study we identified and characterized the overlapping genes in a set of 13,484 pairs of human-mouse orthologous genes.ResultsAbout 10% of the genes under study are overlapping genes, the majority of which are different-strand overlaps. The majority of the same-strand overlaps are embedded forms, whereas most different-strand overlaps are not embedded and in the convergent transcription orientation. Most of the same-strand overlapping gene pairs show at least a tenfold difference in length, much larger than the length difference between non-overlapping neighboring gene pairs. The length difference between the two different-strand overlapping genes is less dramatic. Over 27% of the different-strand-overlap relationships are shared between human and mouse, compared to only ~8% conservation for same-strand-overlap relationships. More than 96% of the same-strand and different-strand overlaps that are not shared between human and mouse have both genes located on the same chromosomes in the species that does not show the overlap. We examined the causes of transition between the overlapping and non-overlapping states in the two species and found that 3' UTR change plays an important role in the transition.ConclusionOur study contributes to the understanding of the evolutionary transition between overlapping genes and non-overlapping genes and demonstrates the high rates of evolutionary changes in the un-translated regions.
Highlights
Increasing evidence suggests that overlapping genes are much more common in eukaryotic genomes than previously thought
Most of the recent largescale analyses in higher eukaryotes have been restricted to different-strand-overlap genes, which are potential senseantisense gene pairs in which the overlap can affect the regulation of gene expression at the level of transcription
Because some large genes overlap with multiple genes, the numbers of unique genes involved in overlap in human and mouse are not 2 × 669 = 1338 and 1108 but are only 1219 (1219/13484 = 9.0%) and 1004 (7.4%), respectively
Summary
Increasing evidence suggests that overlapping genes are much more common in eukaryotic genomes than previously thought. In this study we identified and characterized the overlapping genes in a set of 13,484 pairs of human-mouse orthologous genes. Overlapping genes are known to be common in viruses, mitochondria, bacteria, and plasmids [1], but are thought to be rare in eukaryotes. This view is changing because recent studies have suggested the existence of many overlapping genes in eukaryotic genomes, including human [2,3,4,5], mouse [6], rat [7], fish [8], and flies [9,10]. We studied the evolutionary conservation of overlapping relationships between human and mouse and the possible mechanisms of transition between the overlapping and non-overlapping states
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