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Overlapping genes in the human and mouse genomes.

Sanna CR, Li WH, Zhang L - BMC Genomics (2008)

Bottom Line: Over 27% of the different-strand-overlap relationships are shared between human and mouse, compared to only approximately 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Computer Science, Virginia Tech, Blacksburg, USA. csanna@vt.edu

ABSTRACT

Background: 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.

Results: About 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 approximately 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.

Conclusion: Our 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.

Show MeSH
The cumulative distribution of the lengths of overlapping regions. Different – strand overlaps were divided into divergent, convergent, and embedded types.
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Figure 1: The cumulative distribution of the lengths of overlapping regions. Different – strand overlaps were divided into divergent, convergent, and embedded types.

Mentions: Figure 1 shows the cumulative distribution of overlap lengths. The two species show very similar patterns. The overlap lengths of the two genes in different-strand overlaps tend to be much shorter than those for same-strand overlaps. For example, ~43% of the overlap regions of different-strand overlaps are shorter than 1 kb, whereas less than 2% of the overlap regions of same-strand overlaps are shorter than 1 kb. For the majority of same-strand overlaps, overlap regions account for 90–100% of the shorter gene but less than 10% of the longer gene, consistent with the observation that the majority of same-strand overlaps are embedded forms (Table 2). For different-strand overlaps, in ~37–46% of the cases the overlap regions account for less than 10% of the length of the shorter gene, and in ~30–34% of the cases the overlap regions account for 90–100% of the length of the shorter gene.


Overlapping genes in the human and mouse genomes.

Sanna CR, Li WH, Zhang L - BMC Genomics (2008)

The cumulative distribution of the lengths of overlapping regions. Different – strand overlaps were divided into divergent, convergent, and embedded types.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2335118&req=5

Figure 1: The cumulative distribution of the lengths of overlapping regions. Different – strand overlaps were divided into divergent, convergent, and embedded types.
Mentions: Figure 1 shows the cumulative distribution of overlap lengths. The two species show very similar patterns. The overlap lengths of the two genes in different-strand overlaps tend to be much shorter than those for same-strand overlaps. For example, ~43% of the overlap regions of different-strand overlaps are shorter than 1 kb, whereas less than 2% of the overlap regions of same-strand overlaps are shorter than 1 kb. For the majority of same-strand overlaps, overlap regions account for 90–100% of the shorter gene but less than 10% of the longer gene, consistent with the observation that the majority of same-strand overlaps are embedded forms (Table 2). For different-strand overlaps, in ~37–46% of the cases the overlap regions account for less than 10% of the length of the shorter gene, and in ~30–34% of the cases the overlap regions account for 90–100% of the length of the shorter gene.

Bottom Line: Over 27% of the different-strand-overlap relationships are shared between human and mouse, compared to only approximately 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Computer Science, Virginia Tech, Blacksburg, USA. csanna@vt.edu

ABSTRACT

Background: 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.

Results: About 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 approximately 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.

Conclusion: Our 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.

Show MeSH