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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 distributions of the ratios of the lengths of short vs. long genes in overlapping genes (white bars) and in the non-overlapping neighboring gene pairs (black bars). A. Same-strand overlaps. B. Different-strand overlaps.
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Figure 2: The distributions of the ratios of the lengths of short vs. long genes in overlapping genes (white bars) and in the non-overlapping neighboring gene pairs (black bars). A. Same-strand overlaps. B. Different-strand overlaps.

Mentions: We calculated the ratios of the lengths of shorter and longer genes for overlapping gene pairs and compared them with the ratios of the lengths of the non-overlapping neighboring genes (shorter vs. longer genes) in the sample of 13,484 genes (Figure 2). The permutation tests show that genes involved in the same-strand overlaps have much lower length ratio than neighboring non-overlapping genes (Figure 3, p-value << 0.001 for both species). This makes intuitive sense because most of the same-strand overlaps are in the form of one gene residing in the other gene's introns. For different-strand overlaps, this restriction on gene lengths appears to be not as pronounced, because the vast majority of different-strand overlaps are not embedded forms. However, in different-strand overlaps the length ratio is still significantly lower than the ratios in non-overlapping neighboring genes (p-values < 0.01).


Overlapping genes in the human and mouse genomes.

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

The distributions of the ratios of the lengths of short vs. long genes in overlapping genes (white bars) and in the non-overlapping neighboring gene pairs (black bars). A. Same-strand overlaps. B. Different-strand overlaps.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: The distributions of the ratios of the lengths of short vs. long genes in overlapping genes (white bars) and in the non-overlapping neighboring gene pairs (black bars). A. Same-strand overlaps. B. Different-strand overlaps.
Mentions: We calculated the ratios of the lengths of shorter and longer genes for overlapping gene pairs and compared them with the ratios of the lengths of the non-overlapping neighboring genes (shorter vs. longer genes) in the sample of 13,484 genes (Figure 2). The permutation tests show that genes involved in the same-strand overlaps have much lower length ratio than neighboring non-overlapping genes (Figure 3, p-value << 0.001 for both species). This makes intuitive sense because most of the same-strand overlaps are in the form of one gene residing in the other gene's introns. For different-strand overlaps, this restriction on gene lengths appears to be not as pronounced, because the vast majority of different-strand overlaps are not embedded forms. However, in different-strand overlaps the length ratio is still significantly lower than the ratios in non-overlapping neighboring genes (p-values < 0.01).

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