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Comparing the retention mechanisms of tandem duplicates and retrogenes in human and mouse genomes.

Wang Z, Dong X, Ding G, Li Y - Genet. Sel. Evol. (2010)

Bottom Line: The duplicability of tandem duplicates is also higher than that of retrogenes.However, positive selection seems to play significant roles in the retention of both types of duplicates.We propose that dosage effect is more prevalent in the retention of tandem duplicates, while 'escape from adaptive conflict' (EAC) effect is more prevalent in the retention of retrogenes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, PR China.

ABSTRACT

Background: Multiple models have been proposed to interpret the retention of duplicated genes. In this study, we attempted to compare whether the duplicates arising from tandem duplications and retropositions are retained by the same mechanisms in human and mouse genomes.

Results: Both sequence and expression similarity analyses revealed that tandem duplicates tend to be more conserved, whereas retrogenes tend to be more divergent. The duplicability of tandem duplicates is also higher than that of retrogenes. However, positive selection seems to play significant roles in the retention of both types of duplicates.

Conclusions: We propose that dosage effect is more prevalent in the retention of tandem duplicates, while 'escape from adaptive conflict' (EAC) effect is more prevalent in the retention of retrogenes.

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Percentage of tissues with duplicates co-expressed. Medians for tandem duplicates and retrogenes in mouse genomes are 8.5 and 1.8, respectively (p = 0.002, one-tailed rank sum test); medians for the both of duplicates in human genomes are 7.9 and 2.0, respectively (p = 0.036)
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Figure 3: Percentage of tissues with duplicates co-expressed. Medians for tandem duplicates and retrogenes in mouse genomes are 8.5 and 1.8, respectively (p = 0.002, one-tailed rank sum test); medians for the both of duplicates in human genomes are 7.9 and 2.0, respectively (p = 0.036)

Mentions: In addition to the coding sequences, the evolution of regulatory elements is also important to determine the fate of duplicates. In fact, the differentiation of regulatory motifs can increase the expression specificity of the duplicates among various tissues and developmental stages, which is perhaps the most common form of subfunctionalization [29]. Previous reports have found that a rapid expression divergence exists between duplicates [30], and that the expression diversity is also increased compared to singletons [31]. However, as tandem duplications directly occur at the DNA level, it is more likely that the new duplicates preserve their original regulatory motifs and expression patterns. In contrast, as retrogenes are randomly inserted into the genome via mRNAs, they are more likely to acquire distinct regulatory motifs and expression patterns. To test this hypothesis, we compared the expression similarity for tandem duplicates and retrogenes by using microarray data across diverse tissues (Figure 3). Although a lot of duplicates have been quite differentiated for both types, the expression similarity between tandem duplicates is still significantly higher than that between retrogenes (human: p = 0.036, mouse: p = 0.002, rank sum test). Therefore, the gene expression profiles also support the difference in functional divergence for both types of duplications.


Comparing the retention mechanisms of tandem duplicates and retrogenes in human and mouse genomes.

Wang Z, Dong X, Ding G, Li Y - Genet. Sel. Evol. (2010)

Percentage of tissues with duplicates co-expressed. Medians for tandem duplicates and retrogenes in mouse genomes are 8.5 and 1.8, respectively (p = 0.002, one-tailed rank sum test); medians for the both of duplicates in human genomes are 7.9 and 2.0, respectively (p = 0.036)
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2902415&req=5

Figure 3: Percentage of tissues with duplicates co-expressed. Medians for tandem duplicates and retrogenes in mouse genomes are 8.5 and 1.8, respectively (p = 0.002, one-tailed rank sum test); medians for the both of duplicates in human genomes are 7.9 and 2.0, respectively (p = 0.036)
Mentions: In addition to the coding sequences, the evolution of regulatory elements is also important to determine the fate of duplicates. In fact, the differentiation of regulatory motifs can increase the expression specificity of the duplicates among various tissues and developmental stages, which is perhaps the most common form of subfunctionalization [29]. Previous reports have found that a rapid expression divergence exists between duplicates [30], and that the expression diversity is also increased compared to singletons [31]. However, as tandem duplications directly occur at the DNA level, it is more likely that the new duplicates preserve their original regulatory motifs and expression patterns. In contrast, as retrogenes are randomly inserted into the genome via mRNAs, they are more likely to acquire distinct regulatory motifs and expression patterns. To test this hypothesis, we compared the expression similarity for tandem duplicates and retrogenes by using microarray data across diverse tissues (Figure 3). Although a lot of duplicates have been quite differentiated for both types, the expression similarity between tandem duplicates is still significantly higher than that between retrogenes (human: p = 0.036, mouse: p = 0.002, rank sum test). Therefore, the gene expression profiles also support the difference in functional divergence for both types of duplications.

Bottom Line: The duplicability of tandem duplicates is also higher than that of retrogenes.However, positive selection seems to play significant roles in the retention of both types of duplicates.We propose that dosage effect is more prevalent in the retention of tandem duplicates, while 'escape from adaptive conflict' (EAC) effect is more prevalent in the retention of retrogenes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, PR China.

ABSTRACT

Background: Multiple models have been proposed to interpret the retention of duplicated genes. In this study, we attempted to compare whether the duplicates arising from tandem duplications and retropositions are retained by the same mechanisms in human and mouse genomes.

Results: Both sequence and expression similarity analyses revealed that tandem duplicates tend to be more conserved, whereas retrogenes tend to be more divergent. The duplicability of tandem duplicates is also higher than that of retrogenes. However, positive selection seems to play significant roles in the retention of both types of duplicates.

Conclusions: We propose that dosage effect is more prevalent in the retention of tandem duplicates, while 'escape from adaptive conflict' (EAC) effect is more prevalent in the retention of retrogenes.

Show MeSH