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Weak correlation between sequence conservation in promoter regions and in protein-coding regions of human-mouse orthologous gene pairs.

Chiba H, Yamashita R, Kinoshita K, Nakai K - BMC Genomics (2008)

Bottom Line: A number of studies have compared protein sequences or promoter sequences between mammals, which provided many insights into genomics.Remarkably, the 'ribosome' category showed significantly low promoter conservation, despite its high protein conservation, and the 'extracellular matrix' category showed significantly high promoter conservation, in spite of its low protein conservation.Our results show the relation of gene function to protein conservation and promoter conservation, and revealed that there seem to be nonparallel components between protein and promoter sequence evolution.

View Article: PubMed Central - HTML - PubMed

Affiliation: Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan. hchiba@hgc.jp <hchiba@hgc.jp>

ABSTRACT

Background: Interspecies sequence comparison is a powerful tool to extract functional or evolutionary information from the genomes of organisms. A number of studies have compared protein sequences or promoter sequences between mammals, which provided many insights into genomics. However, the correlation between protein conservation and promoter conservation remains controversial.

Results: We examined promoter conservation as well as protein conservation for 6,901 human and mouse orthologous genes, and observed a very weak correlation between them. We further investigated their relationship by decomposing it based on functional categories, and identified categories with significant tendencies. Remarkably, the 'ribosome' category showed significantly low promoter conservation, despite its high protein conservation, and the 'extracellular matrix' category showed significantly high promoter conservation, in spite of its low protein conservation.

Conclusion: Our results show the relation of gene function to protein conservation and promoter conservation, and revealed that there seem to be nonparallel components between protein and promoter sequence evolution.

Show MeSH
Scatter plot of protein conservation and promoter conservation for two subsets of ribosomal proteins. Crosses represent cytoplasmic ribosomal proteins (58 genes). Dots represent mitochondrial ribosomal proteins (41 genes). The conspicuous outlier corresponding to (56, 302) does not seem to be an actual ribosomal protein, and might have been erroneously annotated by an electronic procedure (see Additional file 9).
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Figure 4: Scatter plot of protein conservation and promoter conservation for two subsets of ribosomal proteins. Crosses represent cytoplasmic ribosomal proteins (58 genes). Dots represent mitochondrial ribosomal proteins (41 genes). The conspicuous outlier corresponding to (56, 302) does not seem to be an actual ribosomal protein, and might have been erroneously annotated by an electronic procedure (see Additional file 9).

Mentions: Besides the protein conservation, we examined the promoter conservation tendency for the two subsets of the C:ribosome category, cytoplasmic and mitochondrial ribosomal proteins. In contrast to the protein conservation, we could not observe a significant difference in the conservation levels between these two subgroups (P-value = 0.34 by Wilcoxon rank sum test; see Additional file 10 for details of the distributions). The plot of promoter conservation levels against protein conservation is shown in Figure 4. Apparently, the protein conservation is drastically different between cytoplasmic and mitochondrial ribosomal proteins, whereas the distribution of promoter conservation is quite similar. This result underscores the decoupled property of protein and promoter sequence evolution.


Weak correlation between sequence conservation in promoter regions and in protein-coding regions of human-mouse orthologous gene pairs.

Chiba H, Yamashita R, Kinoshita K, Nakai K - BMC Genomics (2008)

Scatter plot of protein conservation and promoter conservation for two subsets of ribosomal proteins. Crosses represent cytoplasmic ribosomal proteins (58 genes). Dots represent mitochondrial ribosomal proteins (41 genes). The conspicuous outlier corresponding to (56, 302) does not seem to be an actual ribosomal protein, and might have been erroneously annotated by an electronic procedure (see Additional file 9).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2335122&req=5

Figure 4: Scatter plot of protein conservation and promoter conservation for two subsets of ribosomal proteins. Crosses represent cytoplasmic ribosomal proteins (58 genes). Dots represent mitochondrial ribosomal proteins (41 genes). The conspicuous outlier corresponding to (56, 302) does not seem to be an actual ribosomal protein, and might have been erroneously annotated by an electronic procedure (see Additional file 9).
Mentions: Besides the protein conservation, we examined the promoter conservation tendency for the two subsets of the C:ribosome category, cytoplasmic and mitochondrial ribosomal proteins. In contrast to the protein conservation, we could not observe a significant difference in the conservation levels between these two subgroups (P-value = 0.34 by Wilcoxon rank sum test; see Additional file 10 for details of the distributions). The plot of promoter conservation levels against protein conservation is shown in Figure 4. Apparently, the protein conservation is drastically different between cytoplasmic and mitochondrial ribosomal proteins, whereas the distribution of promoter conservation is quite similar. This result underscores the decoupled property of protein and promoter sequence evolution.

Bottom Line: A number of studies have compared protein sequences or promoter sequences between mammals, which provided many insights into genomics.Remarkably, the 'ribosome' category showed significantly low promoter conservation, despite its high protein conservation, and the 'extracellular matrix' category showed significantly high promoter conservation, in spite of its low protein conservation.Our results show the relation of gene function to protein conservation and promoter conservation, and revealed that there seem to be nonparallel components between protein and promoter sequence evolution.

View Article: PubMed Central - HTML - PubMed

Affiliation: Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan. hchiba@hgc.jp <hchiba@hgc.jp>

ABSTRACT

Background: Interspecies sequence comparison is a powerful tool to extract functional or evolutionary information from the genomes of organisms. A number of studies have compared protein sequences or promoter sequences between mammals, which provided many insights into genomics. However, the correlation between protein conservation and promoter conservation remains controversial.

Results: We examined promoter conservation as well as protein conservation for 6,901 human and mouse orthologous genes, and observed a very weak correlation between them. We further investigated their relationship by decomposing it based on functional categories, and identified categories with significant tendencies. Remarkably, the 'ribosome' category showed significantly low promoter conservation, despite its high protein conservation, and the 'extracellular matrix' category showed significantly high promoter conservation, in spite of its low protein conservation.

Conclusion: Our results show the relation of gene function to protein conservation and promoter conservation, and revealed that there seem to be nonparallel components between protein and promoter sequence evolution.

Show MeSH