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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
Distribution of percentage identities of human and mouse protein sequences. For the high conservation tendency, actin cytoskeleton (A) and ribosome (D), for the low conservation tendency, extracellular matrix (B) and lysosome (C). For each of A-D, the solid line shows the distribution of the identities for genes with the specific GO term, and the dashed line shows the distribution for the control gene set (see Materials and Methods for details).
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Figure 3: Distribution of percentage identities of human and mouse protein sequences. For the high conservation tendency, actin cytoskeleton (A) and ribosome (D), for the low conservation tendency, extracellular matrix (B) and lysosome (C). For each of A-D, the solid line shows the distribution of the identities for genes with the specific GO term, and the dashed line shows the distribution for the control gene set (see Materials and Methods for details).

Mentions: The protein conservation tendencies were examined in a similar manner to those of the promoter conservation, using protein sequences obtained from the RefSeq database. Since the alignment score largely depends on the protein length, we used the percentage identity for protein sequences, instead of the alignment scores. GO terms showing high protein conservation are listed in Table 3, and those with low conservation are in Table 4 (only terms with a P-value < 0.01; for the complete list of results, see Additional file 5). Figure 3 shows the distributions of conservation levels for several GO terms with significant tendencies (all of the distributions for the GO terms in Table 3 and 4 are shown in Additional file 6). When we tried global alignment, we obtained quite similar tendencies (data not shown), which is reasonable, given that the coverages of the local alignments were mostly over 95% (data not shown).


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)

Distribution of percentage identities of human and mouse protein sequences. For the high conservation tendency, actin cytoskeleton (A) and ribosome (D), for the low conservation tendency, extracellular matrix (B) and lysosome (C). For each of A-D, the solid line shows the distribution of the identities for genes with the specific GO term, and the dashed line shows the distribution for the control gene set (see Materials and Methods for details).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Distribution of percentage identities of human and mouse protein sequences. For the high conservation tendency, actin cytoskeleton (A) and ribosome (D), for the low conservation tendency, extracellular matrix (B) and lysosome (C). For each of A-D, the solid line shows the distribution of the identities for genes with the specific GO term, and the dashed line shows the distribution for the control gene set (see Materials and Methods for details).
Mentions: The protein conservation tendencies were examined in a similar manner to those of the promoter conservation, using protein sequences obtained from the RefSeq database. Since the alignment score largely depends on the protein length, we used the percentage identity for protein sequences, instead of the alignment scores. GO terms showing high protein conservation are listed in Table 3, and those with low conservation are in Table 4 (only terms with a P-value < 0.01; for the complete list of results, see Additional file 5). Figure 3 shows the distributions of conservation levels for several GO terms with significant tendencies (all of the distributions for the GO terms in Table 3 and 4 are shown in Additional file 6). When we tried global alignment, we obtained quite similar tendencies (data not shown), which is reasonable, given that the coverages of the local alignments were mostly over 95% (data not shown).

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