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Exploration for functional nucleotide sequence candidates within coding regions of mammalian genes.

Suzuki R, Saitou N - DNA Res. (2011)

Bottom Line: Therefore, synonymous sites of codons, which do not change the encoded amino acid, are regarded as evolving neutrally.No strong influence of conventional factors that affect synonymous substitution was observed in SCCSs.These results imply that SCCSs may have double function as nucleotide element and protein coding sequence and retained in the course of mammalian evolution.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, School of Life Science, Graduate University for Advanced Studies, Mishima 411-8540, Japan.

ABSTRACT
The primary role of a protein coding gene is to encode amino acids. Therefore, synonymous sites of codons, which do not change the encoded amino acid, are regarded as evolving neutrally. However, if a certain region of a protein coding gene contains a functional nucleotide element (e.g. splicing signals), synonymous sites in the region may have selective pressure. The existence of such elements would be detected by searching regions of low nucleotide substitution. We explored invariant nucleotide sequences in 10,790 orthologous genes of six mammalian species (Homo sapiens, Macaca mulatta, Mus musculus, Rattus norvegicus, Bos taurus, and Canis familiaris), and extracted 4150 sequences whose conservation is significantly stronger than other regions of the gene and named them significantly conserved coding sequences (SCCSs). SCCSs are observed in 2273 genes. The genes are mainly involved with development, transcriptional regulation, and the neurons, and are expressed in the nervous system and the head and neck organs. No strong influence of conventional factors that affect synonymous substitution was observed in SCCSs. These results imply that SCCSs may have double function as nucleotide element and protein coding sequence and retained in the course of mammalian evolution.

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GC content of the first (GC1), the second (GC2), and the third (GC3) position of codons in SCCSs: (A) GC1, (B) GC2, (C) GC3. X-axis represents the length of SCCSs, and Y-axis represents GC content of the sequences. Classes whose sample size < 20 were combined. Error bars represent 1 SE.
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DSR010F4: GC content of the first (GC1), the second (GC2), and the third (GC3) position of codons in SCCSs: (A) GC1, (B) GC2, (C) GC3. X-axis represents the length of SCCSs, and Y-axis represents GC content of the sequences. Classes whose sample size < 20 were combined. Error bars represent 1 SE.

Mentions: In mammals, of the influence GC content on nucleotide change as a result of CpG hyper mutability. We investigated GC content of SCCSs. GC content in the first (GC1), second (GC2), and third position (GC3) of codons show different patterns along the sequence length (Fig. 4). GC1 is mostly constant but GC2 increases while GC3 decreases as the length of SCCS increases. Because mammalian genomes prefer GC-ending codons, the decrease of GC3 corresponds to the decrease of preferred codons. The decrease of GC3 seems to be complementary with the increase of GC2 because GC content as a whole is constant (Supplementary Fig. S1).Figure 4.


Exploration for functional nucleotide sequence candidates within coding regions of mammalian genes.

Suzuki R, Saitou N - DNA Res. (2011)

GC content of the first (GC1), the second (GC2), and the third (GC3) position of codons in SCCSs: (A) GC1, (B) GC2, (C) GC3. X-axis represents the length of SCCSs, and Y-axis represents GC content of the sequences. Classes whose sample size < 20 were combined. Error bars represent 1 SE.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3111233&req=5

DSR010F4: GC content of the first (GC1), the second (GC2), and the third (GC3) position of codons in SCCSs: (A) GC1, (B) GC2, (C) GC3. X-axis represents the length of SCCSs, and Y-axis represents GC content of the sequences. Classes whose sample size < 20 were combined. Error bars represent 1 SE.
Mentions: In mammals, of the influence GC content on nucleotide change as a result of CpG hyper mutability. We investigated GC content of SCCSs. GC content in the first (GC1), second (GC2), and third position (GC3) of codons show different patterns along the sequence length (Fig. 4). GC1 is mostly constant but GC2 increases while GC3 decreases as the length of SCCS increases. Because mammalian genomes prefer GC-ending codons, the decrease of GC3 corresponds to the decrease of preferred codons. The decrease of GC3 seems to be complementary with the increase of GC2 because GC content as a whole is constant (Supplementary Fig. S1).Figure 4.

Bottom Line: Therefore, synonymous sites of codons, which do not change the encoded amino acid, are regarded as evolving neutrally.No strong influence of conventional factors that affect synonymous substitution was observed in SCCSs.These results imply that SCCSs may have double function as nucleotide element and protein coding sequence and retained in the course of mammalian evolution.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, School of Life Science, Graduate University for Advanced Studies, Mishima 411-8540, Japan.

ABSTRACT
The primary role of a protein coding gene is to encode amino acids. Therefore, synonymous sites of codons, which do not change the encoded amino acid, are regarded as evolving neutrally. However, if a certain region of a protein coding gene contains a functional nucleotide element (e.g. splicing signals), synonymous sites in the region may have selective pressure. The existence of such elements would be detected by searching regions of low nucleotide substitution. We explored invariant nucleotide sequences in 10,790 orthologous genes of six mammalian species (Homo sapiens, Macaca mulatta, Mus musculus, Rattus norvegicus, Bos taurus, and Canis familiaris), and extracted 4150 sequences whose conservation is significantly stronger than other regions of the gene and named them significantly conserved coding sequences (SCCSs). SCCSs are observed in 2273 genes. The genes are mainly involved with development, transcriptional regulation, and the neurons, and are expressed in the nervous system and the head and neck organs. No strong influence of conventional factors that affect synonymous substitution was observed in SCCSs. These results imply that SCCSs may have double function as nucleotide element and protein coding sequence and retained in the course of mammalian evolution.

Show MeSH