Substitution pattern of the CArG element in human and mouse genomes

cis-Elements CArG bound by serum response factor (SRF) are presently being intensively studied, but little is known about the substitution pattern of functional CArG elements. Here, we have performed the first evolutionary analysis of CArGome in the human and mouse genome through bioinformatic metho...

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Bibliographic Details
Published inGenome Vol. 54; no. 2; pp. 144 - 150
Main Authors Shen, Xia, Mao, Haimei, Miao, Shan
Format Journal Article
LanguageEnglish
Published Canada NRC Research Press 01.02.2011
Canadian Science Publishing NRC Research Press
Subjects
analyse évolutive
Animals
Binding sites
bioinformatics
bioinformatique
CArG elements
Computational biology
Computational Biology - methods
DNA
Evolution & development
Evolution, Molecular
evolutionary analysis
Gene expression
Gene Expression Regulation
Genetic aspects
Genome
Genomics
génome humain
génome murin
Human genome
Humans
Mice
mode de substitution
Molecular structure
mouse genome
Physiological aspects
Promoter Regions, Genetic
Protein Binding
Rodents
Serum
Serum Response Element
Serum Response Factor - genetics
substitution pattern
éléments CArG
China
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Summary:cis-Elements CArG bound by serum response factor (SRF) are presently being intensively studied, but little is known about the substitution pattern of functional CArG elements. Here, we have performed the first evolutionary analysis of CArGome in the human and mouse genome through bioinformatic methods and statistical tests. We calculated the substitution rate at each site of the functional CArG elements. The results showed that the core sites of the functional CArG elements evolved faster than did the background DNA, indicating that these sites were likely to evolve under positive selection. Moreover, a strong TATA "motif" was evident in the core region within the functional CArG elements in both human and mouse promoters. This motif could probably be a major contribution to the formation of the spatial structure, which was important for CArG-SRF recognition. Thus, the study further revealed the sequence character and substitution pattern of CArG elements and provided useful information for the study of the SRF-binding efficiencies of CArG promoters in functional assays.
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ISSN:0831-2796
1480-3321
DOI:10.1139/G10-105