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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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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Abstract 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.
AbstractList 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.
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. Key words: CArG elements, substitution pattern, evolutionary analysis, bioinformatics, mouse genome, human genome. Les elements cis CArG lies par le facteur de reponse au serum (SRF) font presentement l'objet de nombreux travaux, mais peu de choses sont connues au sujet des substitutions entre elements CArG fonctionnels. Dans ce travail, les auteurs ont realise la premiere analyse de revolution du CArGome au sein des genomes de l'humain et de la souris via une approche bioinformatique et des tests statistiques. Les auteurs ont calcule; le taux de substitution a chacun des sites chez les elements CArG fonctionnels. Les resultats montrent que les sites au centre des elements CArG fonctionnels ont evolue plus rapidement que le reste de l'ADN, ce qui suggere que ces sites auraient evoluee sous l'impulsion d'une selection positive. De plus, un fort << motif >> TATA etait evident au sein de la region centrale chez les elements CArG fonctionnels presents dans les promoteurs humains et murins. Ce << motif >> pourrait apporter une contribution majeure a la formation de la structure spatiale qui est importante pour la reconnaissance CArG-SRF. Cette etude a ainsi revele les proprietes de ces sequences et le type de substitutions qui caracterisent les elements CArG en plus de fournir des informations utiles pour l'etude de l'intensite de liaison des facteurs SRF sur les promoteurs CArG lors d'analyses fonctionnelles. Mots-cles: elements CArG, mode de substitution, analyse evolutive, bioinformatique, genome murin, genome humain. [Traduit par la Redaction]
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. [PUBLICATION ABSTRACT]
Abstract_FL Les éléments cis CArG liés par le facteur de réponse au sérum (SRF) font présentement l'objet de nombreux travaux, mais peu de choses sont connues au sujet des substitutions entre éléments CArG fonctionnels. Dans ce travail, les auteurs ont réalisé la première analyse de l'évolution du CArGome au sein des génomes de l'humain et de la souris via une approche bioinformatique et des tests statistiques. Les auteurs ont calculé le taux de substitution à chacun des sites chez les éléments CArG fonctionnels. Les résultats montrent que les sites au centre des éléments CArG fonctionnels ont évolué plus rapidement que le reste de l'ADN, ce qui suggère que ces sites auraient évolué sous l'impulsion d'une sélection positive. De plus, un fort « motif » TATA était évident au sein de la région centrale chez les éléments CArG fonctionnels présents dans les promoteurs humains et murins. Ce « motif » pourrait apporter une contribution majeure à la formation de la structure spatiale qui est importante pour la reconnaissance CArG-SRF. Cette étude a ainsi révélé les propriétés de ces séquences et le type de substitutions qui caractérisent les éléments CArG en plus de fournir des informations utiles pour l'étude de l'intensité de liaison des facteurs SRF sur les promoteurs CArG lors d'analyses fonctionnelles.
Audience Academic
Author Miao, Shan
Mao, Haimei
Shen, Xia
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Snippet cis-Elements CArG bound by serum response factor (SRF) are presently being intensively studied, but little is known about the substitution pattern of...
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SubjectTerms 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
Title Substitution pattern of the CArG element in human and mouse genomes
URI http://www.nrcresearchpress.com/doi/abs/10.1139/G10-105
https://www.ncbi.nlm.nih.gov/pubmed/21326370
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