The correlations of the function and positional distribution of the cis-elements CArG around the TSS in the genes of Mus musculus

Xia Shen, James "Bruce" Walsh, Jing J. Li, Hong X. Pang, Wen J. Wang, Shi H. Tao

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

While many studies of cis-elements CArG bound by serum response factor (SRF) are in progress, little is known about the positional distribution of the functional CArG elements around the transcription start site (TSS) of genes that they influence. We use a validated CArG data set to calculate the distance distribution of functional CArG elements around the TSS. Distances between adjacent CArGs were also analyzed. We compare these distributions with those derived using a control set of randomly selected CArGs (that were not experimentally validated for function). Our results show that most functional CArG elements (108 of 152, 71%) exist upstream of the annotated TSS, with copy number increasing as one moves closer to the TSS. Moreover, the average number of the CArG elements in the CArG-containing genes is significantly more than that in the control genes. Our study extends earlier bioinformatic analyses of functional CArG elements and provides an application of comparative sequence data to the identification of transcription factor binding sites.

Original languageEnglish (US)
Pages (from-to)217-221
Number of pages5
JournalGenome
Volume52
Issue number3
DOIs
StatePublished - Mar 2009

Fingerprint

Transcription Initiation Site
Genes
Serum Response Factor
Computational Biology
Transcription Factors
Binding Sites

Keywords

  • Bioinformatics
  • CArG elements
  • Cis-elements
  • Mouse genome
  • Positional distribution
  • TSS

ASJC Scopus subject areas

  • Biotechnology
  • Genetics
  • Molecular Biology

Cite this

The correlations of the function and positional distribution of the cis-elements CArG around the TSS in the genes of Mus musculus. / Shen, Xia; Walsh, James "Bruce"; Li, Jing J.; Pang, Hong X.; Wang, Wen J.; Tao, Shi H.

In: Genome, Vol. 52, No. 3, 03.2009, p. 217-221.

Research output: Contribution to journalArticle

Shen, Xia ; Walsh, James "Bruce" ; Li, Jing J. ; Pang, Hong X. ; Wang, Wen J. ; Tao, Shi H. / The correlations of the function and positional distribution of the cis-elements CArG around the TSS in the genes of Mus musculus. In: Genome. 2009 ; Vol. 52, No. 3. pp. 217-221.
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AU - Wang, Wen J.

AU - Tao, Shi H.

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