Exploring the characteristics of sequence elements in proximal promoters of human genes

Minou Bina, Phillip Wyss, Wenhui Ren, Wojciech Szpankowski, Elizabeth Thomas, Ranjit Randhawa, Sreedeepti Reddy, Priya M. John, Elsie I. Pares-Matos, Arnold Stein, Hao Xu, Sheryl A. Lazarus

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16 Scopus citations

Abstract

Central to reconstruction of cis-regulatory networks is identification and classification of naturally occurring transcription factor-binding sites according to the genes that they control. We have examined salient characteristics of 9-mers that occur in various orders and combinations in the proximal promoters of human genes. In evaluations of a dataset derived with respect to experimentally defined transcription initiation sites, in some cases we observed a clear correspondence of highly ranked 9-mers with protein-binding sites in genomic DNA. Evaluations of the larger dataset, derived with respect to the 5′ end of human ESTs, revealed that a subset of the highly ranked 9-mers corresponded to sites for several known transcription factor families (including CREB, ETS, EGR-1, SP1, KLF, MAZ, HIF-1, and STATs) that play important roles in the regulation of vertebrate genes. We identified several highly ranked CpG-containing 9-mers, defining sites for interactions with the CREB and ETS families of proteins, and identified potential target genes for these proteins. The results of the studies imply that the CpG-containing transcription factor-binding sites regulate the expression of genes with important roles in pathways leading to cell-type-specific gene expression and pathways controlled by the complex networks of signaling systems.

Original languageEnglish (US)
Pages (from-to)929-940
Number of pages12
JournalGenomics
Volume84
Issue number6
DOIs
Publication statusPublished - Dec 1 2004

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Keywords

  • Codes in human DNA
  • Gene regulation
  • Human genome
  • Sequence context of human genomic DNA
  • Transcription factor binding sites

ASJC Scopus subject areas

  • Genetics

Cite this

Bina, M., Wyss, P., Ren, W., Szpankowski, W., Thomas, E., Randhawa, R., ... Lazarus, S. A. (2004). Exploring the characteristics of sequence elements in proximal promoters of human genes. Genomics, 84(6), 929-940. https://doi.org/10.1016/j.ygeno.2004.08.013