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

Bina, M., Wyss, P., Ren, W. H., Szpankowski, W., Thomas, E., Randhawa, R., Reddy, S., John, P. M., Pares-Matos, E. I., Stein, A., Xu, H., Lazarus, S. A. (December 2004) Exploring the characteristics of sequence elements in proximal promoters of human genes. Genomics, 84 (6). pp. 929-940. ISSN 0888-7543

URL: http://www.ncbi.nlm.nih.gov/pubmed/15533710
DOI: 10.1016/j.ygeno.2004.08.013

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. (C) 2004 Elsevier Inc. All rights reserved.

Item Type: Paper
Uncontrolled Keywords: human genome gene regulation transcription factor binding sites sequence context of human genomic DNA codes in human DNA TRANSCRIPTION FACTORS HUMAN GENOME MEDIATES INDUCTION CPG METHYLATION ETS PROTEINS BINDING-SITE FAMILY CAMP IDENTIFICATION ACTIVATION
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification
bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function
organism description > animal > mammal > primates > hominids > human
CSHL Authors:
Communities: CSHL labs > Wigler lab
Watson School > Publications
Depositing User: Matt Covey
Date: December 2004
Date Deposited: 04 Mar 2013 21:08
Last Modified: 26 Sep 2014 14:12
Related URLs:
URI: http://repository.cshl.edu/id/eprint/27718

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