TY - JOUR
T1 - Exploring the characteristics of sequence elements in proximal promoters of human genes
AU - Bina, Minou
AU - Wyss, Phillip
AU - Ren, Wenhui
AU - Szpankowski, Wojciech
AU - Thomas, Elizabeth
AU - Randhawa, Ranjit
AU - Reddy, Sreedeepti
AU - John, Priya M.
AU - Pares-Matos, Elsie I.
AU - Stein, Arnold
AU - Xu, Hao
AU - Lazarus, Sheryl A.
PY - 2004/12/1
Y1 - 2004/12/1
N2 - 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.
AB - 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.
KW - Codes in human DNA
KW - Gene regulation
KW - Human genome
KW - Sequence context of human genomic DNA
KW - Transcription factor binding sites
UR - http://www.scopus.com/inward/record.url?scp=7944234271&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=7944234271&partnerID=8YFLogxK
U2 - 10.1016/j.ygeno.2004.08.013
DO - 10.1016/j.ygeno.2004.08.013
M3 - Article
C2 - 15533710
AN - SCOPUS:7944234271
VL - 84
SP - 929
EP - 940
JO - Genomics
JF - Genomics
SN - 0888-7543
IS - 6
ER -