Abstract
The processes that take place during development and differentiation are directed through coordinated regulation of expression of a large number of genes. One such gene regulatory network provides cell cycle control in eukaryotic organisms. In this work, we have studied the structural features of the 5′ regulatory regions of cell cycle-related genes. We developed a new method for identifying composite substructures (modules) in regulatory regions of genes consisting of a binding site for a key transcription factor and additional contextual motifs: potential targets for other transcription factors that may synergistically regulate gene transcription. Applying this method to cell cycle-related promoters, we created a program for context-specific identification of binding sites for transcription factors of the E2F family which are key regulators of the cell cycle. We found that E2F composite modules are found at a high frequency and in close proximity to the start of transcription in cell cycle-related promoters in comparison with other promoters. Using this information, we then searched for E2F sites in genomic sequences with the goal of identifying new genes which play important roles in controlling cell proliferation, differentiation and apoptosis. Using a chromatin immunoprecipitation assay, we then experimentally verified the binding of E2F in vivo to the promoters predicted by the computer-assisted methods. Our identification of new E2F target genes provides new insight into gene regulatory networks and provides a framework for continued analysis of the role of contextual promoter features in transcriptional regulation. The tools described are available at http://compel.bionet.nsc.ru/FunSite/SiteScan.html.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 99-120 |
| Number of pages | 22 |
| Journal | Journal of Molecular Biology |
| Volume | 309 |
| Issue number | 1 |
| DOIs | |
| State | Published - May 25 2001 |
| Externally published | Yes |
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Keywords
- Cell cycle
- Composite elements
- Computer-associated prediction
- E2F transcription factors
- Weight matrix
ASJC Scopus subject areas
- Virology
Cite this
Computer-assisted identification of cell cycle-related genes : New targets for E2F transcription factors. / Kel, Alexander E.; Kel-Margoulis, Olga V.; Farnham, Peggy J.; Bartley, Stephanie M.; Wingender, Edgar; Zhang, Michael Q.
In: Journal of Molecular Biology, Vol. 309, No. 1, 25.05.2001, p. 99-120.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Computer-assisted identification of cell cycle-related genes
T2 - New targets for E2F transcription factors
AU - Kel, Alexander E.
AU - Kel-Margoulis, Olga V.
AU - Farnham, Peggy J.
AU - Bartley, Stephanie M.
AU - Wingender, Edgar
AU - Zhang, Michael Q.
PY - 2001/5/25
Y1 - 2001/5/25
N2 - The processes that take place during development and differentiation are directed through coordinated regulation of expression of a large number of genes. One such gene regulatory network provides cell cycle control in eukaryotic organisms. In this work, we have studied the structural features of the 5′ regulatory regions of cell cycle-related genes. We developed a new method for identifying composite substructures (modules) in regulatory regions of genes consisting of a binding site for a key transcription factor and additional contextual motifs: potential targets for other transcription factors that may synergistically regulate gene transcription. Applying this method to cell cycle-related promoters, we created a program for context-specific identification of binding sites for transcription factors of the E2F family which are key regulators of the cell cycle. We found that E2F composite modules are found at a high frequency and in close proximity to the start of transcription in cell cycle-related promoters in comparison with other promoters. Using this information, we then searched for E2F sites in genomic sequences with the goal of identifying new genes which play important roles in controlling cell proliferation, differentiation and apoptosis. Using a chromatin immunoprecipitation assay, we then experimentally verified the binding of E2F in vivo to the promoters predicted by the computer-assisted methods. Our identification of new E2F target genes provides new insight into gene regulatory networks and provides a framework for continued analysis of the role of contextual promoter features in transcriptional regulation. The tools described are available at http://compel.bionet.nsc.ru/FunSite/SiteScan.html.
AB - The processes that take place during development and differentiation are directed through coordinated regulation of expression of a large number of genes. One such gene regulatory network provides cell cycle control in eukaryotic organisms. In this work, we have studied the structural features of the 5′ regulatory regions of cell cycle-related genes. We developed a new method for identifying composite substructures (modules) in regulatory regions of genes consisting of a binding site for a key transcription factor and additional contextual motifs: potential targets for other transcription factors that may synergistically regulate gene transcription. Applying this method to cell cycle-related promoters, we created a program for context-specific identification of binding sites for transcription factors of the E2F family which are key regulators of the cell cycle. We found that E2F composite modules are found at a high frequency and in close proximity to the start of transcription in cell cycle-related promoters in comparison with other promoters. Using this information, we then searched for E2F sites in genomic sequences with the goal of identifying new genes which play important roles in controlling cell proliferation, differentiation and apoptosis. Using a chromatin immunoprecipitation assay, we then experimentally verified the binding of E2F in vivo to the promoters predicted by the computer-assisted methods. Our identification of new E2F target genes provides new insight into gene regulatory networks and provides a framework for continued analysis of the role of contextual promoter features in transcriptional regulation. The tools described are available at http://compel.bionet.nsc.ru/FunSite/SiteScan.html.
KW - Cell cycle
KW - Composite elements
KW - Computer-associated prediction
KW - E2F transcription factors
KW - Weight matrix
UR - http://www.scopus.com/inward/record.url?scp=0035946917&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=0035946917&partnerID=8YFLogxK
U2 - 10.1006/jmbi.2001.4650
DO - 10.1006/jmbi.2001.4650
M3 - Article
C2 - 11491305
AN - SCOPUS:0035946917
VL - 309
SP - 99
EP - 120
JO - Journal of Molecular Biology
JF - Journal of Molecular Biology
SN - 0022-2836
IS - 1
ER -