29 May 2002
Eli Koren & Tal Zohar
CSLS, Hebrew University of Jerusalem, Israel
____________________________________________________________________
Location analysis of transcription factors binding sites
Abstract
1
Understanding how DNA binding proteins control global gene expression requires
knowledge of the chromosomal locations at which these proteins function in vivo. A
microarray method that reveals the genome-wide location of DNA-bound proteins
was developed and used to monitor binding of gene-specific transcription activators in
yeast. A combination of location and expression profiles was used to identify genes
whose expression is directly controlled by certain transcription factors. Genome-wide
location analysis will facilitate investigation of gene regulatory networks, gene
function, and genome maintenance.
2
Genome-wide location analysis was used to determine how the yeast cell cycle gene
expression program is regulated by each of the nine known cell cycle transcriptional
activators. Results have shown that cell cycle transcriptional activators that function
during one stage of the cell cycle regulate transcriptional activators that function
during the next stage. This serial regulation of transcriptional activators forms a
connected regulatory network that is itself a cycle.
3
The E2F transcription factor family is known to play a key role in the timely
expression of genes required for cell cycle progression and proliferation, but only a
few E2F target genes have been identified. The possibility that E2F regulators play a
broader role by identifying additional genes bound by E2F in living human cells was
explored. A protocol was developed to identify genomic binding sites for DNAbinding factors in mammalian cells that combines immunoprecipitation of crosslinked protein-DNA complexes with DNA microarray analysis. Most previously
identified target genes known to have roles in DNA replication and cell cycle control
and represented on the microarray were confirmed by this analysis. The data indicates
that E2F directly links cell cycle progression with the coordinate regulation of genes
essential for both the synthesis of DNA as well as its surveillance.
1
Bing Ren, Francois Robert, John J. Wyrick, Oscar Aparicio
Genome–Wide Location and Function of DNA Binding Proteins SCIENCE, December 22, 2000, Vol 290, 2306 – 2309
2
Itamar Simon, John Barnett, Nancy Hannett, Christopher T. Harbison, Nicola J. Rinaldi
Serial Regulation of Transcriptional Regulators in the Yeast Cell Cycle –
Cell, September 21, 2001, Vol 106, 697 - 708
3
Bing Ren, Hieu Cam, Yasuhiko Takahashi, Thomas Volkert, Jolyon Terragn
E2F integrates cell cycle progression with DNA repair, replication, and G2/M checkpoints
Genes & Dev. January 15, 2002, Vol 16, 245-256