A new cis-acting regulatory element driving gene expression in the zebrafish pineal gland.
BACKGROUND
The identification of functional cis-acting DNA regulatory elements is a crucial step towards understanding gene regulation. Ab initio motif detection algorithms have been extensively used in search of regulatory elements. Yet, their success in providing experimentally validated regulatory elements in vertebrates has been limited.


RESULTS
Here we report in silico identification and in vivo validation of regulatory elements that determine enhanced gene expression in the pineal gland of zebrafish. Microarray data enabled detection of genes that exhibit high expression in the pineal gland. The promoter regions of these genes were computationally analyzed in order to identify overrepresented motifs. The highest ranking motif identified is a CRX/OTX binding site, known to govern expression in the pineal gland and retina. The second highest ranking motif was not reported before; we experimentally validated its function in vivo by mutational analysis. The methodology presented here may be applicable as a general scheme for finding regulatory elements that contribute to tissue-specific gene expression.
Alon
Shahar
S
Department of Neurobiology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
Eisenberg
Eli
E
Jacob-Hirsch
Jasmine
J
Rechavi
Gideon
G
Vatine
Gad
G
Toyama
Reiko
R
Coon
Steven L
SL
Klein
David C
DC
Gothilf
Yoav
Y
D000818:Animals; D019295:Computational Biology / Q000379:methods*; D005786:Gene Expression Regulation; D010870:Pineal Gland / Q000378:metabolism*; D011401:Promoter Regions, Genetic; D050436:Regulatory Elements, Transcriptional; D015027:Zebrafish / Q000235:genetics* / Q000378:metabolism