Journal Article

A new <i>cis</i>-acting regulatory element driving gene expression in the zebrafish pineal gland

Shahar Alon, Eli Eisenberg, Jasmine Jacob-Hirsch, Gideon Rechavi, Gad Vatine, Reiko Toyama, Steven L. Coon, David C. Klein and Yoav Gothilf

in Bioinformatics

Volume 25, issue 5, pages 559-562
Published in print March 2009 | ISSN: 1367-4803
Published online January 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp031
A new cis-acting regulatory element driving gene expression in the zebrafish pineal gland

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Motivation: 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.

Contacts: yoavg@tauex.tau.ac.il; elieis@post.tau.ac.il

Supplementary information:Supplementary data are available at Bioinformatics online.

Journal Article.  3415 words. 

Subjects: Bioinformatics and Computational Biology

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