ZFIN ID: ZDB-PUB-090123-7
A new cis-acting regulatory element driving gene expression in the zebrafish pineal gland
Alon, S., Eisenberg, E., Jacob-Hirsch, J., Rechavi, G., Vatine, G., Toyama, R., Coon, S.L., Klein, D.C., and Gothilf, Y.
Date: 2009
Source: Bioinformatics (Oxford, England)   25(5): 559-562 (Journal)
Registered Authors: Gothilf, Yoav, Klein, David C., Toyama, Reiko
Keywords: none
Microarrays: GEO:GSE13196
MeSH Terms:
  • Animals
  • Computational Biology/methods*
  • Gene Expression Regulation*
  • Pineal Gland/metabolism*
  • Promoter Regions, Genetic
  • Regulatory Elements, Transcriptional*
  • Zebrafish/genetics*
  • Zebrafish/metabolism
PubMed: 19147662 Full text @ Bioinformatics
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 over-represented 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. AVAILABILITY: http://odin.mdacc.tmc.edu/jhu/lysatearray-analysis/. Contacts: yoavg@tauex.tau.ac.il; elieis@post.tau.ac.il.