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  Expression profiling and comparative genomics identify a conserved regulatory region controlling midline expression in the zebrafish embryo

Dickmeis, T., Plessy, C., Rastegar, S., Aanstad, P., Herwig, R., Chalmel, F., et al. (2004). Expression profiling and comparative genomics identify a conserved regulatory region controlling midline expression in the zebrafish embryo. Genome Research, 14(2), 228-238. doi:10.1101/gr.1819204.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-88E3-F Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-88E4-D
Genre: Journal Article
Alternative Title : Genome Res

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 Creators:
Dickmeis, Thomas, Author
Plessy, Charles, Author
Rastegar, Sepand, Author
Aanstad, Pia1, Author
Herwig, Ralf2, Author              
Chalmel, Frédéric, Author
Fischer, Nadine, Author
Strähle, Uwe, Author
Affiliations:
1Max Planck Society, ou_persistent13              
2Bioinformatics (Ralf Herwig), Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479648              

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 Abstract: Differential gene transcription is a fundamental regulatory mechanism of biological systems during development, body homeostasis, and disease. Comparative genomics is believed to be a rapid means for the identification of regulatory sequences in genomes. We tested this approach to identify regulatory sequences that control expression in the midline of the zebrafish embryo. We first isolated a set of genes that are coexpressed in the midline of the zebrafish embryo during somitogenesis stages by gene array analysis and subsequent rescreens by in situ hybridization. We subjected 45 of these genes to Compare and DotPlot analysis to detect conserved sequences in noncoding regions of orthologous loci in the zebrafish and Takifugu genomes. The regions of homology that were scored in nonconserved regions were inserted into expression vectors and tested for their regulatory activity by transient transgenesis in the zebrafish embryo. We identified one conserved region from the connective tissue growth factor gene (ctgf), which was able to drive expression in the midline of the embryo. This region shares sequence similarity with other floor plate/notochord-specific regulatory regions. Our results demonstrate that an unbiased comparative approach is a relevant method for the identification of tissue-specific cis-regulatory sequences in the zebrafish embryo. [Supplemental material is available online at www.genome.org. The sequence data from this study have been submitted to GenBank under accession nos.AY428026-AY428035, CD777505-CD777543, and CD777544-CD778191.]

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Language(s): eng - English
 Dates: 2004-02
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Type: -
 Identifiers: eDoc: 173722
DOI: 10.1101/gr.1819204
 Degree: -

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Title: Genome Research
  Alternative Title : Genome Res
Source Genre: Journal
 Creator(s):
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Publ. Info: -
Pages: - Volume / Issue: 14 (2) Sequence Number: - Start / End Page: 228 - 238 Identifier: ISSN: 1088-9051