Expressed sequence tag analysis of zebrafish eye tissues for NEIBank

Thomas S. Vihtelic, James M. Fadool, James Gao, Kimberley A. Thornton, David R. Hyde, Graeme Wistow

Research output: Contribution to journalArticle

45 Citations (Scopus)

Abstract

Purpose: To characterize gene expression patterns in various tissues of the zebrafish (Danio rerio) eye and identify zebrafish orthologs of human genes by expressed sequence tag (EST) analysis for NEIBank. Methods: mRNA was extracted from adult zebrafish eye tissues, including lenses, anterior segments (minus lens), retinas, posterior segments lacking retinas, and whole eyes. Five different cDNA libraries were constructed in the pCMVSport6 vector. Approximately 4,000 clones from each library were sequenced and analyzed using various bioinformatics programs. Results: The analysis yielded approximately 2,500 different gene clusters for each library. Combining data from the five libraries produced 10,392 unique gene clusters. GenBank accession numbers were identified for 37.6% (3,906) of the total gene clusters in the combined libraries and approximately 50% were linked to Unigene clusters in the current database. Several new crystallin genes, including two γN-crystallins, and a second major intrinsic protein (MIP) were identified in the lens library. In addition, a zebrafish homolog of cochlin (COCH), a gene that may play a role in the pathogenesis of human glaucoma, was identified in the anterior segment library. Surprisingly, no clear ortholog of the major retinal transcription factor Nrl was identified. Conclusions: The zebrafish eye tissue cDNA libraries are a useful resource for comparative gene expression analysis. These libraries will complement the cDNA libraries made for the Zebrafish Gene Collection (ZGC) and provide an additional source for gene identification and characterization in the vertebrate eye.

Original languageEnglish (US)
Pages (from-to)1083-1100
Number of pages18
JournalMolecular Vision
Volume11
StatePublished - Dec 13 2005
Externally publishedYes

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Expressed Sequence Tags
Zebrafish
Libraries
Sequence Analysis
Multigene Family
Gene Library
Lenses
Crystallins
Genes
Retina
Gene Expression
Nucleic Acid Databases
Computational Biology
Glaucoma
Vertebrates
Transcription Factors
Clone Cells
Databases
Messenger RNA
Proteins

ASJC Scopus subject areas

  • Ophthalmology

Cite this

Vihtelic, T. S., Fadool, J. M., Gao, J., Thornton, K. A., Hyde, D. R., & Wistow, G. (2005). Expressed sequence tag analysis of zebrafish eye tissues for NEIBank. Molecular Vision, 11, 1083-1100.

Expressed sequence tag analysis of zebrafish eye tissues for NEIBank. / Vihtelic, Thomas S.; Fadool, James M.; Gao, James; Thornton, Kimberley A.; Hyde, David R.; Wistow, Graeme.

In: Molecular Vision, Vol. 11, 13.12.2005, p. 1083-1100.

Research output: Contribution to journalArticle

Vihtelic, TS, Fadool, JM, Gao, J, Thornton, KA, Hyde, DR & Wistow, G 2005, 'Expressed sequence tag analysis of zebrafish eye tissues for NEIBank', Molecular Vision, vol. 11, pp. 1083-1100.
Vihtelic TS, Fadool JM, Gao J, Thornton KA, Hyde DR, Wistow G. Expressed sequence tag analysis of zebrafish eye tissues for NEIBank. Molecular Vision. 2005 Dec 13;11:1083-1100.
Vihtelic, Thomas S. ; Fadool, James M. ; Gao, James ; Thornton, Kimberley A. ; Hyde, David R. ; Wistow, Graeme. / Expressed sequence tag analysis of zebrafish eye tissues for NEIBank. In: Molecular Vision. 2005 ; Vol. 11. pp. 1083-1100.
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