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First published online 27 July 2005
doi: 10.1242/dev.01951

Development 132, 3799-3811 (2005)
Published by The Company of Biologists 2005
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Large-scale enhancer detection in the zebrafish genome

Staale Ellingsen*, Mary A. Laplante, Melanie König, Hiroshi Kikuta, Tomasz Furmanek, Erling A. Hoivik{dagger} and Thomas S. Becker{ddagger}

Sars International Centre for Marine Molecular Biology at the University of Bergen, Thormoehlensgate 55, 5008 Bergen, Norway

{ddagger} Author for correspondence (e-mail: tom.becker{at}sars.uib.no)

Accepted 29 June 2005

Murine retroviral vectors carrying an enhancer detection cassette were used to generate 95 transgenic lines of fish in which reporter expression is observed in distinct patterns during embryonic development. We mapped 65 insertion sites to the as yet unfinished zebrafish genome sequence. Many integrations map close to previously known developmental genes, including transcription factors of the Pax, Hox, Sox, Pou, Otx, Emx, zinc-finger and bHLH gene families. In most cases, the activated provirus is located in, or within a 15 kb interval around, the corresponding transcriptional unit. The exceptions include four insertions into a gene desert on chromosome 20 upstream of sox11b, and an insertion upstream of otx1. In these cases, the activated insertions are found at a distance of between 32 kb and 132 kb from the coding region. These as well as seven other insertions described here identify genes that have recently been associated with ultra conserved non-coding elements found in all vertebrate genomes.

Key words: Cis-regulatory sequence, Synteny, In vivo imaging, Zebrafish




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