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Zebrafish promoter microarrays identify actively transcribed embryonic genes

Fiona C Wardle1*, Duncan T Odom2, George W Bell2, Bingbing Yuan2, Timothy W Danford3, Elizabeth L Wiellette24, Elizabeth Herbolsheimer2, Hazel L Sive2, Richard A Young2 and James C Smith1

Author Affiliations

1 Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Zoology, Cambridge University, Cambridge CB2 1QN, UK

2 Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA

3 Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Vassar Street, Cambridge, MA 02139, USA

4 Novartis Institutes for Biomedical Research, Mass Ave, Cambridge, MA 02139, USA

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Genome Biology 2006, 7:R71  doi:10.1186/gb-2006-7-8-r71

Published: 4 August 2006

Abstract

We have designed a zebrafish genomic microarray to identify DNA-protein interactions in the proximal promoter regions of over 11,000 zebrafish genes. Using these microarrays, together with chromatin immunoprecipitation with an antibody directed against tri-methylated lysine 4 of Histone H3, we demonstrate the feasibility of this method in zebrafish. This approach will allow investigators to determine the genomic binding locations of DNA interacting proteins during development and expedite the assembly of the genetic networks that regulate embryogenesis.