Zebrafish promoter microarrays identify actively transcribed embryonic genes

Fiona C Wardle¹ , Duncan T Odom² , George W Bell² , Bingbing Yuan², Timothy W Danford³ , Elizabeth L Wiellette²^,4 , Elizabeth Herbolsheimer² , Hazel L Sive² , Richard A Young² and James C Smith¹

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

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

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

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

author email corresponding author email

Genome Biology 2006, 7:R71doi:10.1186/gb-2006-7-8-r71


Published:	4 August 2006

Subject areas: Genome studies, Development, Model organisms

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.