Chromatin immunoprecipitation would be a powerful tool for deciphering transcriptional regulation during development. However, most ChIP studies have involved cultured cells. On p. 34, Havis et al. describe a ChIP assay that can be used with whole zebrafish embryos. The method, which can be used up to 12 hours postfertilization, uses a pronase digestion for dechorionation, followed by homogenization and centrifugation. The pelleted nuclei are treated with formaldehyde for DNA-protein cross-linking, then lysed, and the chromatin is fragmented by sonication. The authors describe the appropriate conditions for adequate shearing of the chromatin and show that subsequent ChIP yields the expected results for antibodies against acetylated histone H4. Havis et al. further demonstrate the efficacy of their system by successful ChIP analysis of a transcription factor, in this case, exogenously introduced Myc-tagged Meis. Given the importance of Danio rerio in developmental biology and drug discovery, a well-optimized ChIP protocol for zebrafish embryos should have wide application in mapping target genes of transcription factors.

• Genes / Markers (5)