Microarray-based analysis of early development in Xenopus laevis

In order to examine transcriptional regulation globally, during early verte brate embryonic development, we have prepared Xenopus laevis cDNA microarra ys. These prototype embryonic arrays contain 864 sequenced gastrula cDNA. I n order to analyze and store array data, a microarray analysis pipeline was developed and integrated with sequence analysis and annotation tools. In t hree independent experimental settings, we demonstrate the power of these g lobal approaches and provide optimized protocols for their application to m olecular embryology. in the first set, by comparing maternal versus zygotic transcription, we document groups of genes that are temporally regulated. This analytical approach resulted in the discovery of novel temporally regu lated genes. In the second, we examine changes in gene expression spatially during development by comparing dorsal and ventral mesoderm dissected from early gastrula embryos. We have discovered novel genes with spatial enrich ment from these experiments. Finally, we use the prototype microarray to ex amine transcriptional responses from embryonic explants treated with activi n. We selected genes (two of which are novel) regulated by activin for furt her characterization. All results obtained by the arrays were independently tested by RT-PCR or by in situ hybridization to provide a direct assessmen t of the accuracy and reproducibility of these approaches in the context of molecular embryology. (C) 2001 Academic Press.