Transcriptome Analysis of Zebrafish Embryogenesis Using Microarrays

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Abstract
Zebrafish (Danio rerio) is a well-recognized model for the study of vertebrate developmental genetics, yet at the same time little is known about the transcriptional events that underlie zebrafish embryogenesis. Here we have employed microarray analysis to study the temporal activity of developmentally regulated genes during zebrafish embryogenesis. Transcriptome analysis at 12 different embryonic time points covering five different developmental stages (maternal, blastula, gastrula, segmentation, and pharyngula) revealed a highly dynamic transcriptional profile. Hierarchical clustering, stage-specific clustering, and algorithms to detect onset and peak of gene expression revealed clearly demarcated transcript clusters with maximum gene activity at distinct developmental stages as well as co-regulated expression of gene groups involved in dedicated functions such as organogenesis. Our study also revealed a previously unidentified cohort of genes that are transcribed prior to the mid-blastula transition, a time point earlier than when the zygotic genome was traditionally thought to become active. Here we provide, for the first time to our knowledge, a comprehensive list of developmentally regulated zebrafish genes and their expression profiles during embryogenesis, including novel information on the temporal expression of several thousand previously uncharacterized genes. The expression data generated from this study are accessible to all interested scientists from our institute resource database (http://giscompute.gis.a-star.edu.sg/~govind/zebrafish/data_download.html). In an effort to shed light on the mysterious molecular process of embryogenesis, scientists have employed the powerful technological approach of high-density microarrays to analyze for the first time (to our knowledge) the expression patterns of over 16,000 zebrafish genes during the major stages of embryonic development. They determined that developmentally regulated genes in zebrafish could be grouped based upon their time of transcript accumulation onset (activation) and their peak of activity (peak accumulation). For example, genes encoding transcriptional regulators are activated en masse earlier than the target genes that they control. Thus, the developmental gene expression profile in zebrafish can be grouped into successive waves of gene activation followed by peak activity. One very novel group of genes that was discovered in this study is a set of about 100 genes that are activated even earlier than what was previously thought to be the earliest time of embryonic transcriptional activation. These genes are likely to be important for preparing the embryonic cells for subsequent high-level genome activation and normal development.