Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis

Open Access
Publisher Website
Google Scholar
Abstract
Time‐series analysis of whole‐genome expression data during Drosophila melanogaster development indicates that up to 86% of its genes change their relative transcript level during embryogenesis. By applying conservative filtering criteria and requiring ‘sharp’ transcript changes, we identified 1534 maternal genes, 792 transient zygotic genes, and 1053 genes whose transcript levels increase during embryogenesis. Each of these three categories is dominated by groups of genes where all transcript levels increase and/or decrease at similar times, suggesting a common mode of regulation. For example, 34% of the transiently expressed genes fall into three groups, with increased transcript levels between 2.5–12, 11–20, and 15–20 h of development, respectively. We highlight common and distinctive functional features of these expression groups and identify a coupling between downregulation of transcript levels and targeted protein degradation. By mapping the groups to the protein network, we also predict and experimentally confirm new functional associations. ### Synopsis Developmental biologists have been studying the fruitfly D. melanogaster for close to one hundred years. It has proven a valuable organism for developmentalists owing to its ease of culture, its short 2‐week lifespan and its transparent embryo, resulting in an extensive knowledge base of tissue differentiation, segmentation, and organ development. Furthermore, painstaking knockout experiments have revealed many of the genetic mechanisms behind the development of Drosophila . With the advent of microarray technology, large‐scale studies of the networks of genetic regulation can be undertaken. We have studied the first comprehensive expression data of roughly 13 000 Drosophila gene transcripts and attempt to correlate the levels of transcripts to a priori knowledge of development. Our expression data span the whole‐embryo stage of Drosophila . During the first ca. 24 h, the embryo has segregated its nuclei, undergone cell differentiation, gastrulation, and segmentation, before the embryo undergoes the transition to the pupal stage. Over this period, we have taken samples at 30 time points, with a higher frequency of sampling in the first hours of embryogenesis. We study the profiles of these transcript levels and categorize them by their behavior. Three major classes of transcripts were found ([Figure 2][1]), I , transcripts that are maternally inherited; II , transcripts that appear to be under stringent regulation and that may be tied to specific phases of development; and III , transcripts that are not under tight regulation. Using a comprehensive array of a priori knowledge, such as annotation, in situ data, pathway members, orthology, and others, we attempt to predict functions of hitherto unclassified genes, that share expression patterns. For instance, we identify a few heavily overrepresented subclasses within class II. One of these groups of genes with a plateau of increased transcript levels start at 3–6 h and decrease at 12–13 h, which is consistent with the time of cellularization and gastrulation in the embryo. For this subclass of genes, we find several central regulators and effectors, among other members of the Notch and Delta pathways that are involved in cell differentiation. The a priori data also underline the importance of genes in this subclass and the need for stringent regulation not only of their transcript levels but also their protein levels. As a result, we propose a number of genes, which so far have been poorly understood, as potential members of pathways involved in cell differentiation and gastrulation. To validate this approach, we chose four such proposed genes and performed in situ colocalization experiments. This staining of embryos revealed a colocalization with Delta, suggesting a regulative relationship with the Delta pathway ([Figure 5][2]). It also showed a non‐random patterning of transcript expression in various tissues over time, lending further support that many of these genes are involved in either the Notch or Delta pathway. Mol Syst Biol. 3: 72 [1]: #F2 [2]: #F5