Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis
Sean D Hooper1,a, Stephanie Boué1,a, Roland Krause2,3,a, Lars J Jensen1, Christopher E Mason4, Murad Ghanim4, Kevin P White4, Eileen EM Furlong1 & Peer Bork1
- Structural and Computational Biology Unit, EMBL, Heidelberg, Germany
- Department Vingron, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
- Department Zychlinsky, Max-Planck-Institute for Infection Biology, Berlin, Germany
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
Correspondence to: Eileen EM Furlong1
Gene Expression Unit, EMBL Heidelberg, Meyerhofstra
e 1, 69117 Heidelberg, Germany. Tel.: +49 6221 387 8416; Email: furlong@embl.de
Correspondence to: Peer Bork1 Structural and Computational Biology Unit, EMBL, Meyerhofstrasse 1, Heidelberg 69117, Germany. Tel.: +49 622 1387 8526; Fax: +49 622 1387 8517; E-mail: Email: bork@embl.de
Received 12 December 2005; Accepted 3 November 2006; Published online 16 January 2007
aThese authors contributed equally to this work
Top of pageArticle highlights
- We identify the most dramatic time points in embryogenesis, with regard to a relay effect of genes and pathways.
- We correlate the phenotype and genotype of developmental phases.
- We suggest a correlation between regulation on the transcript level and the protein level.
- We propose and experimentally validate a selection of hitherto unknown genes as having important functions in developmental pathways.
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), 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.
Figure 2
Major classes of transcript levels, as determined by global convolution. Arcs represent the dominant subgroups within class I, II, and III transcripts. For instance, class I is dominated by two main subgroups I:a and I:b, represented by the pink and red arcs, respectively. Time is in hours, and yellow rectangles signify measurement points. The time of increase and decrease of the transcript groups coincides with those derived by local convolution (Supplementary Figure S1). Note the interplay between groups as a decrease of one transcript group is followed by an increase of another.
Full figure and legend (172K)Figures & Tables indexUsing 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). 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.
Figure 5
Spatial colocalization of worniu, pdm2, CG13333 and CG4440 with Delta in embryos stage 11–12. Columns 1 and 2 show stainings individually and column 3 shows colocalization. CG4440 exhibits an anti-correlation, suggesting colocalization with Notch rather than Delta.
Full figure and legend (613K)Figures & Tables indexAcknowledgements
We thank Tobias Doerks for his transcription factor expertise, as well as Florian Raible and members of the Bork group for helpful discussions. This work was partly supported by EU grants LSHG-CT-2003503329 and QLRT-2001-02062. SD Hooper was supported by the Knut and Alice Wallenberg Foundation.
