Abstract
Regulation of transcription is one of the mechanisms involved in animal development, directing changes in patterning and cell fate specification. Large temporal data series, based on microarrays across the life cycle of the fly Drosophila melanogaster, revealed the existence of groups of genes which expression increases or decreases temporally correlated during the life cycle. These groups of genes are enriched in different biological functions. Here, instead of searching for temporal coincidence in gene expression using the entire genome expression data, we searched for temporal coincidence in gene expression only within predefined catalogues of functionally related genes and investigated whether a catalogue's expression profile can be used to generate larger catalogues, enriched in genes necessary for the same function. We analyzed the expression profiles from genes already associated with early neurodevelopment and late neurodifferentiation, at embryonic stages 16 and 17 of Drosophila life cycle. We hypothesized that during this interval we would find global downregulation of genes important for early neuronal development together with global upregulation of genes necessary for the final differentiation of neurons. Our results were consistent with this hypothesis. We then investigated if the expression profile of gene catalogues representing particular processes of neural development matched the temporal sequence along which these processes occur. The profiles of genes involved in patterning, neurogenesis, axogenesis or synaptic transmission matched the prediction, with largest transcript values at the time when the corresponding biological process takes place in the embryo. Furthermore, we obtained catalogues enriched in genes involved in temporally matching functions by performing a genome-wide systematic search for genes with their highest expression levels at the corresponding embryonic intervals. These findings imply the use of gene expression data in combination with known biological information to predict the involvement of functionally uncharacterized genes in particular biological events.
Highlights
Regulation of transcription is the first step in the regulation of protein expression, which determines cell fate and patterning during development, working under the control of several signaling pathways
Making use of the great amount of data derived from genomic studies, the transcriptional profile of groups of genes involved in the same developmental processes can be analyzed
We showed here that during Drosophila embryonic development the expression profile of functional catalogues correlates with the temporal windows of the biological processes they represent and that many of the genes within each catalogue have similar expression profiles during development
Summary
Regulation of transcription is the first step in the regulation of protein expression, which determines cell fate and patterning during development, working under the control of several signaling pathways. Clusters of genes that increase or decrease their expression within well-defined temporal windows along the life cycle of Drosophila melanogaster have been identified using DNA microarrays [1,2,3,4]. Three basic classes of genes were defined according to their coherent pattern of temporal expression: downregulated, upregulated or transiently expressed [2,3]. A group enriched in genes important for muscle formation was found to be upregulated at the end of embryonic and pupal stages, when larval and adult muscles are formed, respectively [1]. Groups enriched in genes associated with cuticle secretion showed transient, short and substantial transcriptional upregulation during late embryonic development, at the time when the cuticle is secreted by the epidermis [2,3]
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