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Mapping the complexity of transcription control in higher eukaryotes

DOI: 10.1186/gb-2010-11-4-115

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The complexity of life does not correlate with an increased size of the list of parts (the genes) from which organisms are built, but rather with an increased complexity in how these parts are regulated and combined into networks to specify the correct tissue-specific expression of genes. Analyses of yeast had shown a fairly simple hierarchical regulatory architecture, in which master regulators drive expression of many genes and any given gene is typically regulated by at most a handful of transcription factors (TFs) [1]. Some studies in animals, including studies of the early development of Drosophila, suggested a straightforward extension of the concept of a small number of highly specific TFs that define expression domains. Recent studies, including one by Adryan and Teichmann in this issue of Genome Biology [2], put the idea to the test by evaluating large genomic datasets, and their conclusions challenge this hypothesis.Adryan and Teichmann's study is based on datasets obtained by two popular methods for analyzing gene expression [3,4]. Transcriptional profiling using microarrays requires substantial amounts of biological material and is thus typically used on intact multicellular specimens or cultured cell lines. RNA in situ hybridization is used to visualize spatial and temporal gene expression, but is limited for several reasons: some classes of eukaryotic genes, such as microRNAs, are difficult to study in this way; many tissues, such as brains, cannot be permeabilized enough to deliver the probe throughout the sample; temporal resolution is limited; and there is a lack of reliable quantification methods. Systematic RNA in situ surveys are therefore routinely combined with microarray analysis to counter the drawbacks of the two methods [4].Drosophila embryonic development is particularly amenable to analysis by both in situ hybridization and microarray analysis. Large numbers of approximately staged embryos enable the isolation of sufficient amounts of RNA


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